Structured Review

Agilent technologies microarray scanner
Identification of robust candidate genes allowing discrimination of different radiation qualities. (A, B) DNAJC1 and PRTFDC1 6 h after withdrawal of 123 IUdR versus 24 h after γ-irradiation; (C) PPP1R14C 6 h after withdrawal of 123 IUdR versus 6 h after γ-irradiation; (D) KLF10 24 h after γ-irradiation versus 24 h after α-irradiation; (E) TNFAIP8L1 6 h after withdrawal of 123 IUdR versus 6 h after γ- and α-irradiation. Solid bars show the data of the quantitative real-time PCR in comparison with the <t>microarray</t> data (white bars with dashed lines). The error bars represent the standard deviation of the mean ( n = 3, * P
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1) Product Images from "Comparative gene expression analysis after exposure to 123I-iododeoxyuridine, γ- and α-radiation—potential biomarkers for the discrimination of radiation qualities"

Article Title: Comparative gene expression analysis after exposure to 123I-iododeoxyuridine, γ- and α-radiation—potential biomarkers for the discrimination of radiation qualities

Journal: Journal of Radiation Research

doi: 10.1093/jrr/rry038

Identification of robust candidate genes allowing discrimination of different radiation qualities. (A, B) DNAJC1 and PRTFDC1 6 h after withdrawal of 123 IUdR versus 24 h after γ-irradiation; (C) PPP1R14C 6 h after withdrawal of 123 IUdR versus 6 h after γ-irradiation; (D) KLF10 24 h after γ-irradiation versus 24 h after α-irradiation; (E) TNFAIP8L1 6 h after withdrawal of 123 IUdR versus 6 h after γ- and α-irradiation. Solid bars show the data of the quantitative real-time PCR in comparison with the microarray data (white bars with dashed lines). The error bars represent the standard deviation of the mean ( n = 3, * P
Figure Legend Snippet: Identification of robust candidate genes allowing discrimination of different radiation qualities. (A, B) DNAJC1 and PRTFDC1 6 h after withdrawal of 123 IUdR versus 24 h after γ-irradiation; (C) PPP1R14C 6 h after withdrawal of 123 IUdR versus 6 h after γ-irradiation; (D) KLF10 24 h after γ-irradiation versus 24 h after α-irradiation; (E) TNFAIP8L1 6 h after withdrawal of 123 IUdR versus 6 h after γ- and α-irradiation. Solid bars show the data of the quantitative real-time PCR in comparison with the microarray data (white bars with dashed lines). The error bars represent the standard deviation of the mean ( n = 3, * P

Techniques Used: Irradiation, Real-time Polymerase Chain Reaction, Microarray, Standard Deviation

2) Product Images from "Analysis of Differential Expression Patterns of mRNA and Protein During Cold-acclimation and De-acclimation in Arabidopsis *"

Article Title: Analysis of Differential Expression Patterns of mRNA and Protein During Cold-acclimation and De-acclimation in Arabidopsis *

Journal: Molecular & Cellular Proteomics : MCP

doi: 10.1074/mcp.M114.039081

Expression patterns of mRNAs and proteins of regulated targets and cold inducible genes during CA and DA. A , Relative expression patterns of ribosomal protein genes and B , well-known CA-related genes. Left panel shows mRNA expression patterns and right panel contains protein expression patterns. mRNAs were analyzed using microarray data and proteins were evaluated using shotgun proteomics data.
Figure Legend Snippet: Expression patterns of mRNAs and proteins of regulated targets and cold inducible genes during CA and DA. A , Relative expression patterns of ribosomal protein genes and B , well-known CA-related genes. Left panel shows mRNA expression patterns and right panel contains protein expression patterns. mRNAs were analyzed using microarray data and proteins were evaluated using shotgun proteomics data.

Techniques Used: Expressing, Microarray

mRNA and protein expression patterns of mMDH1 during CA and DA. Total RNA was extracted and converted into cDNA to serve as a template for qRT-PCR analyses. mRNA expression was analyzed using qRT-PCR and protein expression was analyzed by western blot analysis. After normalization to ACT2 mRNA, the relative expression pattern of mMDH1 was presented (left bottom). Data are shown as the means of three biological replicates. Total protein extracts were separated by SDS-PAGE and signal was detected using a MDH antibody (MDH2, Abcam). Relative expression was analyzed using ImageJ software. Data are shown as the means of three biological replicates. Microarray data (left) and shotgun data (right) are presented in the top panel.
Figure Legend Snippet: mRNA and protein expression patterns of mMDH1 during CA and DA. Total RNA was extracted and converted into cDNA to serve as a template for qRT-PCR analyses. mRNA expression was analyzed using qRT-PCR and protein expression was analyzed by western blot analysis. After normalization to ACT2 mRNA, the relative expression pattern of mMDH1 was presented (left bottom). Data are shown as the means of three biological replicates. Total protein extracts were separated by SDS-PAGE and signal was detected using a MDH antibody (MDH2, Abcam). Relative expression was analyzed using ImageJ software. Data are shown as the means of three biological replicates. Microarray data (left) and shotgun data (right) are presented in the top panel.

Techniques Used: Expressing, Quantitative RT-PCR, Western Blot, SDS Page, Software, Microarray

3) Product Images from "Transcriptomics in lung tissue upon respiratory syncytial virus infection reveals aging as important modulator of immune activation and matrix maintenance"

Article Title: Transcriptomics in lung tissue upon respiratory syncytial virus infection reveals aging as important modulator of immune activation and matrix maintenance

Journal: Scientific Reports

doi: 10.1038/s41598-018-35180-2

Distinct effects by aging and RSV on gene expression. Panel A shows each individual animal in a principal component analysis (PCA) of the microarray data of lung samples derived at day 0 (mock-inoculated, black, n = 4/group), or at day 2 (red, n = 5/group) or day 5 (green, n = 5/group) after inoculation with RSV. Aging-regulated expression appears by PC1, RSV-regulated gene expression appears along PC2. Y, young (circles); O, old (triangles); M, mock control; R, RSV-inoculated. Panel B shows a Venn-diagram depicting numbers of genes that are significantly upregulated (↑), downregulated (↓), or show no significant response (−). The three symbols indicate from left to right: response to RSV in young mice, response to RSV in old mice, response to aging, respectively.
Figure Legend Snippet: Distinct effects by aging and RSV on gene expression. Panel A shows each individual animal in a principal component analysis (PCA) of the microarray data of lung samples derived at day 0 (mock-inoculated, black, n = 4/group), or at day 2 (red, n = 5/group) or day 5 (green, n = 5/group) after inoculation with RSV. Aging-regulated expression appears by PC1, RSV-regulated gene expression appears along PC2. Y, young (circles); O, old (triangles); M, mock control; R, RSV-inoculated. Panel B shows a Venn-diagram depicting numbers of genes that are significantly upregulated (↑), downregulated (↓), or show no significant response (−). The three symbols indicate from left to right: response to RSV in young mice, response to RSV in old mice, response to aging, respectively.

Techniques Used: Expressing, Microarray, Derivative Assay, Mouse Assay

4) Product Images from "Overexpression of CtCHS1 Increases Accumulation of Quinochalcone in Safflower"

Article Title: Overexpression of CtCHS1 Increases Accumulation of Quinochalcone in Safflower

Journal: Frontiers in Plant Science

doi: 10.3389/fpls.2017.01409

Microarray expression abundance of differential genes at different flower stages in Y and W line. HCL cluster of genes was performed. The color key was set from –1 to +1. The data were retrieved from the safflower microarray data set (unpublished).
Figure Legend Snippet: Microarray expression abundance of differential genes at different flower stages in Y and W line. HCL cluster of genes was performed. The color key was set from –1 to +1. The data were retrieved from the safflower microarray data set (unpublished).

Techniques Used: Microarray, Expressing

5) Product Images from "Aptamer-Based Multiplexed Proteomic Technology for Biomarker DiscoveryUnlocking Biomarker Discovery: Large Scale Application of Aptamer Proteomic Technology for Early Detection of Lung Cancer"

Article Title: Aptamer-Based Multiplexed Proteomic Technology for Biomarker DiscoveryUnlocking Biomarker Discovery: Large Scale Application of Aptamer Proteomic Technology for Early Detection of Lung Cancer

Journal: PLoS ONE

doi: 10.1371/journal.pone.0015004

Principle of multiplex SOMAmer affinity assay. (A) Binding. SOMAmers and samples are mixed in 96-well microwell plates and allowed to bind. Cognate and non-cognate SOMAmer-target protein complexes form. Free SOMAmer and protein are also present. (B–H) Schematic sequence of assay steps leading to quantitative readout of target proteins. (B) SOMAmer-protein binding: DNA-based SOMAmer molecules (gold, blue, and green) have unique shapes selected to bind to a specific protein. SOMAmers contain biotin (B), a photo-cleavable linker (L) and a fluorescent tag at the 5′ end. Most SOMAmers (gold and green) bind to cognate proteins (red), but some (blue) form non-cognate complexes. (C) Catch-1. SOMAmers are captured onto a bead coated with streptavidin (SA) which binds biotin. Un-complexed proteins are washed away. (D) Proteins are tagged with NHS-biotin. (E) Photocleavage and kinetic challenge. UV light (hν) cleaves the linker and SOMAmers are released from beads, leaving biotin on bead. Samples are challenged with anionic competitor (dextran sulfate). Non-cognate complexes (blue SOMAmer) preferentially dissociate. (F) Catch-2 SOMAmer-protein complexes are captured onto new avidin coated beads by protein biotin tag. Free SOMAmers are washed away. (G) SOMAmers are released from complexes into solution at high pH. (H) Remaining SOMAmers are quantified by hybridization to microarray containing single-stranded DNA probes complementary to SOMAmer DNA sequence, which form a double-stranded helix. Hybridized SOMAmers are detected by fluorescent tags when the array is scanned.
Figure Legend Snippet: Principle of multiplex SOMAmer affinity assay. (A) Binding. SOMAmers and samples are mixed in 96-well microwell plates and allowed to bind. Cognate and non-cognate SOMAmer-target protein complexes form. Free SOMAmer and protein are also present. (B–H) Schematic sequence of assay steps leading to quantitative readout of target proteins. (B) SOMAmer-protein binding: DNA-based SOMAmer molecules (gold, blue, and green) have unique shapes selected to bind to a specific protein. SOMAmers contain biotin (B), a photo-cleavable linker (L) and a fluorescent tag at the 5′ end. Most SOMAmers (gold and green) bind to cognate proteins (red), but some (blue) form non-cognate complexes. (C) Catch-1. SOMAmers are captured onto a bead coated with streptavidin (SA) which binds biotin. Un-complexed proteins are washed away. (D) Proteins are tagged with NHS-biotin. (E) Photocleavage and kinetic challenge. UV light (hν) cleaves the linker and SOMAmers are released from beads, leaving biotin on bead. Samples are challenged with anionic competitor (dextran sulfate). Non-cognate complexes (blue SOMAmer) preferentially dissociate. (F) Catch-2 SOMAmer-protein complexes are captured onto new avidin coated beads by protein biotin tag. Free SOMAmers are washed away. (G) SOMAmers are released from complexes into solution at high pH. (H) Remaining SOMAmers are quantified by hybridization to microarray containing single-stranded DNA probes complementary to SOMAmer DNA sequence, which form a double-stranded helix. Hybridized SOMAmers are detected by fluorescent tags when the array is scanned.

Techniques Used: Multiplex Assay, Binding Assay, Sequencing, Protein Binding, Avidin-Biotin Assay, Hybridization, Microarray

6) Product Images from "Highly Enhanced Expression of CD70 on Human T-Lymphotropic Virus Type 1-Carrying T-Cell Lines and Adult T-Cell Leukemia Cells "

Article Title: Highly Enhanced Expression of CD70 on Human T-Lymphotropic Virus Type 1-Carrying T-Cell Lines and Adult T-Cell Leukemia Cells

Journal: Journal of Virology

doi: 10.1128/JVI.02013-07

Genes upregulated more than 10-fold in the HTLV-1-carrying T-cell lines S1T, MT-2, and M8166 compared with the genes in HTLV-1-negative T-cell line MOLT-4. The genes of which products are considered to be expressed on the cell surface are shown. All data represent means ± standard deviations (error bars) for three independent microarray experiments.
Figure Legend Snippet: Genes upregulated more than 10-fold in the HTLV-1-carrying T-cell lines S1T, MT-2, and M8166 compared with the genes in HTLV-1-negative T-cell line MOLT-4. The genes of which products are considered to be expressed on the cell surface are shown. All data represent means ± standard deviations (error bars) for three independent microarray experiments.

Techniques Used: Microarray

7) Product Images from "Increased Expression of Matrix Extracellular Phosphoglycoprotein (MEPE) in Cortical Bone of the Rat Tibia after Mechanical Loading: Identification by Oligonucleotide Microarray"

Article Title: Increased Expression of Matrix Extracellular Phosphoglycoprotein (MEPE) in Cortical Bone of the Rat Tibia after Mechanical Loading: Identification by Oligonucleotide Microarray

Journal: PLoS ONE

doi: 10.1371/journal.pone.0079672

Real-time RT-PCR results of MEPE (A‑B), creatinine kinase (muscle form) (C‑D) and troponin‑C (E‑F) mRNA expression in the loaded tibiae and their contralateral controls represented per rat. Different markers represent different rats. Lines connect the right and left tibia of the same rat. For each gene, two primers were used, primer set I, which contained a sequence of the oligonucleotide as spotted on the microarray (A, C, E) and primer set II, which contained a fragment of the gene that was not present on the microarray (B, D, F). a P
Figure Legend Snippet: Real-time RT-PCR results of MEPE (A‑B), creatinine kinase (muscle form) (C‑D) and troponin‑C (E‑F) mRNA expression in the loaded tibiae and their contralateral controls represented per rat. Different markers represent different rats. Lines connect the right and left tibia of the same rat. For each gene, two primers were used, primer set I, which contained a sequence of the oligonucleotide as spotted on the microarray (A, C, E) and primer set II, which contained a fragment of the gene that was not present on the microarray (B, D, F). a P

Techniques Used: Quantitative RT-PCR, Expressing, Sequencing, Microarray

8) Product Images from "Whole transcriptome characterization of the effects of dehydration and rehydration on Cladonia rangiferina, the grey reindeer lichen"

Article Title: Whole transcriptome characterization of the effects of dehydration and rehydration on Cladonia rangiferina, the grey reindeer lichen

Journal: BMC Genomics

doi: 10.1186/1471-2164-14-870

The validation of the microarray results using quantitative real-time RT-PCR. The qRT-PCR values are the mean of four replicate measurements of each of the three samples in the sample group. The microarray values are obtained from linear modelling results, which are calculated from the average expression intensities of the three replicates in each sample group, and therefore variance values are not available. Both microarray and qRT-PCR results are compared to the Dry sample group.
Figure Legend Snippet: The validation of the microarray results using quantitative real-time RT-PCR. The qRT-PCR values are the mean of four replicate measurements of each of the three samples in the sample group. The microarray values are obtained from linear modelling results, which are calculated from the average expression intensities of the three replicates in each sample group, and therefore variance values are not available. Both microarray and qRT-PCR results are compared to the Dry sample group.

Techniques Used: Microarray, Quantitative RT-PCR, Expressing

9) Product Images from "Genome-wide analysis of aberrantly expressed lncRNAs and miRNAs with associated co-expression and ceRNA networks in β-thalassemia and hereditary persistence of fetal hemoglobin"

Article Title: Genome-wide analysis of aberrantly expressed lncRNAs and miRNAs with associated co-expression and ceRNA networks in β-thalassemia and hereditary persistence of fetal hemoglobin

Journal: Oncotarget

doi: 10.18632/oncotarget.18263

Validation of microarray data by qRT-PCR (A) Three up-regulated lncRNAs and (B) three up-regulated miRNAs were validated by qRT-PCR using RNA extracted from reticulocytes of 13 subjects with HPFH and β-thalassemia minor with high HbF and 13 controls. The relative expression level of each RNA was normalized, and the data displayed in histograms are expressed as the means ± SD, **P
Figure Legend Snippet: Validation of microarray data by qRT-PCR (A) Three up-regulated lncRNAs and (B) three up-regulated miRNAs were validated by qRT-PCR using RNA extracted from reticulocytes of 13 subjects with HPFH and β-thalassemia minor with high HbF and 13 controls. The relative expression level of each RNA was normalized, and the data displayed in histograms are expressed as the means ± SD, **P

Techniques Used: Microarray, Quantitative RT-PCR, Expressing

10) Product Images from "Expression of MicroRNAs in the Stem Cell Niche of the Adult Mouse Incisor"

Article Title: Expression of MicroRNAs in the Stem Cell Niche of the Adult Mouse Incisor

Journal: PLoS ONE

doi: 10.1371/journal.pone.0024536

miRNA expression analysis of distinct cell populations in the adult mouse incisor. (A) Cartoon depiction of the adult mouse incisor. (A') Three distinct regions of the adult mouse incisor were isolated for miRNA microarray analysis. liCL, lingual cervical loop; laCL, labial cervical loop; Am, ameloblasts. (B) The number of miRNA transcripts that showed greater than 1.5-fold differential expression (p
Figure Legend Snippet: miRNA expression analysis of distinct cell populations in the adult mouse incisor. (A) Cartoon depiction of the adult mouse incisor. (A') Three distinct regions of the adult mouse incisor were isolated for miRNA microarray analysis. liCL, lingual cervical loop; laCL, labial cervical loop; Am, ameloblasts. (B) The number of miRNA transcripts that showed greater than 1.5-fold differential expression (p

Techniques Used: Expressing, Isolation, Microarray

11) Product Images from "HOXA7, HOXA9, and HOXA10 are differentially expressed in clival and sacral chordomas"

Article Title: HOXA7, HOXA9, and HOXA10 are differentially expressed in clival and sacral chordomas

Journal: Scientific Reports

doi: 10.1038/s41598-017-02174-5

Hierarchical cluster analysis of nine sacral (blue) and three clivus (red) chordoma cell lines. The gene expression was tested using the 4 × 44 K whole genome microarray (Agilent Technologies). Each cell line was tested at least in duplicates.
Figure Legend Snippet: Hierarchical cluster analysis of nine sacral (blue) and three clivus (red) chordoma cell lines. The gene expression was tested using the 4 × 44 K whole genome microarray (Agilent Technologies). Each cell line was tested at least in duplicates.

Techniques Used: Expressing, Microarray

Expression of several HOX gene family members. ( a ) Box plot illustration of the differences in the expression of HOXA2 , - A4 , - A5 , - A7 , - A9 , - A10 , - B3 , - B7 , and - C9 between clivus ( c ) and sacrum (S) chordoma cell lines. Measurements represent the results of microarray expression profiling of three clivus and nine sacrum chordoma cell lines (each cell line was tested at least in duplicates). ( b ) Validation of the expression of HOXA7 , - A9 and - A10 in the chordoma cell lines via qPCR shown as measured ΔCT values. High ΔCT values represent lower expression of the corresponding gene. Measurements were performed in triplicates. Differences in expression were tested by t-tests. p
Figure Legend Snippet: Expression of several HOX gene family members. ( a ) Box plot illustration of the differences in the expression of HOXA2 , - A4 , - A5 , - A7 , - A9 , - A10 , - B3 , - B7 , and - C9 between clivus ( c ) and sacrum (S) chordoma cell lines. Measurements represent the results of microarray expression profiling of three clivus and nine sacrum chordoma cell lines (each cell line was tested at least in duplicates). ( b ) Validation of the expression of HOXA7 , - A9 and - A10 in the chordoma cell lines via qPCR shown as measured ΔCT values. High ΔCT values represent lower expression of the corresponding gene. Measurements were performed in triplicates. Differences in expression were tested by t-tests. p

Techniques Used: Expressing, Microarray, Real-time Polymerase Chain Reaction

12) Product Images from "Biological outcome and mapping of total factor cascades in response to HIF induction during regenerative angiogenesis"

Article Title: Biological outcome and mapping of total factor cascades in response to HIF induction during regenerative angiogenesis

Journal: Oncotarget

doi: 10.18632/oncotarget.7728

Analysis of differentially regulated genes during regeneration and/or HIF induction A. Cluster and heat map analysis. Genes that were differentially expressed during regeneration under normoxic control conditions were obtained through comparison of genes expressed in normoxic control fins (NCf) and genes expressed in normoxic control regenerated area (blastema) (NB) after 3 dpa. Genes that were differentially expressed during HIF induction were derived from the comparison of genes expressed in normoxic control fins (NCf) and genes expressed in CoCl 2 -treated control fins (HCf). Genes that were differentially expressed in CoCl 2 regenerates were obtained through comparison of genes expressed in control normoxic blastema (NB) and genes expressed in CoCl 2 -treated blastema (HB). The heat map indicates the level of genes expression and expressed as log 2 (green is a decrease and red an increase relative to control). The color scale is shown at the top. B. Summary of number of up-regulated and down-regulated genes during regeneration, HIF induction or both obtained by microarray analysis.
Figure Legend Snippet: Analysis of differentially regulated genes during regeneration and/or HIF induction A. Cluster and heat map analysis. Genes that were differentially expressed during regeneration under normoxic control conditions were obtained through comparison of genes expressed in normoxic control fins (NCf) and genes expressed in normoxic control regenerated area (blastema) (NB) after 3 dpa. Genes that were differentially expressed during HIF induction were derived from the comparison of genes expressed in normoxic control fins (NCf) and genes expressed in CoCl 2 -treated control fins (HCf). Genes that were differentially expressed in CoCl 2 regenerates were obtained through comparison of genes expressed in control normoxic blastema (NB) and genes expressed in CoCl 2 -treated blastema (HB). The heat map indicates the level of genes expression and expressed as log 2 (green is a decrease and red an increase relative to control). The color scale is shown at the top. B. Summary of number of up-regulated and down-regulated genes during regeneration, HIF induction or both obtained by microarray analysis.

Techniques Used: Derivative Assay, Expressing, Microarray

13) Product Images from "?9-Tetrahydrocannabinol Disrupts Estrogen-Signaling through Up-Regulation of Estrogen Receptor β (ERβ)"

Article Title: ?9-Tetrahydrocannabinol Disrupts Estrogen-Signaling through Up-Regulation of Estrogen Receptor β (ERβ)

Journal: Chemical research in toxicology

doi: 10.1021/tx4000446

Δ 9 -THC up-regulates ER β . (A) Results of DNA microarray analysis. Data are expressed as fold induction vs vehicle-treated groups. MCF-7 cells were treated with vehicle or 25 μ M Δ 9 -THC for 48 h, followed by mRNA isolation. Details of microarray conditions are described under Materials and Methods. (B) RT-PCR analysis of ER α , ER β , and Ki-67 transcript levels after treatment with 5 or 25 μ M Δ 9 -THC or without Δ 9 -THC (indicated as −). β -Actin was used as an RNA normalization control. A 100-bp DNA ladder marker was also loaded. A representative data image is shown. (C) Western immunoblot analysis of ER β . MCF-7 cells were treated with 5 μ M or 25 μ M Δ 9 -THC (indicated as 5 or 25) or vehicle (indicated as −) for 48 h. The cell lysates derived from transient transfection of human ER β cDNA-expression plasmid (transfected plasmids: 0.0025, 0.25, and 2.5 μ g) were also loaded. Total cell lysates were prepared, and Western immunoblot analyses were performed using antibodies specific for ER β and β -actin, respectively. The band intensity of ER β (−/− lane as 1.0), which was quantified by using NIH Image, version 1.61, software, is shown beneath the blot image. β -Actin was used an internal loading control.
Figure Legend Snippet: Δ 9 -THC up-regulates ER β . (A) Results of DNA microarray analysis. Data are expressed as fold induction vs vehicle-treated groups. MCF-7 cells were treated with vehicle or 25 μ M Δ 9 -THC for 48 h, followed by mRNA isolation. Details of microarray conditions are described under Materials and Methods. (B) RT-PCR analysis of ER α , ER β , and Ki-67 transcript levels after treatment with 5 or 25 μ M Δ 9 -THC or without Δ 9 -THC (indicated as −). β -Actin was used as an RNA normalization control. A 100-bp DNA ladder marker was also loaded. A representative data image is shown. (C) Western immunoblot analysis of ER β . MCF-7 cells were treated with 5 μ M or 25 μ M Δ 9 -THC (indicated as 5 or 25) or vehicle (indicated as −) for 48 h. The cell lysates derived from transient transfection of human ER β cDNA-expression plasmid (transfected plasmids: 0.0025, 0.25, and 2.5 μ g) were also loaded. Total cell lysates were prepared, and Western immunoblot analyses were performed using antibodies specific for ER β and β -actin, respectively. The band intensity of ER β (−/− lane as 1.0), which was quantified by using NIH Image, version 1.61, software, is shown beneath the blot image. β -Actin was used an internal loading control.

Techniques Used: Microarray, Isolation, Reverse Transcription Polymerase Chain Reaction, Marker, Western Blot, Derivative Assay, Transfection, Expressing, Plasmid Preparation, Software

14) Product Images from "Wnt activity and basal niche position sensitize intestinal stem and progenitor cells to DNA damage"

Article Title: Wnt activity and basal niche position sensitize intestinal stem and progenitor cells to DNA damage

Journal: The EMBO Journal

doi: 10.15252/embj.201490700

Enhanced induction of p53-dependent apoptosis in response to irradiation in LGR5 hi cells compared to LGR5 lo cells A mRNA gene expression analysis by microarray. The figure shows the number of differentially expressed genes (#dg) and the median absolute fold change (med. Abs. FC) for genes that are regulated in both LGR5 hi cells and LGR5 lo cells in response to IR ( n = 4–5 samples per group). NIR, non-irradiated; IR, irradiated. Wilcoxon test. B, C LGR5 hi and LGR5 lo cells were freshly isolated from 3-month-old LGR5-GFP ki mice 6 h after 12 Gy γ-irradiation (IR) or from non-irradiated (NIR) mice ( n = 3 mice per group). (B) qPCR analysis of relative mRNA expression of apoptosis-related genes compared to GAPDH . Mean values ± SEM are given. Unpaired two-tailed Student's t -test. (C) Representative Western blot analysis of cell lysates for the expression of phospho-p53 and cleaved caspase-3. D, E Three-month-old mTerc +/+ mice were γ-irradiated with 12 Gy. Small intestinal tissue was collected at 3 h after IR ( n = 3 mice per group). (D) Representative picture of TUNEL staining. Arrowheads and numbers indicate ISPC positions in the crypts. Scale bar: 20 μm. (E) Percentage of TUNEL-positive ISPCs at indicated positions in basal crypts. Mean values ± SEM are given. Unpaired two-tailed Student's t -test. F, P Two-month-old LGR5-GFP ki , p53 +/+ mice and LGR5-GFP ki , p53 −/− mice were exposed to 12 Gy γ-irradiation ( n = 4 mice per group). Basal crypts were isolated at 24 h after IR. (F–H) Flow cytometry analysis of the survival rate of LGR5 + cells (F), LGR5 hi and LGR5 lo cells (G), and LGR5 hi-high and LGR5 hi-low cells (H) of irradiated mice (24 h after IR) compared to non-irradiated mice (NIR). Mean values ± SEM are given. Unpaired two-tailed Student's t -test. (I–P) Representative FACS plots of LGR5 + cells in freshly isolated basal crypts from irradiated and non-irradiated mice of indicated genotypes. Note the stronger rescue of survival rate of LGR5 hi-high than the LGR5 hi-low cells upon p53 deletion. NIR, non-irradiated; IR, irradiated.
Figure Legend Snippet: Enhanced induction of p53-dependent apoptosis in response to irradiation in LGR5 hi cells compared to LGR5 lo cells A mRNA gene expression analysis by microarray. The figure shows the number of differentially expressed genes (#dg) and the median absolute fold change (med. Abs. FC) for genes that are regulated in both LGR5 hi cells and LGR5 lo cells in response to IR ( n = 4–5 samples per group). NIR, non-irradiated; IR, irradiated. Wilcoxon test. B, C LGR5 hi and LGR5 lo cells were freshly isolated from 3-month-old LGR5-GFP ki mice 6 h after 12 Gy γ-irradiation (IR) or from non-irradiated (NIR) mice ( n = 3 mice per group). (B) qPCR analysis of relative mRNA expression of apoptosis-related genes compared to GAPDH . Mean values ± SEM are given. Unpaired two-tailed Student's t -test. (C) Representative Western blot analysis of cell lysates for the expression of phospho-p53 and cleaved caspase-3. D, E Three-month-old mTerc +/+ mice were γ-irradiated with 12 Gy. Small intestinal tissue was collected at 3 h after IR ( n = 3 mice per group). (D) Representative picture of TUNEL staining. Arrowheads and numbers indicate ISPC positions in the crypts. Scale bar: 20 μm. (E) Percentage of TUNEL-positive ISPCs at indicated positions in basal crypts. Mean values ± SEM are given. Unpaired two-tailed Student's t -test. F, P Two-month-old LGR5-GFP ki , p53 +/+ mice and LGR5-GFP ki , p53 −/− mice were exposed to 12 Gy γ-irradiation ( n = 4 mice per group). Basal crypts were isolated at 24 h after IR. (F–H) Flow cytometry analysis of the survival rate of LGR5 + cells (F), LGR5 hi and LGR5 lo cells (G), and LGR5 hi-high and LGR5 hi-low cells (H) of irradiated mice (24 h after IR) compared to non-irradiated mice (NIR). Mean values ± SEM are given. Unpaired two-tailed Student's t -test. (I–P) Representative FACS plots of LGR5 + cells in freshly isolated basal crypts from irradiated and non-irradiated mice of indicated genotypes. Note the stronger rescue of survival rate of LGR5 hi-high than the LGR5 hi-low cells upon p53 deletion. NIR, non-irradiated; IR, irradiated.

Techniques Used: Irradiation, Expressing, Microarray, Isolation, Mouse Assay, Real-time Polymerase Chain Reaction, Two Tailed Test, Western Blot, TUNEL Assay, Staining, Flow Cytometry, Cytometry, FACS

15) Product Images from "Redox-dependent condensation of the mycobacterial nucleoid by WhiB4"

Article Title: Redox-dependent condensation of the mycobacterial nucleoid by WhiB4

Journal: Redox Biology

doi: 10.1016/j.redox.2018.08.006

WhiB4 mediated regulation of gene expression in response to oxidative stress in Mtb . Wt Mtb, Mtb Δ whiB4, and whiB4-Comp strains were grown and exposed to 250 μM CHP for 2 h. Total RNA was isolated and subjected to microarray analysis. Heat maps depicting the comparison of gene expression (Log 2 fold-change, p value ≤ 0.05) coordinating respiration, CCM, DNA damage, PE-PPE and redox balance between wt Mtb [T] vs wt Mtb [UT]; Mtb ∆ whiB4 [T] vs wt Mtb [T] and whiB4-Comp [T] vs wt Mtb [T] from two biological samples. UT- untreated, T- CHP treated.
Figure Legend Snippet: WhiB4 mediated regulation of gene expression in response to oxidative stress in Mtb . Wt Mtb, Mtb Δ whiB4, and whiB4-Comp strains were grown and exposed to 250 μM CHP for 2 h. Total RNA was isolated and subjected to microarray analysis. Heat maps depicting the comparison of gene expression (Log 2 fold-change, p value ≤ 0.05) coordinating respiration, CCM, DNA damage, PE-PPE and redox balance between wt Mtb [T] vs wt Mtb [UT]; Mtb ∆ whiB4 [T] vs wt Mtb [T] and whiB4-Comp [T] vs wt Mtb [T] from two biological samples. UT- untreated, T- CHP treated.

Techniques Used: Expressing, Isolation, Microarray

16) Product Images from "Genome-wide analysis of aberrantly expressed lncRNAs and miRNAs with associated co-expression and ceRNA networks in β-thalassemia and hereditary persistence of fetal hemoglobin"

Article Title: Genome-wide analysis of aberrantly expressed lncRNAs and miRNAs with associated co-expression and ceRNA networks in β-thalassemia and hereditary persistence of fetal hemoglobin

Journal: Oncotarget

doi: 10.18632/oncotarget.18263

Validation of microarray data by qRT-PCR (A) Three up-regulated lncRNAs and (B) three up-regulated miRNAs were validated by qRT-PCR using RNA extracted from reticulocytes of 13 subjects with HPFH and β-thalassemia minor with high HbF and 13 controls. The relative expression level of each RNA was normalized, and the data displayed in histograms are expressed as the means ± SD, **P
Figure Legend Snippet: Validation of microarray data by qRT-PCR (A) Three up-regulated lncRNAs and (B) three up-regulated miRNAs were validated by qRT-PCR using RNA extracted from reticulocytes of 13 subjects with HPFH and β-thalassemia minor with high HbF and 13 controls. The relative expression level of each RNA was normalized, and the data displayed in histograms are expressed as the means ± SD, **P

Techniques Used: Microarray, Quantitative RT-PCR, Expressing

17) Product Images from "Microarray Analysis of Gene Expression Changes in Neuroplastin 65-Knockout Mice: Implications for Abnormal Cognition and Emotional Disorders"

Article Title: Microarray Analysis of Gene Expression Changes in Neuroplastin 65-Knockout Mice: Implications for Abnormal Cognition and Emotional Disorders

Journal: Neuroscience Bulletin

doi: 10.1007/s12264-018-0251-5

Relative expression levels of selected genes in Np65 -KO and WT mice. A Results of quantitative real-time PCR (RT-PCR) ( n = 4 mice). B RT-PCR and microarray experimental results for relative gene expression in Np65 -KO and WT mice. The relative expression levels were calculated as the ratio of the target gene expression level to the β-actin expression level in the same sample. Fold changes are shown as mean ± SEM. * P
Figure Legend Snippet: Relative expression levels of selected genes in Np65 -KO and WT mice. A Results of quantitative real-time PCR (RT-PCR) ( n = 4 mice). B RT-PCR and microarray experimental results for relative gene expression in Np65 -KO and WT mice. The relative expression levels were calculated as the ratio of the target gene expression level to the β-actin expression level in the same sample. Fold changes are shown as mean ± SEM. * P

Techniques Used: Expressing, Mouse Assay, Real-time Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, Microarray

Differentially-expressed genes in the hippocampus of Np65 -KO mice. A Scatter plot of normalized intensity derived from microarray chips with WT and Np65 -KO mice. Dots above the red line denote upregulated genes, and dots below the green line denote downregulated genes. B Venn diagram showing the percentages of differentially-expressed genes categorized by fold-change. C Hierarchical clustering of differentially-expressed genes. N1–N3, Np65 -KO mice; W1–W3, WT mice. D Fold changes of differentially-expressed genes in Np65 -KO mice. E Chromosome distributions of differentially-expressed genes in Np65 -KO mice. Red bars, numbers of upregulated genes; green bars, numbers of downregulated genes.
Figure Legend Snippet: Differentially-expressed genes in the hippocampus of Np65 -KO mice. A Scatter plot of normalized intensity derived from microarray chips with WT and Np65 -KO mice. Dots above the red line denote upregulated genes, and dots below the green line denote downregulated genes. B Venn diagram showing the percentages of differentially-expressed genes categorized by fold-change. C Hierarchical clustering of differentially-expressed genes. N1–N3, Np65 -KO mice; W1–W3, WT mice. D Fold changes of differentially-expressed genes in Np65 -KO mice. E Chromosome distributions of differentially-expressed genes in Np65 -KO mice. Red bars, numbers of upregulated genes; green bars, numbers of downregulated genes.

Techniques Used: Mouse Assay, Derivative Assay, Microarray

18) Product Images from "Transcriptome Analyses of a Salt-Tolerant Cytokinin-Deficient Mutant Reveal Differential Regulation of Salt Stress Response by Cytokinin Deficiency"

Article Title: Transcriptome Analyses of a Salt-Tolerant Cytokinin-Deficient Mutant Reveal Differential Regulation of Salt Stress Response by Cytokinin Deficiency

Journal: PLoS ONE

doi: 10.1371/journal.pone.0032124

Confirmation of microarray data by qRT-PCR analysis. Eight genes were selected and their expression profiles were assessed by qRT-PCR in all four plant samples to verify the microarray data. (A) Fold changes were obtained from microarray analysis. (B) Fold changes were obtained from qRT-PCR analysis. Fold changes were calculated from the expression data obtained by qRT-PCR in all four samples. Relative quantitation of expression was calculated using 2 −ΔCt method and UBQ10 as endogenous control. cDNAs were obtained from three biological replicates.
Figure Legend Snippet: Confirmation of microarray data by qRT-PCR analysis. Eight genes were selected and their expression profiles were assessed by qRT-PCR in all four plant samples to verify the microarray data. (A) Fold changes were obtained from microarray analysis. (B) Fold changes were obtained from qRT-PCR analysis. Fold changes were calculated from the expression data obtained by qRT-PCR in all four samples. Relative quantitation of expression was calculated using 2 −ΔCt method and UBQ10 as endogenous control. cDNAs were obtained from three biological replicates.

Techniques Used: Microarray, Quantitative RT-PCR, Expressing, Quantitation Assay

19) Product Images from "Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes"

Article Title: Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes

Journal:

doi: 10.1038/nprot.2007.53

Chromosome 10 array-CGH profile of a colon cancer cell line on a whole-genome tiling path microarray. ( a ) The profile indicates a single copy gain (highlighted in green) and a single copy deletion (highlighted in red) on the q-arm of chromosome 10. (
Figure Legend Snippet: Chromosome 10 array-CGH profile of a colon cancer cell line on a whole-genome tiling path microarray. ( a ) The profile indicates a single copy gain (highlighted in green) and a single copy deletion (highlighted in red) on the q-arm of chromosome 10. (

Techniques Used: Microarray

Principle of array-CGH. Genomic DNA from two cell populations is differentially labeled and hybridized to a microarray in the presence of Cot1 DNA to suppress repeat sequences. The fluorescent ratios on each array spot are calculated and normalized so
Figure Legend Snippet: Principle of array-CGH. Genomic DNA from two cell populations is differentially labeled and hybridized to a microarray in the presence of Cot1 DNA to suppress repeat sequences. The fluorescent ratios on each array spot are calculated and normalized so

Techniques Used: Labeling, Microarray

20) Product Images from "Chromosomal Microarray With Clinical Diagnostic Utility in Children With Developmental Delay or Intellectual Disability"

Article Title: Chromosomal Microarray With Clinical Diagnostic Utility in Children With Developmental Delay or Intellectual Disability

Journal: Annals of Laboratory Medicine

doi: 10.3343/alm.2018.38.5.473

Microarray data of the rarely reported pathogenic copy number variations verified in this study: Agilent Human Genome oligonucleotide CGH showing deletions of 2.98 Mb on 2p21p16.3 (A), 1.46 Mb on 3p21.31 (B), 4.22 Mb on 10p11.22p11.21 (C), and 3.3 Mb on 14q24.2 (D).
Figure Legend Snippet: Microarray data of the rarely reported pathogenic copy number variations verified in this study: Agilent Human Genome oligonucleotide CGH showing deletions of 2.98 Mb on 2p21p16.3 (A), 1.46 Mb on 3p21.31 (B), 4.22 Mb on 10p11.22p11.21 (C), and 3.3 Mb on 14q24.2 (D).

Techniques Used: Microarray

21) Product Images from "Untargeted screening for novel autoantibodies with prognostic value in first-episode psychosis"

Article Title: Untargeted screening for novel autoantibodies with prognostic value in first-episode psychosis

Journal: Translational Psychiatry

doi: 10.1038/tp.2017.160

( a ) General levels of seroreactivity in plasma samples from patients with first-episode psychosis (red bars) and non-psychotic controls (green bars). Results from the untargeted screening with planar microarray assays are shown. The majority of the reactive protein fragments (out of the 2304) were targets for seroreactivity in very few individuals (upper left), whereas a few protein fragments were seropositive in a majority of the samples. ( b ) Distribution of the number of reactive antigens in plasma samples from patients with first-episode psychosis versus non-psychotic controls. Results from the untargeted screening with planar microarray assays are shown. Red dots depict values for patients who subsequently were diagnosed with schizophrenia; yellow dots depict values for patients who developed delusional disorder, schizoaffective disorder, bipolar disorder or unspecified nonorganic psychosis; and blue dots depict values for patients who achieved complete remission.
Figure Legend Snippet: ( a ) General levels of seroreactivity in plasma samples from patients with first-episode psychosis (red bars) and non-psychotic controls (green bars). Results from the untargeted screening with planar microarray assays are shown. The majority of the reactive protein fragments (out of the 2304) were targets for seroreactivity in very few individuals (upper left), whereas a few protein fragments were seropositive in a majority of the samples. ( b ) Distribution of the number of reactive antigens in plasma samples from patients with first-episode psychosis versus non-psychotic controls. Results from the untargeted screening with planar microarray assays are shown. Red dots depict values for patients who subsequently were diagnosed with schizophrenia; yellow dots depict values for patients who developed delusional disorder, schizoaffective disorder, bipolar disorder or unspecified nonorganic psychosis; and blue dots depict values for patients who achieved complete remission.

Techniques Used: Microarray

22) Product Images from "LncRNA ENST00000539653 acts as an oncogenic factor via MAPK signalling in papillary thyroid cancer"

Article Title: LncRNA ENST00000539653 acts as an oncogenic factor via MAPK signalling in papillary thyroid cancer

Journal: BMC Cancer

doi: 10.1186/s12885-019-5533-4

LncRNA microarray analysis in papillary thyroid cancer (PTC) tissues compared with matched adjacent noncancerous thyroid tissues. a Hierarchical clustering analysis of differentially expressed lncRNAs. Red and green colors indicate high and low expression, respectively. In the heat map, columns represent samples and rows represent each lncRNA. b Volcano plot of differentially expressed lncRNAs between PTC and paired noncancerous thyroid tissue. The vertical lines correspond to 2.0-fold upregulation and downregulation, and the horizontal line represents a P value of 0.05
Figure Legend Snippet: LncRNA microarray analysis in papillary thyroid cancer (PTC) tissues compared with matched adjacent noncancerous thyroid tissues. a Hierarchical clustering analysis of differentially expressed lncRNAs. Red and green colors indicate high and low expression, respectively. In the heat map, columns represent samples and rows represent each lncRNA. b Volcano plot of differentially expressed lncRNAs between PTC and paired noncancerous thyroid tissue. The vertical lines correspond to 2.0-fold upregulation and downregulation, and the horizontal line represents a P value of 0.05

Techniques Used: Microarray, Expressing

QRT-PCR validation of selected differentially expressed lncRNAs. a Comparison between microarray and qRT-PCR results. The heights of the columns represent the log-transformed median fold changes (Tumor/Normal tissues) in the expression in 86 paired PTC and noncancerous thyroid tissues. b Relative expression level of ENS-653 in 86 pairs of PTC and noncancerous thyroid tissues. ENS-653 expression was evaluated by qRT-PCR and normalized to GAPDH mRNA expression. Data are expressed as a mean ± SD. c Proportion of cases with positive fold changes of ENS-653 expression in PTC compared with noncancerous thyroid tissues. ** P
Figure Legend Snippet: QRT-PCR validation of selected differentially expressed lncRNAs. a Comparison between microarray and qRT-PCR results. The heights of the columns represent the log-transformed median fold changes (Tumor/Normal tissues) in the expression in 86 paired PTC and noncancerous thyroid tissues. b Relative expression level of ENS-653 in 86 pairs of PTC and noncancerous thyroid tissues. ENS-653 expression was evaluated by qRT-PCR and normalized to GAPDH mRNA expression. Data are expressed as a mean ± SD. c Proportion of cases with positive fold changes of ENS-653 expression in PTC compared with noncancerous thyroid tissues. ** P

Techniques Used: Quantitative RT-PCR, Microarray, Transformation Assay, Expressing

23) Product Images from "Major urinary protein 5, a scent communication protein, is regulated by dietary restriction and subsequent re-feeding in mice"

Article Title: Major urinary protein 5, a scent communication protein, is regulated by dietary restriction and subsequent re-feeding in mice

Journal: Proceedings of the Royal Society B: Biological Sciences

doi: 10.1098/rspb.2013.0101

Dietary restriction leads to deacetylation of the lysine 9 residue in histone 3 (H3K9) close to the Mup5 gene on chromosome 4 (light grey bar). The black bar indicates the region tiled by the microarray. Acetylation of H3K9 within this region in the liver of DR-fed compared with AL-fed mice is indicated with grey bars. Following DR, H3K9 is deacetylated, leading to inhibition of gene expression. Representative results of two mice per group are shown.
Figure Legend Snippet: Dietary restriction leads to deacetylation of the lysine 9 residue in histone 3 (H3K9) close to the Mup5 gene on chromosome 4 (light grey bar). The black bar indicates the region tiled by the microarray. Acetylation of H3K9 within this region in the liver of DR-fed compared with AL-fed mice is indicated with grey bars. Following DR, H3K9 is deacetylated, leading to inhibition of gene expression. Representative results of two mice per group are shown.

Techniques Used: Microarray, Mouse Assay, Inhibition, Expressing

24) Product Images from "The Cortical and Striatal Gene Expression Profile of 100 Hz Electroacupuncture Treatment in 6-Hydroxydopamine-Induced Parkinson's Disease Model"

Article Title: The Cortical and Striatal Gene Expression Profile of 100 Hz Electroacupuncture Treatment in 6-Hydroxydopamine-Induced Parkinson's Disease Model

Journal: Evidence-based Complementary and Alternative Medicine : eCAM

doi: 10.1155/2012/908439

Selected transcripts clustered and validated with real-time PCR. After pathway analysis, we selected genes involved in major pathways (the common pathways in the cortex and STR, Table 7). First, selected genes were clustered using Cluster 3.0 according to the LOG value in the STR groups (a) Red is relatively upregulated and green is relatively downregulated in different samples. The three “Cs” are the three control samples. The three “Ms” are the model samples. The three “Es” are the EA-treated samples. Then, to verify the reliability of the microarray analysis, we verified these selected genes from the clustering diagram using real-time RT-PCR. The real-time PCR primers are listed on Table S1 (devised and synthesized by Takara). The reaction procedure was present on (b). If the level of control was regarded as 1, the corresponding gene expression in model and EA-treated groups were present on (c). These transcripts analyzed here showed coherent profiles with cluster (a).
Figure Legend Snippet: Selected transcripts clustered and validated with real-time PCR. After pathway analysis, we selected genes involved in major pathways (the common pathways in the cortex and STR, Table 7). First, selected genes were clustered using Cluster 3.0 according to the LOG value in the STR groups (a) Red is relatively upregulated and green is relatively downregulated in different samples. The three “Cs” are the three control samples. The three “Ms” are the model samples. The three “Es” are the EA-treated samples. Then, to verify the reliability of the microarray analysis, we verified these selected genes from the clustering diagram using real-time RT-PCR. The real-time PCR primers are listed on Table S1 (devised and synthesized by Takara). The reaction procedure was present on (b). If the level of control was regarded as 1, the corresponding gene expression in model and EA-treated groups were present on (c). These transcripts analyzed here showed coherent profiles with cluster (a).

Techniques Used: Real-time Polymerase Chain Reaction, Microarray, Quantitative RT-PCR, Synthesized, Expressing

The flow-sheet was used for the data analysis of genomic profile. Three biology duplicate samples in each group were used for microarray analyzing. The cortex and right STR were examined, and the differential genes in this figure came from comparison of three groups ( P
Figure Legend Snippet: The flow-sheet was used for the data analysis of genomic profile. Three biology duplicate samples in each group were used for microarray analyzing. The cortex and right STR were examined, and the differential genes in this figure came from comparison of three groups ( P

Techniques Used: Flow Cytometry, Microarray

25) Product Images from "The MalR type regulator AcrC is a transcriptional repressor of acarbose biosynthetic genes in Actinoplanes sp. SE50/110"

Article Title: The MalR type regulator AcrC is a transcriptional repressor of acarbose biosynthetic genes in Actinoplanes sp. SE50/110

Journal: BMC Genomics

doi: 10.1186/s12864-017-3941-x

Differential transcriptional analysis of the deletion mutant Δ acrC compared to the wild type. a Ratio/intensity plot from whole genome microarrays of the strain Actinoplanes sp. SE50/110 Δ acrC compared to the Actinoplanes sp. SE50/110 wild type grown in maltose minimal medium (Mal-MM). Green and red dots represent genes with significantly different transcript levels in the Δ acrC strain. Filled dots show acb genes. b Ratio/intensity plot from whole genome microarrays of the strain Δ acrC compared to the wild type grown in glucose minimal medium (Glc-MM). c Heatmap of the fold change of transcript abundance for the genes of the acb gene cluster, derived from the microarray data shown in 2A and 2B. Significance of p
Figure Legend Snippet: Differential transcriptional analysis of the deletion mutant Δ acrC compared to the wild type. a Ratio/intensity plot from whole genome microarrays of the strain Actinoplanes sp. SE50/110 Δ acrC compared to the Actinoplanes sp. SE50/110 wild type grown in maltose minimal medium (Mal-MM). Green and red dots represent genes with significantly different transcript levels in the Δ acrC strain. Filled dots show acb genes. b Ratio/intensity plot from whole genome microarrays of the strain Δ acrC compared to the wild type grown in glucose minimal medium (Glc-MM). c Heatmap of the fold change of transcript abundance for the genes of the acb gene cluster, derived from the microarray data shown in 2A and 2B. Significance of p

Techniques Used: Mutagenesis, Gas Chromatography, Derivative Assay, Microarray

26) Product Images from "Transcriptome Analysis of the Hierarchical Response of Histone Deacetylase Proteins That Respond in an Antagonistic Manner to Salinity Stress"

Article Title: Transcriptome Analysis of the Hierarchical Response of Histone Deacetylase Proteins That Respond in an Antagonistic Manner to Salinity Stress

Journal: Frontiers in Plant Science

doi: 10.3389/fpls.2019.01323

Microarray analysis of genome-wide transcription in Col-0, hda19-3 , quad , and quint plants under non-stressed and salinity-stressed growth conditions. (A) The survival rate (in percent) of each plant was evaluated 4 days after treatment with 100 mM NaCl or without NaCl (means ± SD; n = 3, where each biological replicate was a collection of 10 plants). P values were calculated using Student’s t test (* P
Figure Legend Snippet: Microarray analysis of genome-wide transcription in Col-0, hda19-3 , quad , and quint plants under non-stressed and salinity-stressed growth conditions. (A) The survival rate (in percent) of each plant was evaluated 4 days after treatment with 100 mM NaCl or without NaCl (means ± SD; n = 3, where each biological replicate was a collection of 10 plants). P values were calculated using Student’s t test (* P

Techniques Used: Microarray, Genome Wide

27) Product Images from "Selective gene expression by rat gastric corpus epithelium"

Article Title: Selective gene expression by rat gastric corpus epithelium

Journal: Physiological Genomics

doi: 10.1152/physiolgenomics.00193.2010

Gene validation by RT-qPCR of selected genes. Based on microarray gene expression data 4 genes previously known to be selectively expressed in 1 segment ( A ) were chosen and mRNA expression assessed by RT-qPCR. Significant enrichment (log ratio > 1)
Figure Legend Snippet: Gene validation by RT-qPCR of selected genes. Based on microarray gene expression data 4 genes previously known to be selectively expressed in 1 segment ( A ) were chosen and mRNA expression assessed by RT-qPCR. Significant enrichment (log ratio > 1)

Techniques Used: Quantitative RT-PCR, Microarray, Expressing

28) Product Images from "Deciphering the Role of RND Efflux Transporters in Burkholderia cenocepacia"

Article Title: Deciphering the Role of RND Efflux Transporters in Burkholderia cenocepacia

Journal: PLoS ONE

doi: 10.1371/journal.pone.0018902

The Phenotype Microarray profile of B. cenocepacia J2315 and the RND mutants. Metabolic plates (from PM 11 to PM20) representing the growth of the three B. cenocepacia mutant strains D4, D9 and D4–D9 versus the wild-type strain J2315, in the presence of toxic compounds is shown.
Figure Legend Snippet: The Phenotype Microarray profile of B. cenocepacia J2315 and the RND mutants. Metabolic plates (from PM 11 to PM20) representing the growth of the three B. cenocepacia mutant strains D4, D9 and D4–D9 versus the wild-type strain J2315, in the presence of toxic compounds is shown.

Techniques Used: Microarray, Mutagenesis

29) Product Images from "Sexually dimorphic gene expression in the heart of mice and men"

Article Title: Sexually dimorphic gene expression in the heart of mice and men

Journal: Journal of Molecular Medicine (Berlin, Germany)

doi: 10.1007/s00109-007-0240-z

Candidate genes identified by microarray approaches. a False colour representation of the 13 overlapping genes (see also intersection in the Venn diagram) identified with sex-biased expression in 2 as well as in 8 months old mice. Fold-changes were calculated from four technical replicates using pooled total RNA isolated from male and female whole mouse hearts of both age groups ( n = 6 per group). Numbers of genes identified with sex-biased expression in each group (90 and 33, respectively) are shown in the Venn diagram. b False colour representation of the 14 overlapping genes (see also intersection in the Venn diagram) identified with sex-biased expression in human left ventricular samples of both age groups. Fold-changes were calculated from four technical replicates using pooled total RNA isolated from three to five samples per group. Numbers of genes identified with sex-biased expression in each age group (93 and 125, respectively) are shown in the Venn diagram. c False colour representation of the 16 genes identified in the Cardiogenomics dataset with sex-biased expression in myocardial tissue of male (mean age = 53.6 years) and female (mean age = 49.3 years) human donors ( n = 7 per group). Note that for some genes sex-biased expression was detected in both species (e.g. Ddx3y and Jarid1d) as well as in both platforms (USP9Y and RPS4Y1). Shades of red represent female-biased expression and blue , male-biased expression in individual samples (FDR
Figure Legend Snippet: Candidate genes identified by microarray approaches. a False colour representation of the 13 overlapping genes (see also intersection in the Venn diagram) identified with sex-biased expression in 2 as well as in 8 months old mice. Fold-changes were calculated from four technical replicates using pooled total RNA isolated from male and female whole mouse hearts of both age groups ( n = 6 per group). Numbers of genes identified with sex-biased expression in each group (90 and 33, respectively) are shown in the Venn diagram. b False colour representation of the 14 overlapping genes (see also intersection in the Venn diagram) identified with sex-biased expression in human left ventricular samples of both age groups. Fold-changes were calculated from four technical replicates using pooled total RNA isolated from three to five samples per group. Numbers of genes identified with sex-biased expression in each age group (93 and 125, respectively) are shown in the Venn diagram. c False colour representation of the 16 genes identified in the Cardiogenomics dataset with sex-biased expression in myocardial tissue of male (mean age = 53.6 years) and female (mean age = 49.3 years) human donors ( n = 7 per group). Note that for some genes sex-biased expression was detected in both species (e.g. Ddx3y and Jarid1d) as well as in both platforms (USP9Y and RPS4Y1). Shades of red represent female-biased expression and blue , male-biased expression in individual samples (FDR

Techniques Used: Microarray, Expressing, Mouse Assay, Isolation

Experimental design to screen for genes with sex-biased expression in the heart of mice and human donors. Total RNA was isolated from mouse whole heart samples and from myocardial tissue of human donors. Cyanine dye labelled cDNAs generated from pooled RNAs were hybridised on Agilent cDNA microarrays. In addition, human myocardial expression datasets were downloaded from CardioGenomics and filtered for sex-biased genes. Candidate gene lists were compared to identify sexual dimorphisms in young as well as aged individuals and both species and platforms. Expression levels of several candidate genes were quantified individually by real-time PCR (QPCR) in the same samples used for microarray analysis and in left ventricular samples from female mice at different stages of the oestrous as well as from males ( n = 8 per group). Numbers of individuals analysed by QPCR are shown in brackets . FDR , false discovery rate; y , years; mon , months
Figure Legend Snippet: Experimental design to screen for genes with sex-biased expression in the heart of mice and human donors. Total RNA was isolated from mouse whole heart samples and from myocardial tissue of human donors. Cyanine dye labelled cDNAs generated from pooled RNAs were hybridised on Agilent cDNA microarrays. In addition, human myocardial expression datasets were downloaded from CardioGenomics and filtered for sex-biased genes. Candidate gene lists were compared to identify sexual dimorphisms in young as well as aged individuals and both species and platforms. Expression levels of several candidate genes were quantified individually by real-time PCR (QPCR) in the same samples used for microarray analysis and in left ventricular samples from female mice at different stages of the oestrous as well as from males ( n = 8 per group). Numbers of individuals analysed by QPCR are shown in brackets . FDR , false discovery rate; y , years; mon , months

Techniques Used: Expressing, Mouse Assay, Isolation, Generated, Real-time Polymerase Chain Reaction, Microarray

30) Product Images from "Microarray Analysis of Gene Expression Changes in Neuroplastin 65-Knockout Mice: Implications for Abnormal Cognition and Emotional Disorders"

Article Title: Microarray Analysis of Gene Expression Changes in Neuroplastin 65-Knockout Mice: Implications for Abnormal Cognition and Emotional Disorders

Journal: Neuroscience Bulletin

doi: 10.1007/s12264-018-0251-5

Differentially-expressed genes in the hippocampus of Np65 -KO mice. A Scatter plot of normalized intensity derived from microarray chips with WT and Np65 -KO mice. Dots above the red line denote upregulated genes, and dots below the green line denote downregulated genes. B Venn diagram showing the percentages of differentially-expressed genes categorized by fold-change. C Hierarchical clustering of differentially-expressed genes. N1–N3, Np65 -KO mice; W1–W3, WT mice. D Fold changes of differentially-expressed genes in Np65 -KO mice. E Chromosome distributions of differentially-expressed genes in Np65 -KO mice. Red bars, numbers of upregulated genes; green bars, numbers of downregulated genes.
Figure Legend Snippet: Differentially-expressed genes in the hippocampus of Np65 -KO mice. A Scatter plot of normalized intensity derived from microarray chips with WT and Np65 -KO mice. Dots above the red line denote upregulated genes, and dots below the green line denote downregulated genes. B Venn diagram showing the percentages of differentially-expressed genes categorized by fold-change. C Hierarchical clustering of differentially-expressed genes. N1–N3, Np65 -KO mice; W1–W3, WT mice. D Fold changes of differentially-expressed genes in Np65 -KO mice. E Chromosome distributions of differentially-expressed genes in Np65 -KO mice. Red bars, numbers of upregulated genes; green bars, numbers of downregulated genes.

Techniques Used: Mouse Assay, Derivative Assay, Microarray

Relative expression levels of selected genes in Np65 -KO and WT mice. A Results of quantitative real-time PCR (RT-PCR) ( n = 4 mice). B RT-PCR and microarray experimental results for relative gene expression in Np65 -KO and WT mice. The relative expression levels were calculated as the ratio of the target gene expression level to the β-actin expression level in the same sample. Fold changes are shown as mean ± SEM. * P
Figure Legend Snippet: Relative expression levels of selected genes in Np65 -KO and WT mice. A Results of quantitative real-time PCR (RT-PCR) ( n = 4 mice). B RT-PCR and microarray experimental results for relative gene expression in Np65 -KO and WT mice. The relative expression levels were calculated as the ratio of the target gene expression level to the β-actin expression level in the same sample. Fold changes are shown as mean ± SEM. * P

Techniques Used: Expressing, Mouse Assay, Real-time Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, Microarray

31) Product Images from "Surface Glycosylation Profiles of Urine Extracellular Vesicles"

Article Title: Surface Glycosylation Profiles of Urine Extracellular Vesicles

Journal: PLoS ONE

doi: 10.1371/journal.pone.0074801

Graphical representation of results of lectin microarrays of intact urine uEVs after glycosidase and amidase treatment. Combined panels represent the complete set of microarray features containing 43 lectins and two negative controls (PBS and BSA). All data shown represent the mean ± average deviation of 3 technical replicates carried out on a single biological sample.
Figure Legend Snippet: Graphical representation of results of lectin microarrays of intact urine uEVs after glycosidase and amidase treatment. Combined panels represent the complete set of microarray features containing 43 lectins and two negative controls (PBS and BSA). All data shown represent the mean ± average deviation of 3 technical replicates carried out on a single biological sample.

Techniques Used: Microarray

Schematic of lectin microarray profiling process.
Figure Legend Snippet: Schematic of lectin microarray profiling process.

Techniques Used: Microarray

Unsupervised hierarchical clustering of lectin microarray profiles for intact urine uEVs and purified THP from three healthy individuals. LM data for all uEV (donors D1, D2, and D3) and THP samples (donors D1, D2 and D4) normalized by rescaling (range 0 to 65200). Individual technical replicates are indicated by designation of 1 to 5. Two groups are evident at 0.28 similarity, three groups at 0.57 similarity. Clustering based on Euclidean distance, complete linkage method. Responses and clustering shown are typical of those obtained from a minimum of 10 healthy uEV enrichment and profiling experiments.
Figure Legend Snippet: Unsupervised hierarchical clustering of lectin microarray profiles for intact urine uEVs and purified THP from three healthy individuals. LM data for all uEV (donors D1, D2, and D3) and THP samples (donors D1, D2 and D4) normalized by rescaling (range 0 to 65200). Individual technical replicates are indicated by designation of 1 to 5. Two groups are evident at 0.28 similarity, three groups at 0.57 similarity. Clustering based on Euclidean distance, complete linkage method. Responses and clustering shown are typical of those obtained from a minimum of 10 healthy uEV enrichment and profiling experiments.

Techniques Used: Microarray, Purification

Competitive inhibition of uEV interactions with lectin microarray using six different sugars. Data normalized to the response of LEL to show the relative inhibition through competition with 50( A ) Lac, ( B ) Gal, ( C ) Man, ( D ) GalNAc, and ( E ) and Fuc ( F ). To evaluate 50 mM GlcNAc inhibition ( F ), data was normalized to the response of RCA-I. Mean data is representative of inhibition for a single biological sample experiment conducted with 3 technical replicates. Error bars represent ± average deviation. Significance (** = p ≤0.01, * = p ≤0.05) determined by two-tailed, two-sampled unequal variance Student’s t-test. Arrows mark reductions in intensity greater than 20% with p > 0.05.
Figure Legend Snippet: Competitive inhibition of uEV interactions with lectin microarray using six different sugars. Data normalized to the response of LEL to show the relative inhibition through competition with 50( A ) Lac, ( B ) Gal, ( C ) Man, ( D ) GalNAc, and ( E ) and Fuc ( F ). To evaluate 50 mM GlcNAc inhibition ( F ), data was normalized to the response of RCA-I. Mean data is representative of inhibition for a single biological sample experiment conducted with 3 technical replicates. Error bars represent ± average deviation. Significance (** = p ≤0.01, * = p ≤0.05) determined by two-tailed, two-sampled unequal variance Student’s t-test. Arrows mark reductions in intensity greater than 20% with p > 0.05.

Techniques Used: Inhibition, Microarray, Two Tailed Test

32) Product Images from "Identifying MicroRNA-mRNA regulatory network in colorectal cancer by a combination of expression profile and bioinformatics analysis"

Article Title: Identifying MicroRNA-mRNA regulatory network in colorectal cancer by a combination of expression profile and bioinformatics analysis

Journal: BMC Systems Biology

doi: 10.1186/1752-0509-6-68

Step 1, both miRNA and mRNA microarray tests for identifying significantly dysregulated miRNAs and mRNAs in colorectal cancer. Step 2, Pearson correlation analysis for anti-correlationship of dysregulated miRNAs and mRNAs. Step 3, TargetScan and Mirnada predicting the target-relationship miRNA-mRNA pairs.
Figure Legend Snippet: Step 1, both miRNA and mRNA microarray tests for identifying significantly dysregulated miRNAs and mRNAs in colorectal cancer. Step 2, Pearson correlation analysis for anti-correlationship of dysregulated miRNAs and mRNAs. Step 3, TargetScan and Mirnada predicting the target-relationship miRNA-mRNA pairs.

Techniques Used: Microarray

33) Product Images from "Heterochromatin protein 1 promotes self-renewal and triggers regenerative proliferation in adult stem cells"

Article Title: Heterochromatin protein 1 promotes self-renewal and triggers regenerative proliferation in adult stem cells

Journal: The Journal of Cell Biology

doi: 10.1083/jcb.201207172

Microarray analysis of genes affected by HP1-1 knockdown. (A) Heat map of altered genes ( > 1.5-fold) shared among the four profiles of Control, Smedwi-2, HP1-1 , and HP1-2(RNAi) regenerating worms at 3 dpa; log 2 -based scale. Numbers in parentheses represent replicate samples. (B and C) Microarray (B) and qRT-PCR (C) showing the relative expression levels of lineage markers. Error bars show SDs, n = 2 (B) or 3 (C). *, P
Figure Legend Snippet: Microarray analysis of genes affected by HP1-1 knockdown. (A) Heat map of altered genes ( > 1.5-fold) shared among the four profiles of Control, Smedwi-2, HP1-1 , and HP1-2(RNAi) regenerating worms at 3 dpa; log 2 -based scale. Numbers in parentheses represent replicate samples. (B and C) Microarray (B) and qRT-PCR (C) showing the relative expression levels of lineage markers. Error bars show SDs, n = 2 (B) or 3 (C). *, P

Techniques Used: Microarray, Quantitative RT-PCR, Expressing

34) Product Images from "Mycobacterium tuberculosis WhiB3 Responds to Vacuolar pH-induced Changes in Mycothiol Redox Potential to Modulate Phagosomal Maturation and Virulence *"

Article Title: Mycobacterium tuberculosis WhiB3 Responds to Vacuolar pH-induced Changes in Mycothiol Redox Potential to Modulate Phagosomal Maturation and Virulence *

Journal: The Journal of Biological Chemistry

doi: 10.1074/jbc.M115.684597

WhiB3 regulates gene expression in response to acidic pH in vitro . WT M. tuberculosis and Mtb Δ whiB3 strains were grown to an A 600 nm of ∼0.3 and exposed to acidic pH of 4.5 for 2 h at 37 °C. Total RNA was isolated and subjected to microarray analysis as described under “Experimental Procedures.” A , genes with > 2-fold ( p
Figure Legend Snippet: WhiB3 regulates gene expression in response to acidic pH in vitro . WT M. tuberculosis and Mtb Δ whiB3 strains were grown to an A 600 nm of ∼0.3 and exposed to acidic pH of 4.5 for 2 h at 37 °C. Total RNA was isolated and subjected to microarray analysis as described under “Experimental Procedures.” A , genes with > 2-fold ( p

Techniques Used: Expressing, In Vitro, Isolation, Microarray

35) Product Images from "The transcriptional landscape of dorsal root ganglia after sciatic nerve transection"

Article Title: The transcriptional landscape of dorsal root ganglia after sciatic nerve transection

Journal: Scientific Reports

doi: 10.1038/srep16888

Cascade regulation of transcription factors. ( A ) Networks showing the connections and interactions between up-regulated (red) and down-regulated (green) transcription factors. ( B ) RT-qPCR validation of microarray analysis for the differential expression of several key transcription factors. R stands for the correlation coefficient between microarray and RT-qPCR data.
Figure Legend Snippet: Cascade regulation of transcription factors. ( A ) Networks showing the connections and interactions between up-regulated (red) and down-regulated (green) transcription factors. ( B ) RT-qPCR validation of microarray analysis for the differential expression of several key transcription factors. R stands for the correlation coefficient between microarray and RT-qPCR data.

Techniques Used: Quantitative RT-PCR, Microarray, Expressing

Dynamic changes of differentially expressed genes associated with neurite/axon growth. ( A ) Up-regulation (red), down-regulation (green) and unchange (no color) of genes associated with neurite/axon growth at different time points post nerve injury (PNI), where solid lines and dashed lines represent the activating and inhibitory roles of the corresponding genes on neurite/axon growth respectively. ( B ) The networks showing the connections and interactions among differential expressions (up-regulation labeled by red and down-regulation labeled by green) of genes associated with neurite/axon growth (circle) and their upstream regulatory genes (pentagon). (C) RT-qPCR validation of microarray analysis for the differential expression of several genes associated with neurite/axon growth. R stands for the correlation coefficient between microarray and RT-qPCR data.
Figure Legend Snippet: Dynamic changes of differentially expressed genes associated with neurite/axon growth. ( A ) Up-regulation (red), down-regulation (green) and unchange (no color) of genes associated with neurite/axon growth at different time points post nerve injury (PNI), where solid lines and dashed lines represent the activating and inhibitory roles of the corresponding genes on neurite/axon growth respectively. ( B ) The networks showing the connections and interactions among differential expressions (up-regulation labeled by red and down-regulation labeled by green) of genes associated with neurite/axon growth (circle) and their upstream regulatory genes (pentagon). (C) RT-qPCR validation of microarray analysis for the differential expression of several genes associated with neurite/axon growth. R stands for the correlation coefficient between microarray and RT-qPCR data.

Techniques Used: Labeling, Quantitative RT-PCR, Microarray, Expressing

36) Product Images from "Widespread changes in mRNA stability contribute to quiescence-specific gene expression patterns in a fibroblast model of quiescence"

Article Title: Widespread changes in mRNA stability contribute to quiescence-specific gene expression patterns in a fibroblast model of quiescence

Journal: BMC Genomics

doi: 10.1186/s12864-017-3521-0

Gene expression and RNA stability heatmap for the top upregulated a and downregulated b genes with quiescence. Columns 1 and 2 are the log 2 fold change in gene expression with quiescence \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \left({ \log}_2\left(\frac{CI7 Abundance}{PAbundance}\right)\right) $$\end{document} ( log 2 ( C I 7 A b u n d a n c e P A b u n d a n c e ) ) from microarray gene expression profiling of 7-day contact inhibited (CI7) and 14-day contact inhibited (CI14) fibroblasts. Column 3 is the log difference in decay constants ( K D proliferation − K D quiescence ) shrunken by the local false discovery rate (see Methods ) scaled to fit within the bounds of the gene expression values between CI7 and P fibroblasts. Gene ontology terms that are significantly enriched in a cluster are marked to the right of the heatmap
Figure Legend Snippet: Gene expression and RNA stability heatmap for the top upregulated a and downregulated b genes with quiescence. Columns 1 and 2 are the log 2 fold change in gene expression with quiescence \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \left({ \log}_2\left(\frac{CI7 Abundance}{PAbundance}\right)\right) $$\end{document} ( log 2 ( C I 7 A b u n d a n c e P A b u n d a n c e ) ) from microarray gene expression profiling of 7-day contact inhibited (CI7) and 14-day contact inhibited (CI14) fibroblasts. Column 3 is the log difference in decay constants ( K D proliferation − K D quiescence ) shrunken by the local false discovery rate (see Methods ) scaled to fit within the bounds of the gene expression values between CI7 and P fibroblasts. Gene ontology terms that are significantly enriched in a cluster are marked to the right of the heatmap

Techniques Used: Expressing, Microarray

37) Product Images from "Comparative transcriptome analysis of green/white variegated sectors in Arabidopsis yellow variegated2: responses to oxidative and other stresses in white sectors"

Article Title: Comparative transcriptome analysis of green/white variegated sectors in Arabidopsis yellow variegated2: responses to oxidative and other stresses in white sectors

Journal: Journal of Experimental Botany

doi: 10.1093/jxb/erq075

Microarray expression profile in Columbia and var2 white/green sectors. (A) A pie graph representation of the rate of up- or down-regulated probes in var2 white sectors ( var2 W) compared to var2 green sectors ( var2 G). The rates of each category (RNA metabolism, Stress response and Photosynthesis and chloroplasts) are shown in the bar graph to the right. (B–I) Gene ontology (GO) analysis. Representative categories among down-regulated (B–D) or up-regulated (E–I) genes in var2 white sectors compared to var2 green sectors are shown (see Tables 1 and 2 ). Gene expression profiles according to averaged normalized signal values (see colour scale) in Columbia (WT, left), var2 green sectors (green, middle), and var2 white sectors (white, right) are shown as a heat map. Each horizontal bar represents a single gene. (B) Photosynthesis. (C) Light-harvesting complex. (D) Tetrapyrrole binding. (E) Response to oxidative stress. (F) Response to heat. (G) Response to hydrogen peroxide. (H) Superoxide dismutase activity. (I) Response to stress.
Figure Legend Snippet: Microarray expression profile in Columbia and var2 white/green sectors. (A) A pie graph representation of the rate of up- or down-regulated probes in var2 white sectors ( var2 W) compared to var2 green sectors ( var2 G). The rates of each category (RNA metabolism, Stress response and Photosynthesis and chloroplasts) are shown in the bar graph to the right. (B–I) Gene ontology (GO) analysis. Representative categories among down-regulated (B–D) or up-regulated (E–I) genes in var2 white sectors compared to var2 green sectors are shown (see Tables 1 and 2 ). Gene expression profiles according to averaged normalized signal values (see colour scale) in Columbia (WT, left), var2 green sectors (green, middle), and var2 white sectors (white, right) are shown as a heat map. Each horizontal bar represents a single gene. (B) Photosynthesis. (C) Light-harvesting complex. (D) Tetrapyrrole binding. (E) Response to oxidative stress. (F) Response to heat. (G) Response to hydrogen peroxide. (H) Superoxide dismutase activity. (I) Response to stress.

Techniques Used: Microarray, Expressing, Binding Assay, Activity Assay

38) Product Images from "Long noncoding RNA expression profile in fibroblast-like synoviocytes from patients with rheumatoid arthritis"

Article Title: Long noncoding RNA expression profile in fibroblast-like synoviocytes from patients with rheumatoid arthritis

Journal: Arthritis Research & Therapy

doi: 10.1186/s13075-016-1129-4

Classification analyses of up-regulated lncRNAs a ( Up-regulati on) and down-regulated lncRNAs b ( Down-regulatio n) in rheumatoid arthritis fibroblast-like synoviocytes, as detected by microarray analysis
Figure Legend Snippet: Classification analyses of up-regulated lncRNAs a ( Up-regulati on) and down-regulated lncRNAs b ( Down-regulatio n) in rheumatoid arthritis fibroblast-like synoviocytes, as detected by microarray analysis

Techniques Used: Microarray

39) Product Images from "Affinity proteomics discovers decreased levels of AMFR in plasma from Osteoporosis patients"

Article Title: Affinity proteomics discovers decreased levels of AMFR in plasma from Osteoporosis patients

Journal: Proteomics. Clinical Applications

doi: 10.1002/prca.201400167

Verification of anti‐AMFR antibody. (A) Western blot analysis of tissue and cell lysates and plasma as taken from the Human Protein Atlas portal for HPA029018. (B) Western blot with different dilution of cell lysates (LY) overexpressing AMFR (Supporting Information Fig. 1–4) and nontransfected reference cells (C1–C4). (C) Epitope mapping of anti‐AMFR HPA029018 using a peptide array, and displaying reactive AMFR peptides with common motif (highlighted) and (D) identified peptides representing other proteins. (E) Interaction analysis of HPA029018 using antigen microarray built with 13 363 unique antigens.
Figure Legend Snippet: Verification of anti‐AMFR antibody. (A) Western blot analysis of tissue and cell lysates and plasma as taken from the Human Protein Atlas portal for HPA029018. (B) Western blot with different dilution of cell lysates (LY) overexpressing AMFR (Supporting Information Fig. 1–4) and nontransfected reference cells (C1–C4). (C) Epitope mapping of anti‐AMFR HPA029018 using a peptide array, and displaying reactive AMFR peptides with common motif (highlighted) and (D) identified peptides representing other proteins. (E) Interaction analysis of HPA029018 using antigen microarray built with 13 363 unique antigens.

Techniques Used: Western Blot, Peptide Microarray, Microarray

40) Product Images from "A rationally designed JAZ subtype-selective agonist of jasmonate perception"

Article Title: A rationally designed JAZ subtype-selective agonist of jasmonate perception

Journal: Nature Communications

doi: 10.1038/s41467-018-06135-y

JA responses and microarray analyses in 3 / ent 6 / 8 -treated Arabidopsis seedlings. a WT Arabidopsis seedlings grown for 6 days on 1/2 MS medium containing 3 , ent 6 , or 8 (1 µM). Scale bar, 10 mm. b Quantification of root length or fresh weight of the aerial part in the ligand-treated seedlings shown in a ( n = 18). Significant differences were evaluated by one-way ANOVA/Tukey HSD post hoc test ( p
Figure Legend Snippet: JA responses and microarray analyses in 3 / ent 6 / 8 -treated Arabidopsis seedlings. a WT Arabidopsis seedlings grown for 6 days on 1/2 MS medium containing 3 , ent 6 , or 8 (1 µM). Scale bar, 10 mm. b Quantification of root length or fresh weight of the aerial part in the ligand-treated seedlings shown in a ( n = 18). Significant differences were evaluated by one-way ANOVA/Tukey HSD post hoc test ( p

Techniques Used: Microarray, Mass Spectrometry

41) Product Images from "A rationally designed JAZ subtype-selective agonist of jasmonate perception"

Article Title: A rationally designed JAZ subtype-selective agonist of jasmonate perception

Journal: Nature Communications

doi: 10.1038/s41467-018-06135-y

JA responses and microarray analyses in 3 / ent 6 / 8 -treated Arabidopsis seedlings. a WT Arabidopsis seedlings grown for 6 days on 1/2 MS medium containing 3 , ent 6 , or 8 (1 µM). Scale bar, 10 mm. b Quantification of root length or fresh weight of the aerial part in the ligand-treated seedlings shown in a ( n = 18). Significant differences were evaluated by one-way ANOVA/Tukey HSD post hoc test ( p
Figure Legend Snippet: JA responses and microarray analyses in 3 / ent 6 / 8 -treated Arabidopsis seedlings. a WT Arabidopsis seedlings grown for 6 days on 1/2 MS medium containing 3 , ent 6 , or 8 (1 µM). Scale bar, 10 mm. b Quantification of root length or fresh weight of the aerial part in the ligand-treated seedlings shown in a ( n = 18). Significant differences were evaluated by one-way ANOVA/Tukey HSD post hoc test ( p

Techniques Used: Microarray, Mass Spectrometry

42) Product Images from "Transcriptomic Changes of Piscirickettsia salmonis During Intracellular Growth in a Salmon Macrophage-Like Cell Line"

Article Title: Transcriptomic Changes of Piscirickettsia salmonis During Intracellular Growth in a Salmon Macrophage-Like Cell Line

Journal: Frontiers in Cellular and Infection Microbiology

doi: 10.3389/fcimb.2019.00426

qPCR validation of microarray results. Log 2 ratios (infected/control) of gene expression ( N = 47) calculated from microarrays were plotted against the log 2 ratios derived from qPCR assays. Correlation between microarrays and qPCR was calculated using Pearson correlation ( p
Figure Legend Snippet: qPCR validation of microarray results. Log 2 ratios (infected/control) of gene expression ( N = 47) calculated from microarrays were plotted against the log 2 ratios derived from qPCR assays. Correlation between microarrays and qPCR was calculated using Pearson correlation ( p

Techniques Used: Real-time Polymerase Chain Reaction, Microarray, Infection, Expressing, Derivative Assay

43) Product Images from "Epigenetic stress responses induce muscle stem cell aging by Hoxa9 developmental signals"

Article Title: Epigenetic stress responses induce muscle stem cell aging by Hoxa9 developmental signals

Journal: Nature

doi: 10.1038/nature20603

Overexpression of Hox genes inhibits SC function a , Expression of Hoxa9 in SCs transduced with Hoxa9 cDNA or EGFP as control. b–c , FACS-isolated SCs from young adult mice were transduced with a lentivirus either containing both EGFP and Hoxa9 cDNA or only EGFP. Infected (EGFP + ) cells were isolated after 3 days. (b) Frequency of myogenic colonies from single cell-sorted SCs. (c) Quantification of cell number based on Alamar Blue assay of bulk cultures. d , Frequency of myogenic colonies of SCs overexpressing the indicated Hox genes. e+g , TUNEL (e) or BrdU (g) staining of SCs overexpressing Hoxa9 or EGFP. Infected (EGFP+) cells were isolated 3d after transduction and analyzed 3d later. Nuclei were counterstained with DAPI (blue). Arrowheads mark TUNEL or BrdU positive cells. f+h , Quantification of apoptosis (f) or proliferation (h) based on TUNEL or BrdU staining as in e or g. i , qRT-PCR based expression analysis of various cell-cycle and senescence markers in SCs overexpressing Hoxa9 compared to EGFP-infected controls, day 5 after infection. j , SA-ß-Galactosidase staining of SCs overexpressing Hoxa9 or EGFP at day 5 after infection. Arrowheads mark SA-ß-Gal positive cells. k , Quantification of senescence per field of view (FOV) based on SA-ß-Gal staining in j. l , Heat map displaying log2 fold changes of expression of selected genes from microarray analysis in Fig. 5a . m–o , qRT-PCR validation of differentially expressed genes annotated to Wnt- (m), TGFß- (n) and JAK/STAT pathways (o) as in l. p , Identification of Hoxa9 binding sites by anti-HA ChIP of primary myoblasts overexpressing HA-tagged Hoxa9 cDNA or EGFP as control. Shown is the qRT-PCR for 1 or 2 putative Hoxa9 binding sites at the indicated loci. Hoxa9 binding sites at target genes were identified as described in Methods and are listed in Supplementary Table 1 . A two-sided block bootstrap test on the difference of the percentage of bound DNA for all binding sites being equal to 0 was performed to test the hypothesis of a generally increased binding Hoxa9. q–s , SCs were infected with lentiviruses expressing Hoxa9 , Wnt3a , BMP4 , STAT3 cDNAs or EGFP. qRT-PCR analysis of expression of the indicated target genes at 5 days after infection: Axin2 (q), BMP4 (r) and STAT3 (s). Scale bars = 20 μm for e, g, 50 μm for j. Comparisons by two-sided student’s t-test (a–d, f, h, k, q–s) or two-way ANOVA (i, m–o). n=4 mice for a; n=3 mice for b; n=7 mice for c; n=3 mice for d; n=4 mice for f, h, k; n=3 mice (p15, p21), n=6 mice (p16), n=4 mice (all others) for i; n=4 pools of 3 mice for l; n=4 mice for m–o; n=3 biological replicates for p; n=3 mice (Wnt3a, BMP4, STAT3), n=4 mice (EGFP, Hoxa9) for q–s.
Figure Legend Snippet: Overexpression of Hox genes inhibits SC function a , Expression of Hoxa9 in SCs transduced with Hoxa9 cDNA or EGFP as control. b–c , FACS-isolated SCs from young adult mice were transduced with a lentivirus either containing both EGFP and Hoxa9 cDNA or only EGFP. Infected (EGFP + ) cells were isolated after 3 days. (b) Frequency of myogenic colonies from single cell-sorted SCs. (c) Quantification of cell number based on Alamar Blue assay of bulk cultures. d , Frequency of myogenic colonies of SCs overexpressing the indicated Hox genes. e+g , TUNEL (e) or BrdU (g) staining of SCs overexpressing Hoxa9 or EGFP. Infected (EGFP+) cells were isolated 3d after transduction and analyzed 3d later. Nuclei were counterstained with DAPI (blue). Arrowheads mark TUNEL or BrdU positive cells. f+h , Quantification of apoptosis (f) or proliferation (h) based on TUNEL or BrdU staining as in e or g. i , qRT-PCR based expression analysis of various cell-cycle and senescence markers in SCs overexpressing Hoxa9 compared to EGFP-infected controls, day 5 after infection. j , SA-ß-Galactosidase staining of SCs overexpressing Hoxa9 or EGFP at day 5 after infection. Arrowheads mark SA-ß-Gal positive cells. k , Quantification of senescence per field of view (FOV) based on SA-ß-Gal staining in j. l , Heat map displaying log2 fold changes of expression of selected genes from microarray analysis in Fig. 5a . m–o , qRT-PCR validation of differentially expressed genes annotated to Wnt- (m), TGFß- (n) and JAK/STAT pathways (o) as in l. p , Identification of Hoxa9 binding sites by anti-HA ChIP of primary myoblasts overexpressing HA-tagged Hoxa9 cDNA or EGFP as control. Shown is the qRT-PCR for 1 or 2 putative Hoxa9 binding sites at the indicated loci. Hoxa9 binding sites at target genes were identified as described in Methods and are listed in Supplementary Table 1 . A two-sided block bootstrap test on the difference of the percentage of bound DNA for all binding sites being equal to 0 was performed to test the hypothesis of a generally increased binding Hoxa9. q–s , SCs were infected with lentiviruses expressing Hoxa9 , Wnt3a , BMP4 , STAT3 cDNAs or EGFP. qRT-PCR analysis of expression of the indicated target genes at 5 days after infection: Axin2 (q), BMP4 (r) and STAT3 (s). Scale bars = 20 μm for e, g, 50 μm for j. Comparisons by two-sided student’s t-test (a–d, f, h, k, q–s) or two-way ANOVA (i, m–o). n=4 mice for a; n=3 mice for b; n=7 mice for c; n=3 mice for d; n=4 mice for f, h, k; n=3 mice (p15, p21), n=6 mice (p16), n=4 mice (all others) for i; n=4 pools of 3 mice for l; n=4 mice for m–o; n=3 biological replicates for p; n=3 mice (Wnt3a, BMP4, STAT3), n=4 mice (EGFP, Hoxa9) for q–s.

Techniques Used: Over Expression, Expressing, Transduction, FACS, Isolation, Mouse Assay, Infection, Alamar Blue Assay, TUNEL Assay, Staining, BrdU Staining, Quantitative RT-PCR, Microarray, Binding Assay, Chromatin Immunoprecipitation, Blocking Assay

44) Product Images from "Loss of miR-542-3p enhances IGFBP-1 expression in decidualizing human endometrial stromal cells"

Article Title: Loss of miR-542-3p enhances IGFBP-1 expression in decidualizing human endometrial stromal cells

Journal: Scientific Reports

doi: 10.1038/srep40001

Identification of miRNAs involved in decidualization. ( A ) Scatter plot of miRNA microarray results. Total RNA from three independent HESC cultures, decidualized or not, were labelled and hybridised separately on the Agilent miRNA microarray, and signal intensity, which corresponds to the expression level of each miRNA, was measured. The intensity was averaged and converted to a log2 value. Expression level of each miRNA is shown as a scatter plot. The level of expression in undifferentiated and decidualizing HESCs is shown on the Y-axis and X-axis, respectively. qRT-PCR analysis of miR-542-3p and IGFBP1 mRNA expression in undifferentiated and differentiating HESCs in samples used for microarray experiments. ( B ) The level of miR-542-3p (miR-542-3p/ U6 ratio) expression in HESCs treated with 8-br-cAMP and MPA for 6 days was significantly down-regulated in comparison to untreated HESCs. ( C ) IGFBP1 mRNA expression, normalized to GAPDH mRNA (glyceraldehyde phosphate dehydrogenase), in HESCs treated with 8-br-cAMP and MPA for 6 days was significantly up-regulated in comparison to undifferentiated HESCs. The experiments were performed using three independent primary cell cultures. The data are shown as mean ± SEM. ** P
Figure Legend Snippet: Identification of miRNAs involved in decidualization. ( A ) Scatter plot of miRNA microarray results. Total RNA from three independent HESC cultures, decidualized or not, were labelled and hybridised separately on the Agilent miRNA microarray, and signal intensity, which corresponds to the expression level of each miRNA, was measured. The intensity was averaged and converted to a log2 value. Expression level of each miRNA is shown as a scatter plot. The level of expression in undifferentiated and decidualizing HESCs is shown on the Y-axis and X-axis, respectively. qRT-PCR analysis of miR-542-3p and IGFBP1 mRNA expression in undifferentiated and differentiating HESCs in samples used for microarray experiments. ( B ) The level of miR-542-3p (miR-542-3p/ U6 ratio) expression in HESCs treated with 8-br-cAMP and MPA for 6 days was significantly down-regulated in comparison to untreated HESCs. ( C ) IGFBP1 mRNA expression, normalized to GAPDH mRNA (glyceraldehyde phosphate dehydrogenase), in HESCs treated with 8-br-cAMP and MPA for 6 days was significantly up-regulated in comparison to undifferentiated HESCs. The experiments were performed using three independent primary cell cultures. The data are shown as mean ± SEM. ** P

Techniques Used: Microarray, Expressing, Quantitative RT-PCR

45) Product Images from "Control of Rta expression critically determines transcription of viral and cellular genes following gammaherpesvirus infection"

Article Title: Control of Rta expression critically determines transcription of viral and cellular genes following gammaherpesvirus infection

Journal: The Journal of General Virology

doi: 10.1099/vir.0.82548-0

Q-RT-PCR confirmation of microarray data. 3T3 cells were infected (at an m.o.i. of 5) for 2 h with WT-, 50R- or M50-MHV68 and expression of CPA3, TNFIP6, FGF10, VCAM-1 and VEGF was determined using Q-RT-PCR. Bars show mean fold changes ( n =3 infections) normalized to loading controls ( β -2 microglobulin or glyceraldehyde-3-phosphate dehydrogenase) in cells infected with 50R- (white) and M50- (black) relative to WT-MHV68 (grey). P values according to Student's t -test are shown (*, P
Figure Legend Snippet: Q-RT-PCR confirmation of microarray data. 3T3 cells were infected (at an m.o.i. of 5) for 2 h with WT-, 50R- or M50-MHV68 and expression of CPA3, TNFIP6, FGF10, VCAM-1 and VEGF was determined using Q-RT-PCR. Bars show mean fold changes ( n =3 infections) normalized to loading controls ( β -2 microglobulin or glyceraldehyde-3-phosphate dehydrogenase) in cells infected with 50R- (white) and M50- (black) relative to WT-MHV68 (grey). P values according to Student's t -test are shown (*, P

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Microarray, Infection, Expressing

Viral gene expression 1 h after infection with WT-, 50R- and M50-MHV68. 3T3 cells were infected at an m.o.i. of 5. RNA was extracted and analysed by DNA microarray. Fluorescence intensity (relative expression) of high-expression (fluorescence > 1000) MHV68 ORFs (a) and low-expression (fluorescence
Figure Legend Snippet: Viral gene expression 1 h after infection with WT-, 50R- and M50-MHV68. 3T3 cells were infected at an m.o.i. of 5. RNA was extracted and analysed by DNA microarray. Fluorescence intensity (relative expression) of high-expression (fluorescence > 1000) MHV68 ORFs (a) and low-expression (fluorescence

Techniques Used: Expressing, Infection, Microarray, Fluorescence

46) Product Images from "Activation of p38/JNK Pathway Is Responsible for Embelin Induced Apoptosis in Lung Cancer Cells: Transitional Role of Reactive Oxygen Species"

Article Title: Activation of p38/JNK Pathway Is Responsible for Embelin Induced Apoptosis in Lung Cancer Cells: Transitional Role of Reactive Oxygen Species

Journal: PLoS ONE

doi: 10.1371/journal.pone.0087050

Alterations in pathway based gene expression profile induced by embelin. A549 cells were treated with embelin (15 µM) for 4h. Microarray analysis was performed as described in “Materials and Methods” section. Genes that showed differential regulation by at least 2-fold with p
Figure Legend Snippet: Alterations in pathway based gene expression profile induced by embelin. A549 cells were treated with embelin (15 µM) for 4h. Microarray analysis was performed as described in “Materials and Methods” section. Genes that showed differential regulation by at least 2-fold with p

Techniques Used: Expressing, Microarray

47) Product Images from "PERP regulates enamel formation via effects on cell-cell adhesion and gene expression"

Article Title: PERP regulates enamel formation via effects on cell-cell adhesion and gene expression

Journal: Journal of Cell Science

doi: 10.1242/jcs.078071

Identification of additional genes regulated by PERP. ( A ) qPCR was used to confirm differentially expressed genes determined by microarray analysis. Dmkn , Krt83 , Sost and Lama2 were significantly downregulated in teeth of Perp -null mice. ( B ) Dmkn and
Figure Legend Snippet: Identification of additional genes regulated by PERP. ( A ) qPCR was used to confirm differentially expressed genes determined by microarray analysis. Dmkn , Krt83 , Sost and Lama2 were significantly downregulated in teeth of Perp -null mice. ( B ) Dmkn and

Techniques Used: Real-time Polymerase Chain Reaction, Microarray, Mouse Assay

Relative expression of genes involved in amelogenesis. ( A ) Heat map depiction of candidate genes involved in amelogenesis from the microarray comparison of first lower molars of wild-type and Perp -null mice at P0. Percentage expression changes relative
Figure Legend Snippet: Relative expression of genes involved in amelogenesis. ( A ) Heat map depiction of candidate genes involved in amelogenesis from the microarray comparison of first lower molars of wild-type and Perp -null mice at P0. Percentage expression changes relative

Techniques Used: Expressing, Microarray, Mouse Assay

48) Product Images from "Local Administration of Soluble CD40:Fc to the Salivary Glands of Non-Obese Diabetic Mice Does Not Ameliorate Autoimmune Inflammation"

Article Title: Local Administration of Soluble CD40:Fc to the Salivary Glands of Non-Obese Diabetic Mice Does Not Ameliorate Autoimmune Inflammation

Journal: PLoS ONE

doi: 10.1371/journal.pone.0051375

Network based analysis of genes affected by CD40:Fc treatment. Microarray analysis was performed on SG of CD40:Fc treated and control mice (n = 4 each, treatment at 10 weeks, end of study at 20 weeks) and gene changes greater than 2 fold were used in the analysis and compared for biological functional pathways or biomarkers by an Ingenuity Pathway analysis (IPA). ( A ) The pathway of NF-κB and TGF-β was affected in CD40:Fc treated mice. Green colored shapes indicates upregulated genes, red colored shapes downregulated; gray colored shapes genes in the pathway that were not differentially expressed. Color intensity reflects the degree of differential expression. Triangles represent phosphatases; horizontal diamond, peptidases; vertical diamond, enzymes; horizontal oval, transcription factors; vertical oval, transmembrane receptors; trapezoid, transporters; circle, other type of protein. Dotted lines indicate an indirect interaction; solid line, direct interaction, solid arrow head indicates “acts on”. ( B ) Metacore analysis of pathways linking differentially expressed genes to immune pathways. The differentially expressed genes are indicated along with the direction of change in expression. ( C ) Quantitative-PCR of selected genes shows agreement with microarray results. The results obtained using the microarray platform were validated by examining the correlation between the expression levels in the microarray and qPCR results obtained for a subset of genes.
Figure Legend Snippet: Network based analysis of genes affected by CD40:Fc treatment. Microarray analysis was performed on SG of CD40:Fc treated and control mice (n = 4 each, treatment at 10 weeks, end of study at 20 weeks) and gene changes greater than 2 fold were used in the analysis and compared for biological functional pathways or biomarkers by an Ingenuity Pathway analysis (IPA). ( A ) The pathway of NF-κB and TGF-β was affected in CD40:Fc treated mice. Green colored shapes indicates upregulated genes, red colored shapes downregulated; gray colored shapes genes in the pathway that were not differentially expressed. Color intensity reflects the degree of differential expression. Triangles represent phosphatases; horizontal diamond, peptidases; vertical diamond, enzymes; horizontal oval, transcription factors; vertical oval, transmembrane receptors; trapezoid, transporters; circle, other type of protein. Dotted lines indicate an indirect interaction; solid line, direct interaction, solid arrow head indicates “acts on”. ( B ) Metacore analysis of pathways linking differentially expressed genes to immune pathways. The differentially expressed genes are indicated along with the direction of change in expression. ( C ) Quantitative-PCR of selected genes shows agreement with microarray results. The results obtained using the microarray platform were validated by examining the correlation between the expression levels in the microarray and qPCR results obtained for a subset of genes.

Techniques Used: Microarray, Mouse Assay, Functional Assay, Indirect Immunoperoxidase Assay, Expressing, Real-time Polymerase Chain Reaction

49) Product Images from "Tumor heterogeneity in the recurrence of epithelial ovarian cancer demonstrated by polycomb group proteins"

Article Title: Tumor heterogeneity in the recurrence of epithelial ovarian cancer demonstrated by polycomb group proteins

Journal: OncoTargets and therapy

doi: 10.2147/OTT.S67570

Epigenetic heterogeneity underlying the heterogeneous expression of polycomb group proteins. Notes: (A) miRNA microarray expression profiling of six pairs of primary and recurrent ovarian tumor tissues: heat map shows eight downregulated (fold change > 2) miRNAs in recurrent tumors. ( B ) Luciferase reporter assay: ( B1 ) miR-4261 and miR-298 significantly suppressed the luciferase activity of ZNF207 and ILF3 ( P =0.001, P =0.008); ( B2 ) ZNF207 and ILF3 significantly promoted the luciferase activity of EZH2-promoter reporter plasmid ( P =0.000, P =0.000). ( C ) Transfection of miR-4261 ( C1 and C3 ) and miR-298 ( C2 and C4 ) mimics into ovarian cancer cells, A2780 and OVCAR8, confirmed by real-time polymerase chain reaction and fluorescence. ( D ) Expression of ZNF207, ILF3, and EZH2 in ovarian cancer cells after miR-4261 and miR-298 upregulation: ( D1 , D2 , and D4 ) a significant reduction of ZNF207 and ILF3 at mRNA and protein levels was observed (for ZNF207, P =0.001 both; for ILF3, P =0.000, P =0.001); ( D3 and D4 ) EZH2 expression was only concomitantly reduced significantly by miR-298 overexpression ( P =0.001 both). Abbreviation: miRNA, microRNA.
Figure Legend Snippet: Epigenetic heterogeneity underlying the heterogeneous expression of polycomb group proteins. Notes: (A) miRNA microarray expression profiling of six pairs of primary and recurrent ovarian tumor tissues: heat map shows eight downregulated (fold change > 2) miRNAs in recurrent tumors. ( B ) Luciferase reporter assay: ( B1 ) miR-4261 and miR-298 significantly suppressed the luciferase activity of ZNF207 and ILF3 ( P =0.001, P =0.008); ( B2 ) ZNF207 and ILF3 significantly promoted the luciferase activity of EZH2-promoter reporter plasmid ( P =0.000, P =0.000). ( C ) Transfection of miR-4261 ( C1 and C3 ) and miR-298 ( C2 and C4 ) mimics into ovarian cancer cells, A2780 and OVCAR8, confirmed by real-time polymerase chain reaction and fluorescence. ( D ) Expression of ZNF207, ILF3, and EZH2 in ovarian cancer cells after miR-4261 and miR-298 upregulation: ( D1 , D2 , and D4 ) a significant reduction of ZNF207 and ILF3 at mRNA and protein levels was observed (for ZNF207, P =0.001 both; for ILF3, P =0.000, P =0.001); ( D3 and D4 ) EZH2 expression was only concomitantly reduced significantly by miR-298 overexpression ( P =0.001 both). Abbreviation: miRNA, microRNA.

Techniques Used: Expressing, Microarray, Luciferase, Reporter Assay, Activity Assay, Plasmid Preparation, Transfection, Real-time Polymerase Chain Reaction, Fluorescence, Over Expression

50) Product Images from "Generation of Induced Pluripotent Stem Cells in Rabbits"

Article Title: Generation of Induced Pluripotent Stem Cells in Rabbits

Journal: The Journal of Biological Chemistry

doi: 10.1074/jbc.M110.150540

DNA microarray analysis demonstrating the global gene expression profiles of iPS cells at different passage numbers, of ES cells, and of parental somatic cells. A , unsupervised hierarchical clustering. Rabbit iPS cells were more similar to each other according to their passage number rather than by origin. B , three-dimensional principal component analysis mapping. Consistent with the result of hierarchical clustering in A , iPS cells at similar passage numbers are close to each other. This map clearly demonstrates that these rabbit iPS cells started to resemble ES cells as passage proceeded. Scale bar , 100 μm.
Figure Legend Snippet: DNA microarray analysis demonstrating the global gene expression profiles of iPS cells at different passage numbers, of ES cells, and of parental somatic cells. A , unsupervised hierarchical clustering. Rabbit iPS cells were more similar to each other according to their passage number rather than by origin. B , three-dimensional principal component analysis mapping. Consistent with the result of hierarchical clustering in A , iPS cells at similar passage numbers are close to each other. This map clearly demonstrates that these rabbit iPS cells started to resemble ES cells as passage proceeded. Scale bar , 100 μm.

Techniques Used: Microarray, Expressing

51) Product Images from "Therapeutic Effect of Repurposed Temsirolimus in Lung Adenocarcinoma Model"

Article Title: Therapeutic Effect of Repurposed Temsirolimus in Lung Adenocarcinoma Model

Journal: Frontiers in Pharmacology

doi: 10.3389/fphar.2018.00778

Bioinformatics-based drug-repositioning approach to identify candidate drugs. Schematic representation of the bioinformatics workflow by using the LINCS L1000 data set for the repositioning approach to identifying potential candidate drugs for the treatment of NSCLC. The microarray results of Tg-3m and Tg-6m tumors were subjected to the LINCS L1000 data sets to obtain the most differentially expressed genes. The mouse gene symbols were then converted to human homologous genes and annotated by combining the DrugBank and PubChem results to obtain detailed drug information. The drugs that negatively (K score = –1) correlated with the gene expression from both Tg-3m and Tg-6m lung tumor cell lines were selected for further screening.
Figure Legend Snippet: Bioinformatics-based drug-repositioning approach to identify candidate drugs. Schematic representation of the bioinformatics workflow by using the LINCS L1000 data set for the repositioning approach to identifying potential candidate drugs for the treatment of NSCLC. The microarray results of Tg-3m and Tg-6m tumors were subjected to the LINCS L1000 data sets to obtain the most differentially expressed genes. The mouse gene symbols were then converted to human homologous genes and annotated by combining the DrugBank and PubChem results to obtain detailed drug information. The drugs that negatively (K score = –1) correlated with the gene expression from both Tg-3m and Tg-6m lung tumor cell lines were selected for further screening.

Techniques Used: Microarray, Expressing

52) Product Images from "Comparative gene expression analysis after exposure to 123I-iododeoxyuridine, γ- and α-radiation—potential biomarkers for the discrimination of radiation qualities"

Article Title: Comparative gene expression analysis after exposure to 123I-iododeoxyuridine, γ- and α-radiation—potential biomarkers for the discrimination of radiation qualities

Journal: Journal of Radiation Research

doi: 10.1093/jrr/rry038

Identification of robust candidate genes allowing discrimination of different radiation qualities. (A, B) DNAJC1 and PRTFDC1 6 h after withdrawal of 123 IUdR versus 24 h after γ-irradiation; (C) PPP1R14C 6 h after withdrawal of 123 IUdR versus 6 h after γ-irradiation; (D) KLF10 24 h after γ-irradiation versus 24 h after α-irradiation; (E) TNFAIP8L1 6 h after withdrawal of 123 IUdR versus 6 h after γ- and α-irradiation. Solid bars show the data of the quantitative real-time PCR in comparison with the microarray data (white bars with dashed lines). The error bars represent the standard deviation of the mean ( n = 3, * P
Figure Legend Snippet: Identification of robust candidate genes allowing discrimination of different radiation qualities. (A, B) DNAJC1 and PRTFDC1 6 h after withdrawal of 123 IUdR versus 24 h after γ-irradiation; (C) PPP1R14C 6 h after withdrawal of 123 IUdR versus 6 h after γ-irradiation; (D) KLF10 24 h after γ-irradiation versus 24 h after α-irradiation; (E) TNFAIP8L1 6 h after withdrawal of 123 IUdR versus 6 h after γ- and α-irradiation. Solid bars show the data of the quantitative real-time PCR in comparison with the microarray data (white bars with dashed lines). The error bars represent the standard deviation of the mean ( n = 3, * P

Techniques Used: Irradiation, Real-time Polymerase Chain Reaction, Microarray, Standard Deviation

53) Product Images from "Transcriptomics in lung tissue upon respiratory syncytial virus infection reveals aging as important modulator of immune activation and matrix maintenance"

Article Title: Transcriptomics in lung tissue upon respiratory syncytial virus infection reveals aging as important modulator of immune activation and matrix maintenance

Journal: Scientific Reports

doi: 10.1038/s41598-018-35180-2

Distinct effects by aging and RSV on gene expression. Panel A shows each individual animal in a principal component analysis (PCA) of the microarray data of lung samples derived at day 0 (mock-inoculated, black, n = 4/group), or at day 2 (red, n = 5/group) or day 5 (green, n = 5/group) after inoculation with RSV. Aging-regulated expression appears by PC1, RSV-regulated gene expression appears along PC2. Y, young (circles); O, old (triangles); M, mock control; R, RSV-inoculated. Panel B shows a Venn-diagram depicting numbers of genes that are significantly upregulated (↑), downregulated (↓), or show no significant response (−). The three symbols indicate from left to right: response to RSV in young mice, response to RSV in old mice, response to aging, respectively.
Figure Legend Snippet: Distinct effects by aging and RSV on gene expression. Panel A shows each individual animal in a principal component analysis (PCA) of the microarray data of lung samples derived at day 0 (mock-inoculated, black, n = 4/group), or at day 2 (red, n = 5/group) or day 5 (green, n = 5/group) after inoculation with RSV. Aging-regulated expression appears by PC1, RSV-regulated gene expression appears along PC2. Y, young (circles); O, old (triangles); M, mock control; R, RSV-inoculated. Panel B shows a Venn-diagram depicting numbers of genes that are significantly upregulated (↑), downregulated (↓), or show no significant response (−). The three symbols indicate from left to right: response to RSV in young mice, response to RSV in old mice, response to aging, respectively.

Techniques Used: Expressing, Microarray, Derivative Assay, Mouse Assay

54) Product Images from "Gene Expression Profiling in Cells with Enhanced ?-Secretase Activity"

Article Title: Gene Expression Profiling in Cells with Enhanced ?-Secretase Activity

Journal: PLoS ONE

doi: 10.1371/journal.pone.0006952

Involvement of γ-secretase-dependently transcribed genes in Wnt pathways. Several key players of the canonical Wnt pathway (green panel) were reported by our microarray to increase (red quadrangles) or decrease (blue quadrangles) in transcript levels under conditions of enhanced γ-secretase activity compared to inhibited activity. β-Catenin is a central node connecting Wnt–Frizzled–Dishevelled to a downstream effect influencing the cell cycle (see also Fig. 4 and interactions of encoded proteins). For better understanding, selected genes that were not detected by the microarray are displayed as well (dashed lines black quadrangles). CycD was reported to be regulated by PTPRG, one of the top scoring candidates for γ-secretase affected gene transcription. Nkd, which we found to be increased in transcript levels, connects the canonical Wnt pathway with the planar cell polarity pathway (blue panel). CD44, a well-known γ-secretase substrate, interacts with SPP1. SPP1 and UPP1, two strong candidates are both under the control of the same transcription factor Oct3/4, as has been suggested for TERA [92] . UPP1 directly interacts with Vimentin (see also Fig. 4 ), a known player in AD and a cytoskeletal protein. Crucial genes of the Wnt/Ca 2+ pathway (grey panel) were also found to be differentially expressed in our array. All together, γ-secretase activity influences the transcript levels of genes of the canonical, the planar cell polarity and Ca 2+ Wnt pathways.
Figure Legend Snippet: Involvement of γ-secretase-dependently transcribed genes in Wnt pathways. Several key players of the canonical Wnt pathway (green panel) were reported by our microarray to increase (red quadrangles) or decrease (blue quadrangles) in transcript levels under conditions of enhanced γ-secretase activity compared to inhibited activity. β-Catenin is a central node connecting Wnt–Frizzled–Dishevelled to a downstream effect influencing the cell cycle (see also Fig. 4 and interactions of encoded proteins). For better understanding, selected genes that were not detected by the microarray are displayed as well (dashed lines black quadrangles). CycD was reported to be regulated by PTPRG, one of the top scoring candidates for γ-secretase affected gene transcription. Nkd, which we found to be increased in transcript levels, connects the canonical Wnt pathway with the planar cell polarity pathway (blue panel). CD44, a well-known γ-secretase substrate, interacts with SPP1. SPP1 and UPP1, two strong candidates are both under the control of the same transcription factor Oct3/4, as has been suggested for TERA [92] . UPP1 directly interacts with Vimentin (see also Fig. 4 ), a known player in AD and a cytoskeletal protein. Crucial genes of the Wnt/Ca 2+ pathway (grey panel) were also found to be differentially expressed in our array. All together, γ-secretase activity influences the transcript levels of genes of the canonical, the planar cell polarity and Ca 2+ Wnt pathways.

Techniques Used: Microarray, Activity Assay

Protein-protein interaction network of proteins encoded by genes differentially transcribed in cells with enhanced γ-secretase activity. All interaction partners as reported by experiment based evidence in the string 8.0 database are shown in black and indicated by two headed arrows. Proteins encoded by PCR-validated genes are represented in circles (blue circles for genes of decreased transcription, red circles for genes of increased transcription). Interaction partners encoded by genes identified in our microarray, but having not yet been validated are displayed in quadrangles (blue quadrangles for genes of decreased transcription, red quadrangles for genes of increased transcription). Proteins with blue background are known γ-secretase substrates. The central grey box indicates γ-secretase subunits. Proteins acting directly or indirectly on, or interacting with Wnt pathways are highlighted by a light purple background figure.
Figure Legend Snippet: Protein-protein interaction network of proteins encoded by genes differentially transcribed in cells with enhanced γ-secretase activity. All interaction partners as reported by experiment based evidence in the string 8.0 database are shown in black and indicated by two headed arrows. Proteins encoded by PCR-validated genes are represented in circles (blue circles for genes of decreased transcription, red circles for genes of increased transcription). Interaction partners encoded by genes identified in our microarray, but having not yet been validated are displayed in quadrangles (blue quadrangles for genes of decreased transcription, red quadrangles for genes of increased transcription). Proteins with blue background are known γ-secretase substrates. The central grey box indicates γ-secretase subunits. Proteins acting directly or indirectly on, or interacting with Wnt pathways are highlighted by a light purple background figure.

Techniques Used: Activity Assay, Polymerase Chain Reaction, Microarray

Real time PCR validation of differentially transcribed genes in cells with enhanced γ-secretase activity. Fifty of the top scoring genes identified by microarray analysis to be differentially transcribed with enhanced γ-secretase activity were analyzed by real time PCR with primers based on mouse gene sequences. These primers showed specific and reproducible amplification for 35 genes and a total of 21 genes were validated to be differentially transcribed with enhanced γ-secretase activity. Relative quantification is expressed as fold change of transcript levels compared to inhibited γ-secretase conditions. Fold difference is displayed on the Y-axis and in table below X-axis. Error bars reflect standard deviations of biological triplicates.
Figure Legend Snippet: Real time PCR validation of differentially transcribed genes in cells with enhanced γ-secretase activity. Fifty of the top scoring genes identified by microarray analysis to be differentially transcribed with enhanced γ-secretase activity were analyzed by real time PCR with primers based on mouse gene sequences. These primers showed specific and reproducible amplification for 35 genes and a total of 21 genes were validated to be differentially transcribed with enhanced γ-secretase activity. Relative quantification is expressed as fold change of transcript levels compared to inhibited γ-secretase conditions. Fold difference is displayed on the Y-axis and in table below X-axis. Error bars reflect standard deviations of biological triplicates.

Techniques Used: Real-time Polymerase Chain Reaction, Activity Assay, Microarray, Amplification

Microarray-based strategy for the identification of genes differentially transcribed in cells with enhanced γ-secretase activity. To identify genes whose transcription is affected by γ-secretase activity, two starkly contrasting conditions were analyzed by cDNA microarray: genetically engineered enhanced γ-secretase (left panel) and pharmacologically inhibited γ-secretase (right panel) in CHO cell lines. For a schematic depiction of the strategy, the Notch-1 receptor signaling pathway is used as an example. After processing by the Furin protease and when activated by binding to its ligands Notch-1 is cleaved at the S2 position by the TACE protease, generating a substrate for γ-secretase (1, 7). Under enhanced (left panel) or inhibited (right panel) γ-secretase activity, the cleavage of the substrate controls the release of the Notch intracellular domain (NICD) (2, 8). With enhanced γ-secretase, increased numbers of NICDs enter the nucleus and interact with CSL (3), leading to the transcription of target genes like Hes1 and Hey (4). The Hes1 transcription repressor inhibits transcription of target genes like NC3C1 (5), with the final consequence being reduced production of NC3C1 mRNA (6). Thus, enhancing γ-secretase leads simultaneously to gene-dependent increase (in the case of Hes/Hey) or decrease (in the case of NC3C1) of mRNA copy numbers. With inhibited γ-secretase, reduced numbers of NICDs (9) lead to the transcription of less Hes1/Hey (10), to reduced inhibition of target genes like NC3C1 (11) and consequently to increased production of NC3C1 mRNA (12). Inhibiting γ-secretase thus leads to gene-dependent decrease (in the case of Hes/Hey genes) or increase (in the case of NC3C1) of mRNA copy numbers. Following mouse cDNA microarray analysis of both transcriptomes, top scoring candidates were evaluated and validated by real time PCR and further analyzed for changes of transcript levels between healthy and AD human brain cortices.
Figure Legend Snippet: Microarray-based strategy for the identification of genes differentially transcribed in cells with enhanced γ-secretase activity. To identify genes whose transcription is affected by γ-secretase activity, two starkly contrasting conditions were analyzed by cDNA microarray: genetically engineered enhanced γ-secretase (left panel) and pharmacologically inhibited γ-secretase (right panel) in CHO cell lines. For a schematic depiction of the strategy, the Notch-1 receptor signaling pathway is used as an example. After processing by the Furin protease and when activated by binding to its ligands Notch-1 is cleaved at the S2 position by the TACE protease, generating a substrate for γ-secretase (1, 7). Under enhanced (left panel) or inhibited (right panel) γ-secretase activity, the cleavage of the substrate controls the release of the Notch intracellular domain (NICD) (2, 8). With enhanced γ-secretase, increased numbers of NICDs enter the nucleus and interact with CSL (3), leading to the transcription of target genes like Hes1 and Hey (4). The Hes1 transcription repressor inhibits transcription of target genes like NC3C1 (5), with the final consequence being reduced production of NC3C1 mRNA (6). Thus, enhancing γ-secretase leads simultaneously to gene-dependent increase (in the case of Hes/Hey) or decrease (in the case of NC3C1) of mRNA copy numbers. With inhibited γ-secretase, reduced numbers of NICDs (9) lead to the transcription of less Hes1/Hey (10), to reduced inhibition of target genes like NC3C1 (11) and consequently to increased production of NC3C1 mRNA (12). Inhibiting γ-secretase thus leads to gene-dependent decrease (in the case of Hes/Hey genes) or increase (in the case of NC3C1) of mRNA copy numbers. Following mouse cDNA microarray analysis of both transcriptomes, top scoring candidates were evaluated and validated by real time PCR and further analyzed for changes of transcript levels between healthy and AD human brain cortices.

Techniques Used: Microarray, Activity Assay, Binding Assay, Inhibition, Real-time Polymerase Chain Reaction

55) Product Images from "Oligouridylate Binding Protein 1b Plays an Integral Role in Plant Heat Stress Tolerance"

Article Title: Oligouridylate Binding Protein 1b Plays an Integral Role in Plant Heat Stress Tolerance

Journal: Frontiers in Plant Science

doi: 10.3389/fpls.2016.00853

Microarray analysis of UBP1b -ox and Venu s control plants subjected to heat stress and non-stress conditions . Two-week-old Arabidopsis plants were subjected to 40°C for 1 h. Each sample was composed of five pooled seedlings which were used for extracting total RNA. Three biological replicates were analyzed. (A) Heat map of the microarray expression data obtained for UBP1b -ox (line ox1) and Venu s control plants. Blue color refers to a negative z-score; pink color refers to a positive z-score of the level of gene expression. (B) Venn diagram representation of 1981 heat-inducible genes identified in the microarray analysis. A total of 479 genes exhibited higher levels of expression in UBP1b -ox plants than in Venu s control plants when subjected to non-stress conditions, and 830 genes exhibited higher levels of expression in UBP1b -ox plants than in Venu s control plants when subjected to heat-stress.
Figure Legend Snippet: Microarray analysis of UBP1b -ox and Venu s control plants subjected to heat stress and non-stress conditions . Two-week-old Arabidopsis plants were subjected to 40°C for 1 h. Each sample was composed of five pooled seedlings which were used for extracting total RNA. Three biological replicates were analyzed. (A) Heat map of the microarray expression data obtained for UBP1b -ox (line ox1) and Venu s control plants. Blue color refers to a negative z-score; pink color refers to a positive z-score of the level of gene expression. (B) Venn diagram representation of 1981 heat-inducible genes identified in the microarray analysis. A total of 479 genes exhibited higher levels of expression in UBP1b -ox plants than in Venu s control plants when subjected to non-stress conditions, and 830 genes exhibited higher levels of expression in UBP1b -ox plants than in Venu s control plants when subjected to heat-stress.

Techniques Used: Microarray, Expressing

56) Product Images from "Master and servant: LINC00152 – a STAT3-induced long noncoding RNA regulates STAT3 in a positive feedback in human multiple myeloma"

Article Title: Master and servant: LINC00152 – a STAT3-induced long noncoding RNA regulates STAT3 in a positive feedback in human multiple myeloma

Journal: BMC Medical Genomics

doi: 10.1186/s12920-020-0692-3

Identification of genes regulated by STAiR18 and STAT3. a Differentially regulated STAT3 and STAiR18 target genes determined after STAiR18-Ex1 and STAT3 KD ( n = 4). RNA was isolated 40 h post-transfection and subjected to gene expression microarrays. A minimal fold-change of 1.5-fold and maximum p -value of 0.05 were applied as cutoff criteria, yielding 545 and 721 differentially regulated candidates upon STAT3 and STAiR18 knockdown, respectively. 58 of these candidates are regulated by both knockdowns. b The fold-changes of 58 genes differentially regulated by both the KD of STAT3 and STAiR18 were plotted against each other. c Validation of selected transcripts regulated by both KDs by qPCR using specific primer pairs. Values were normalized to U6 RNA ( n = 4). The detected expression of equivalent genes identified by microarray is shown at the top panel (i) for comparison
Figure Legend Snippet: Identification of genes regulated by STAiR18 and STAT3. a Differentially regulated STAT3 and STAiR18 target genes determined after STAiR18-Ex1 and STAT3 KD ( n = 4). RNA was isolated 40 h post-transfection and subjected to gene expression microarrays. A minimal fold-change of 1.5-fold and maximum p -value of 0.05 were applied as cutoff criteria, yielding 545 and 721 differentially regulated candidates upon STAT3 and STAiR18 knockdown, respectively. 58 of these candidates are regulated by both knockdowns. b The fold-changes of 58 genes differentially regulated by both the KD of STAT3 and STAiR18 were plotted against each other. c Validation of selected transcripts regulated by both KDs by qPCR using specific primer pairs. Values were normalized to U6 RNA ( n = 4). The detected expression of equivalent genes identified by microarray is shown at the top panel (i) for comparison

Techniques Used: Isolation, Transfection, Expressing, Real-time Polymerase Chain Reaction, Microarray

57) Product Images from "Postgenomic Analysis of Streptococcus thermophilus Cocultivated in Milk with Lactobacillus delbrueckii subsp. bulgaricus: Involvement of Nitrogen, Purine, and Iron Metabolism ▿: Involvement of Nitrogen, Purine, and Iron Metabolism ▿ †"

Article Title: Postgenomic Analysis of Streptococcus thermophilus Cocultivated in Milk with Lactobacillus delbrueckii subsp. bulgaricus: Involvement of Nitrogen, Purine, and Iron Metabolism ▿: Involvement of Nitrogen, Purine, and Iron Metabolism ▿ †

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.01984-08

Comparative analysis of protein abundance (black) and gene expression (dots for microarray analysis and hatching for RT-qPCR analyses) for the purine biosynthesis pathway between 2 h 30 min and 5 h 30 min of growth of S. thermophilus . *, not detected
Figure Legend Snippet: Comparative analysis of protein abundance (black) and gene expression (dots for microarray analysis and hatching for RT-qPCR analyses) for the purine biosynthesis pathway between 2 h 30 min and 5 h 30 min of growth of S. thermophilus . *, not detected

Techniques Used: Expressing, Microarray, Quantitative RT-PCR

58) Product Images from "(-)-Xanthatin Selectively Induces GADD45? and Stimulates Caspase-Independent Cell Death in Human Breast Cancer MDA-MB-231 Cells"

Article Title: (-)-Xanthatin Selectively Induces GADD45? and Stimulates Caspase-Independent Cell Death in Human Breast Cancer MDA-MB-231 Cells

Journal: Chemical research in toxicology

doi: 10.1021/tx200046s

(−)-Xanthatin suppresses key genes involved in the G 2 /M checkpoint. (A) GADD45 molecules can inhibit Cdc2/cyclin B1 involved in the G 2 /M checkpoint. (B-a) Results of DNA microarray analysis were presented. Data are expressed as the fold induction
Figure Legend Snippet: (−)-Xanthatin suppresses key genes involved in the G 2 /M checkpoint. (A) GADD45 molecules can inhibit Cdc2/cyclin B1 involved in the G 2 /M checkpoint. (B-a) Results of DNA microarray analysis were presented. Data are expressed as the fold induction

Techniques Used: Microarray

59) Product Images from "Activation of cancer-related and mitogen-activated protein kinase signaling pathways in human mature osteoblasts isolated from patients with type 2 diabetes"

Article Title: Activation of cancer-related and mitogen-activated protein kinase signaling pathways in human mature osteoblasts isolated from patients with type 2 diabetes

Journal: Bone Reports

doi: 10.1016/j.bonr.2019.100199

Real-time PCR confirmation of a subset of differentially regulated genes identified in the RNA microarray analysis. Correlation plot of osteoblast marker genes in the RNA microarray dataset and real-time PCR validation. A high correlation was observed between the two methods.
Figure Legend Snippet: Real-time PCR confirmation of a subset of differentially regulated genes identified in the RNA microarray analysis. Correlation plot of osteoblast marker genes in the RNA microarray dataset and real-time PCR validation. A high correlation was observed between the two methods.

Techniques Used: Real-time Polymerase Chain Reaction, Microarray, Marker

60) Product Images from "Gene expression profiling for human iPS-derived motor neurons from sporadic ALS patients reveals a strong association between mitochondrial functions and neurodegeneration"

Article Title: Gene expression profiling for human iPS-derived motor neurons from sporadic ALS patients reveals a strong association between mitochondrial functions and neurodegeneration

Journal: Frontiers in Cellular Neuroscience

doi: 10.3389/fncel.2015.00289

Mitochondrion gene expression in hiPSC-derived motor neurons . Gene expression normalized signals of 105 genes from GO terms of Cellular Components that are related to the mitochondrion. Bars represent the means ± SEM of the signals from three samples of differentiated motor neurons of non-ALS and ALS patients, as described in the text. The signal values (Cy5) were normalized by microarray reference (Cy3). The genes referred to GO terms mitochondrion (0005739), mitochondrial part (0044429), mitochondrial matrix (0005759), and mitochondrial lumen (0031980). See text and Table S4 for details. Differences within groups were analyzed by One-Way ANOVA followed by Tukey post-test, whereas differences between non-ALS and ALS groups were analyzed according to unpaired t -test ** p
Figure Legend Snippet: Mitochondrion gene expression in hiPSC-derived motor neurons . Gene expression normalized signals of 105 genes from GO terms of Cellular Components that are related to the mitochondrion. Bars represent the means ± SEM of the signals from three samples of differentiated motor neurons of non-ALS and ALS patients, as described in the text. The signal values (Cy5) were normalized by microarray reference (Cy3). The genes referred to GO terms mitochondrion (0005739), mitochondrial part (0044429), mitochondrial matrix (0005759), and mitochondrial lumen (0031980). See text and Table S4 for details. Differences within groups were analyzed by One-Way ANOVA followed by Tukey post-test, whereas differences between non-ALS and ALS groups were analyzed according to unpaired t -test ** p

Techniques Used: Expressing, Derivative Assay, Microarray

61) Product Images from "Inductions of the fatty acid 2-hydroxylase (FA2H) gene by ?9-tetrahydrocannabinol in human breast cancer cells"

Article Title: Inductions of the fatty acid 2-hydroxylase (FA2H) gene by ?9-tetrahydrocannabinol in human breast cancer cells

Journal: The Journal of toxicological sciences

doi:

Comparison of the biological activities of Δ 9 -THC and nTZDpa. (A) Results of DNA microarray analysis. Data are expressed as fold induction vs. vehicle-treated groups. MDA-MB-231 cells were treated with vehicle or 25 μM Δ 9 -THC or
Figure Legend Snippet: Comparison of the biological activities of Δ 9 -THC and nTZDpa. (A) Results of DNA microarray analysis. Data are expressed as fold induction vs. vehicle-treated groups. MDA-MB-231 cells were treated with vehicle or 25 μM Δ 9 -THC or

Techniques Used: Microarray, Multiple Displacement Amplification

62) Product Images from "Comparative Gene Expression Analysis of Two Mouse Models of Autism: Transcriptome Profiling of the BTBR and En2−/− Hippocampus"

Article Title: Comparative Gene Expression Analysis of Two Mouse Models of Autism: Transcriptome Profiling of the BTBR and En2−/− Hippocampus

Journal: Frontiers in Neuroscience

doi: 10.3389/fnins.2016.00396

DEGs commonly expressed in the BTBR and En2 −/− hippocampus. (A) Venn diagram of differentially expressed genes in the BTBR and En2 −/− adult hippocampus. A total of 1016 and 862 differentially expressed genes were identified in BTBR (brown) and En2 −/− (gray) mice, respectively. Among these, 153 show differential expression in both strains. The table shows a subset of these common DEGs, all belonging to inflammatory pathways. (B) qRT-PCR validation of Ccnd1 and Pglyrp1, two genes differentially expressed in both BTBR and En2 −/− hippocampi. qRT-PCR results for both genes were in agreement with microarray results. Values are expressed as each gene/L41 comparative quantitation ratios normalized on the expression of respective control (mean ± s.e.m of three replicates from pools of six animals per genotype; p
Figure Legend Snippet: DEGs commonly expressed in the BTBR and En2 −/− hippocampus. (A) Venn diagram of differentially expressed genes in the BTBR and En2 −/− adult hippocampus. A total of 1016 and 862 differentially expressed genes were identified in BTBR (brown) and En2 −/− (gray) mice, respectively. Among these, 153 show differential expression in both strains. The table shows a subset of these common DEGs, all belonging to inflammatory pathways. (B) qRT-PCR validation of Ccnd1 and Pglyrp1, two genes differentially expressed in both BTBR and En2 −/− hippocampi. qRT-PCR results for both genes were in agreement with microarray results. Values are expressed as each gene/L41 comparative quantitation ratios normalized on the expression of respective control (mean ± s.e.m of three replicates from pools of six animals per genotype; p

Techniques Used: Mouse Assay, Expressing, Quantitative RT-PCR, Microarray, Quantitation Assay

Differentially expressed genes in the BTBR hippocampus. (A) Schematic representation of BTBR hippocampal DEGs, as compared to control B6 mice. A total of 1016 DEGs were identified, (580 down-regulated, 436 up-regulated). (B) qRT-PCR validation of differentially expressed genes. qRT-PCR results for all the evaluated genes were in agreement with microarray results. Values are expressed as each gene/L41 comparative quantitation ratios normalized on the expression of WT (mean ± s.e.m of three replicates from pools of six animals per genotype; p
Figure Legend Snippet: Differentially expressed genes in the BTBR hippocampus. (A) Schematic representation of BTBR hippocampal DEGs, as compared to control B6 mice. A total of 1016 DEGs were identified, (580 down-regulated, 436 up-regulated). (B) qRT-PCR validation of differentially expressed genes. qRT-PCR results for all the evaluated genes were in agreement with microarray results. Values are expressed as each gene/L41 comparative quantitation ratios normalized on the expression of WT (mean ± s.e.m of three replicates from pools of six animals per genotype; p

Techniques Used: Mouse Assay, Quantitative RT-PCR, Microarray, Quantitation Assay, Expressing

63) Product Images from "Phase I clinical study of liver regenerative therapy for cirrhosis by intrahepatic arterial infusion of freshly isolated autologous adipose tissue-derived stromal/stem (regenerative) cell"

Article Title: Phase I clinical study of liver regenerative therapy for cirrhosis by intrahepatic arterial infusion of freshly isolated autologous adipose tissue-derived stromal/stem (regenerative) cell

Journal: Regenerative Therapy

doi: 10.1016/j.reth.2016.12.001

Hierarchical gene expression clustering analysis of peripheral blood, ADRCs, and cADSCs . RNA was extracted from peripheral blood in PAXgene ® tubes and from freshly isolated ADRCs and expanded cADSCs. Gene expression data were obtained by DNA microarray and followed by unsupervised hierarchical clustering analysis. (A) Clustering analysis of gene expression data of peripheral blood and ADRCs. (B) Clustering analysis of gene expression data of ADRCs and cADSCs.
Figure Legend Snippet: Hierarchical gene expression clustering analysis of peripheral blood, ADRCs, and cADSCs . RNA was extracted from peripheral blood in PAXgene ® tubes and from freshly isolated ADRCs and expanded cADSCs. Gene expression data were obtained by DNA microarray and followed by unsupervised hierarchical clustering analysis. (A) Clustering analysis of gene expression data of peripheral blood and ADRCs. (B) Clustering analysis of gene expression data of ADRCs and cADSCs.

Techniques Used: Expressing, Isolation, Microarray

64) Product Images from "Long non-coding RNAs could act as vectors for paternal heredity of high fat diet-induced obesity"

Article Title: Long non-coding RNAs could act as vectors for paternal heredity of high fat diet-induced obesity

Journal: Oncotarget

doi: 10.18632/oncotarget.18138

Validation of microarray data by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) The relative expression levels of eight lncRNAs are shown comparing (A) F0-HFD/F0-normal; (B) F1-HFD/F0-HFD; and (C) F1-HFD/F1-normal. Data are presented as average 2 -ΔCt , n = 10. (D) Comparison between qRT-PCR results and microarray data revealing a good correlation of the two methods. The heights of the columns represent the fold changes (log2 transformed) computed from the qPCR and microarray data.
Figure Legend Snippet: Validation of microarray data by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) The relative expression levels of eight lncRNAs are shown comparing (A) F0-HFD/F0-normal; (B) F1-HFD/F0-HFD; and (C) F1-HFD/F1-normal. Data are presented as average 2 -ΔCt , n = 10. (D) Comparison between qRT-PCR results and microarray data revealing a good correlation of the two methods. The heights of the columns represent the fold changes (log2 transformed) computed from the qPCR and microarray data.

Techniques Used: Microarray, Reverse Transcription Polymerase Chain Reaction, Quantitative RT-PCR, Expressing, Transformation Assay, Real-time Polymerase Chain Reaction

LncRNA scatter plots used to identify differentially expressed lncRNAs in four groups X and Y axes represent averaged normalised signal values of the control and experimental group microarray samples. LncRNAs above the top red line and below the bottom blue line showed greater than 2.0-fold changes in expression between the two compared groups. (A) F0-HFD/F0-NC; (B) F1-HFD/F1-NC; and (C) F1-HFD/F0-HFD.
Figure Legend Snippet: LncRNA scatter plots used to identify differentially expressed lncRNAs in four groups X and Y axes represent averaged normalised signal values of the control and experimental group microarray samples. LncRNAs above the top red line and below the bottom blue line showed greater than 2.0-fold changes in expression between the two compared groups. (A) F0-HFD/F0-NC; (B) F1-HFD/F1-NC; and (C) F1-HFD/F0-HFD.

Techniques Used: Microarray, Expressing

65) Product Images from "Doxorubicin and NRG-1/erbB4-Deficiency Affect Gene Expression Profile: Involving Protein Homeostasis in Mouse"

Article Title: Doxorubicin and NRG-1/erbB4-Deficiency Affect Gene Expression Profile: Involving Protein Homeostasis in Mouse

Journal: ISRN Cardiology

doi: 10.5402/2012/745185

Validat ion of cDNA microarray ratios and functional clustering. The cDNA array ratios were correlated to RT-PCR ratios of differentially expressed genes. (a) Following logarithmic transformation, RT-PCR ratios were plotted against cDNA array ratios. (b) Differentially expressed genes among erbB4-KO, WTD, and erbB4-KOD hearts using the criteria of FDR
Figure Legend Snippet: Validat ion of cDNA microarray ratios and functional clustering. The cDNA array ratios were correlated to RT-PCR ratios of differentially expressed genes. (a) Following logarithmic transformation, RT-PCR ratios were plotted against cDNA array ratios. (b) Differentially expressed genes among erbB4-KO, WTD, and erbB4-KOD hearts using the criteria of FDR

Techniques Used: Microarray, Functional Assay, Reverse Transcription Polymerase Chain Reaction, Transformation Assay

Related Articles

Indirect Immunoperoxidase Assay:

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Centrifugation:

Article Title: Increased Expression of Matrix Extracellular Phosphoglycoprotein (MEPE) in Cortical Bone of the Rat Tibia after Mechanical Loading: Identification by Oligonucleotide Microarray
Article Snippet: .. Slides were dried by centrifugation at 200 g for 3 min. After drying, the slides were scanned at 10 µm resolution for Cy3 and Cy5 intensities using the microarray scanner (Agilent Technologies) operated by Agilent Scan Control software and Feature Extraction software. ..

Amplification:

Article Title: Expression of MicroRNAs in the Stem Cell Niche of the Adult Mouse Incisor
Article Snippet: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturer's protocol (Agilent). .. Arrays were scanned using a microarray scanner and raw signal intensities were extracted with Feature Extraction v10.3 software (Agilent).

Article Title: Transcriptomics in lung tissue upon respiratory syncytial virus infection reveals aging as important modulator of immune activation and matrix maintenance
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Article Title: Highly Enhanced Expression of CD70 on Human T-Lymphotropic Virus Type 1-Carrying T-Cell Lines and Adult T-Cell Leukemia Cells
Article Snippet: The cDNA was transcribed and amplified with T7 RNA polymerase to produce the cRNA labeled with cyanine 3. .. After hybridization, the microarray was washed thoroughly and scanned with a microarray scanner (Agilent).

In Situ:

Article Title: Overexpression of CtCHS1 Increases Accumulation of Quinochalcone in Safflower
Article Snippet: 8 × 15K (Agilent) in situ synthesis of gene chip was used to detect gene expression. .. Then the microarrays were scanned with the Microarray Scanner (Agilent). gProcessed Signal were the value of transcript abundancy.

Synthesized:

Article Title: Analysis of Differential Expression Patterns of mRNA and Protein During Cold-acclimation and De-acclimation in Arabidopsis *
Article Snippet: After isolation, RNAs were synthesized into cDNAs using 500 ng of total RNA. cRNA was labeled with a single color (Cy3) using Quick Amp labeling kit (Agilent Technologies, Palo Alto, CA) and hybridized to an Arabidopsis oligo DNA microarray Ver. .. Arrays were scanned with a microarray scanner (G2505B, Agilent Technologies) and analyzed using GeneSpring Ver.7 (Agilent Technologies).

Software:

Article Title: Expression of MicroRNAs in the Stem Cell Niche of the Adult Mouse Incisor
Article Snippet: .. Arrays were scanned using a microarray scanner and raw signal intensities were extracted with Feature Extraction v10.3 software (Agilent). ..

Article Title: Highly Enhanced Expression of CD70 on Human T-Lymphotropic Virus Type 1-Carrying T-Cell Lines and Adult T-Cell Leukemia Cells
Article Snippet: After hybridization, the microarray was washed thoroughly and scanned with a microarray scanner (Agilent). .. After hybridization, the microarray was washed thoroughly and scanned with a microarray scanner (Agilent).

Article Title: Aptamer-Based Multiplexed Proteomic Technology for Biomarker DiscoveryUnlocking Biomarker Discovery: Large Scale Application of Aptamer Proteomic Technology for Early Detection of Lung Cancer
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Article Title: HOXA7, HOXA9, and HOXA10 are differentially expressed in clival and sacral chordomas
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Article Title: Whole transcriptome characterization of the effects of dehydration and rehydration on Cladonia rangiferina, the grey reindeer lichen
Article Snippet: .. Data analysis The oligonucleotide probe identifiers and signal intensities from the scanned microarray image files were determined using software running on the microarray scanner (Feature Extraction, v 10.5.1.1, Agilent). ..

Article Title: Increased Expression of Matrix Extracellular Phosphoglycoprotein (MEPE) in Cortical Bone of the Rat Tibia after Mechanical Loading: Identification by Oligonucleotide Microarray
Article Snippet: .. Slides were dried by centrifugation at 200 g for 3 min. After drying, the slides were scanned at 10 µm resolution for Cy3 and Cy5 intensities using the microarray scanner (Agilent Technologies) operated by Agilent Scan Control software and Feature Extraction software. ..

Article Title: Biological outcome and mapping of total factor cascades in response to HIF induction during regenerative angiogenesis
Article Snippet: After washing, the slides were scanned using the Microarray Scanner (Agilent Technologies, USA) at 5-μm resolution and at high and low photomultiplier voltages to optimize the dynamic range of image quantification. .. The data were extracted from these images using the Agilent Feature Extraction v.9.5.3 software.

Isolation:

Article Title: Overexpression of CtCHS1 Increases Accumulation of Quinochalcone in Safflower
Article Snippet: Gene Chip RNA of equivalent different developmental stage flower samples from two safflower lines were isolated using trizol and purified. .. Then the microarrays were scanned with the Microarray Scanner (Agilent). gProcessed Signal were the value of transcript abundancy.

Article Title: Analysis of Differential Expression Patterns of mRNA and Protein During Cold-acclimation and De-acclimation in Arabidopsis *
Article Snippet: After isolation, RNAs were synthesized into cDNAs using 500 ng of total RNA. cRNA was labeled with a single color (Cy3) using Quick Amp labeling kit (Agilent Technologies, Palo Alto, CA) and hybridized to an Arabidopsis oligo DNA microarray Ver. .. Arrays were scanned with a microarray scanner (G2505B, Agilent Technologies) and analyzed using GeneSpring Ver.7 (Agilent Technologies).

Generated:

Article Title: HOXA7, HOXA9, and HOXA10 are differentially expressed in clival and sacral chordomas
Article Snippet: The signals were captured by a Microarray Scanner (G2565, Agilent Technologies, Santa Clara, USA). .. The generated data was analysed using the software Genespring 12.1 (Agilent Technologies) and Ingenuity Pathway Analysis (IPA; Qiagen).

Labeling:

Article Title: Expression of MicroRNAs in the Stem Cell Niche of the Adult Mouse Incisor
Article Snippet: Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to custom v3.1 multi-species 8×15k miRNA arrays (Agilent). .. Arrays were scanned using a microarray scanner and raw signal intensities were extracted with Feature Extraction v10.3 software (Agilent).

Article Title: Highly Enhanced Expression of CD70 on Human T-Lymphotropic Virus Type 1-Carrying T-Cell Lines and Adult T-Cell Leukemia Cells
Article Snippet: The cyanine 3-labeled cRNA was purified with RNeasy (Qiagen) and examined for its concentration and labeling quality by a spectrophotometer. .. After hybridization, the microarray was washed thoroughly and scanned with a microarray scanner (Agilent).

Article Title: Analysis of Differential Expression Patterns of mRNA and Protein During Cold-acclimation and De-acclimation in Arabidopsis *
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Article Title: Comparative gene expression analysis after exposure to 123I-iododeoxyuridine, γ- and α-radiation—potential biomarkers for the discrimination of radiation qualities
Article Snippet: Labeled cRNA samples were hybridized for 17 h to 44 k Whole Human Genome DNA microarrays (G4112F, Agilent) using a hybridization oven (Agilent). .. After hybridization and washing, DNA microarrays were scanned with the Microarray Scanner (G2505 B, Agilent) as recommended by Agilent.

Article Title: Increased Expression of Matrix Extracellular Phosphoglycoprotein (MEPE) in Cortical Bone of the Rat Tibia after Mechanical Loading: Identification by Oligonucleotide Microarray
Article Snippet: The probe-hybridization mixture contained 16.0 µl Cy3 and 16.0 µl Cy5 labeled samples and 26.2 µl hybridization mixture (60 µg yeast tRNA, 12 µg polyA and 24 µg human Cot-1 DNA). .. Slides were dried by centrifugation at 200 g for 3 min. After drying, the slides were scanned at 10 µm resolution for Cy3 and Cy5 intensities using the microarray scanner (Agilent Technologies) operated by Agilent Scan Control software and Feature Extraction software.

Article Title: Biological outcome and mapping of total factor cascades in response to HIF induction during regenerative angiogenesis
Article Snippet: The labeled targets were purified using the RNeasy® Mini Kit (Qiagen) and their quality and quantity were confirmed by spectrophotometry and the Bioanalyzer 2100 technology (Agilent Technologies, USA). .. After washing, the slides were scanned using the Microarray Scanner (Agilent Technologies, USA) at 5-μm resolution and at high and low photomultiplier voltages to optimize the dynamic range of image quantification.

Purification:

Article Title: Overexpression of CtCHS1 Increases Accumulation of Quinochalcone in Safflower
Article Snippet: Gene Chip RNA of equivalent different developmental stage flower samples from two safflower lines were isolated using trizol and purified. .. Then the microarrays were scanned with the Microarray Scanner (Agilent). gProcessed Signal were the value of transcript abundancy.

Article Title: Highly Enhanced Expression of CD70 on Human T-Lymphotropic Virus Type 1-Carrying T-Cell Lines and Adult T-Cell Leukemia Cells
Article Snippet: The cyanine 3-labeled cRNA was purified with RNeasy (Qiagen) and examined for its concentration and labeling quality by a spectrophotometer. .. After hybridization, the microarray was washed thoroughly and scanned with a microarray scanner (Agilent).

Article Title: Comparative gene expression analysis after exposure to 123I-iododeoxyuridine, γ- and α-radiation—potential biomarkers for the discrimination of radiation qualities
Article Snippet: Of the total RNA, 400 ng was transcribed into cDNA with an oligo-dT primer, followed by transcription into cRNA labeled with cyanine 3-CTP (Quick-Amp Labeling Kit, One-color, Agilent). cRNA purification was performed with the RNeasy Mini Kit (Qiagen). cRNA yields and the dye incorporation were measured with the NanoDrop-1000 spectrophotometer. .. After hybridization and washing, DNA microarrays were scanned with the Microarray Scanner (G2505 B, Agilent) as recommended by Agilent.

Article Title: Biological outcome and mapping of total factor cascades in response to HIF induction during regenerative angiogenesis
Article Snippet: The labeled targets were purified using the RNeasy® Mini Kit (Qiagen) and their quality and quantity were confirmed by spectrophotometry and the Bioanalyzer 2100 technology (Agilent Technologies, USA). .. After washing, the slides were scanned using the Microarray Scanner (Agilent Technologies, USA) at 5-μm resolution and at high and low photomultiplier voltages to optimize the dynamic range of image quantification.

Concentration Assay:

Article Title: Highly Enhanced Expression of CD70 on Human T-Lymphotropic Virus Type 1-Carrying T-Cell Lines and Adult T-Cell Leukemia Cells
Article Snippet: The cyanine 3-labeled cRNA was purified with RNeasy (Qiagen) and examined for its concentration and labeling quality by a spectrophotometer. .. After hybridization, the microarray was washed thoroughly and scanned with a microarray scanner (Agilent).

Incubation:

Article Title: Biological outcome and mapping of total factor cascades in response to HIF induction during regenerative angiogenesis
Article Snippet: Cy3- and Cy5-labeled cRNA targets were mixed and incubated on microarray slides at 65°C for 17 hours. .. After washing, the slides were scanned using the Microarray Scanner (Agilent Technologies, USA) at 5-μm resolution and at high and low photomultiplier voltages to optimize the dynamic range of image quantification.

Significance Assay:

Article Title: Overexpression of CtCHS1 Increases Accumulation of Quinochalcone in Safflower
Article Snippet: Then the microarrays were scanned with the Microarray Scanner (Agilent). gProcessed Signal were the value of transcript abundancy. .. Differential genes were screened out with appropriate fold change absolutely (FCA) calculated and p-value.

Article Title: HOXA7, HOXA9, and HOXA10 are differentially expressed in clival and sacral chordomas
Article Snippet: The signals were captured by a Microarray Scanner (G2565, Agilent Technologies, Santa Clara, USA). .. Differentially expressed genes with statistical significance (p-value cut-off ≤ 0,005) between the two groups (clivus versus sacrum) were identified using scatter plot filtering.

Imaging:

Article Title: Aptamer-Based Multiplexed Proteomic Technology for Biomarker DiscoveryUnlocking Biomarker Discovery: Large Scale Application of Aptamer Proteomic Technology for Early Detection of Lung Cancer
Article Snippet: .. Microarray Imaging The microarray slides were imaged with a microarray scanner (Agilent G2565CA Microarray Scanner System, Agilent Technologies) in the Cy3-channel at 5 µm resolution at 100% PMT setting and the XRD option enabled at 0.05. .. The resulting tiff images were processed using Agilent feature extraction software version 10.5.1.1 with the GE1_105_Dec08 protocol.

Expressing:

Article Title: Expression of MicroRNAs in the Stem Cell Niche of the Adult Mouse Incisor
Article Snippet: Paragraph title: Microarray and differential expression analysis ... Arrays were scanned using a microarray scanner and raw signal intensities were extracted with Feature Extraction v10.3 software (Agilent).

Article Title: Transcriptomics in lung tissue upon respiratory syncytial virus infection reveals aging as important modulator of immune activation and matrix maintenance
Article Snippet: .. After washing (NimbleGen Arrays User’s Guide – Gene Expression Arrays Version 5.0), slides were scanned in an ozone-free room with a microarray scanner (Agilent DNA microarray scanner G2565CA, Agilent Technologies). .. Feature extraction was performed with NimbleScan v2.5 (Roche NimbleGen) resulting in a table containing individual probe signal intensities for both dyes.

Article Title: Overexpression of CtCHS1 Increases Accumulation of Quinochalcone in Safflower
Article Snippet: 8 × 15K (Agilent) in situ synthesis of gene chip was used to detect gene expression. .. Then the microarrays were scanned with the Microarray Scanner (Agilent). gProcessed Signal were the value of transcript abundancy.

Article Title: Highly Enhanced Expression of CD70 on Human T-Lymphotropic Virus Type 1-Carrying T-Cell Lines and Adult T-Cell Leukemia Cells
Article Snippet: The microarray processing of the samples was carried out with necessary reagent kits provided by Agilent, according to the manufacturer's one-color microarray-based gene expression analysis protocol (version 5.5). .. After hybridization, the microarray was washed thoroughly and scanned with a microarray scanner (Agilent).

Article Title: HOXA7, HOXA9, and HOXA10 are differentially expressed in clival and sacral chordomas
Article Snippet: Paragraph title: Gene Expression Analysis ... The signals were captured by a Microarray Scanner (G2565, Agilent Technologies, Santa Clara, USA).

Article Title: Analysis of Differential Expression Patterns of mRNA and Protein During Cold-acclimation and De-acclimation in Arabidopsis *
Article Snippet: Arrays were scanned with a microarray scanner (G2505B, Agilent Technologies) and analyzed using GeneSpring Ver.7 (Agilent Technologies). .. These data were used for reference data of mRNA expression for corresponding proteins, which was analyzed by shotgun proteomics.

Article Title: Increased Expression of Matrix Extracellular Phosphoglycoprotein (MEPE) in Cortical Bone of the Rat Tibia after Mechanical Loading: Identification by Oligonucleotide Microarray
Article Snippet: Slides were dried by centrifugation at 200 g for 3 min. After drying, the slides were scanned at 10 µm resolution for Cy3 and Cy5 intensities using the microarray scanner (Agilent Technologies) operated by Agilent Scan Control software and Feature Extraction software. .. The dataset is submitted to GEO gene expression omnibus (GSE50707) with platform accession number: GPL: 1397.

Chromatin Immunoprecipitation:

Article Title: Expression of MicroRNAs in the Stem Cell Niche of the Adult Mouse Incisor
Article Snippet: Microarray and differential expression analysis Probe labeling and array hybridizations were performed according to standard protocols from the UCSF Shared Microarray Core Facilities and Agilent Technologies ( http://www.arrays.ucsf.edu and http://www.agilent.com ). miRNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). .. Arrays were scanned using a microarray scanner and raw signal intensities were extracted with Feature Extraction v10.3 software (Agilent).

Article Title: Overexpression of CtCHS1 Increases Accumulation of Quinochalcone in Safflower
Article Snippet: Paragraph title: Gene Chip ... Then the microarrays were scanned with the Microarray Scanner (Agilent). gProcessed Signal were the value of transcript abundancy.

Spectrophotometry:

Article Title: Transcriptomics in lung tissue upon respiratory syncytial virus infection reveals aging as important modulator of immune activation and matrix maintenance
Article Snippet: The yields of amplified RNA and incorporation of CyDye were determined by using a NanoDrop spectrophotometer. .. After washing (NimbleGen Arrays User’s Guide – Gene Expression Arrays Version 5.0), slides were scanned in an ozone-free room with a microarray scanner (Agilent DNA microarray scanner G2565CA, Agilent Technologies).

Article Title: Highly Enhanced Expression of CD70 on Human T-Lymphotropic Virus Type 1-Carrying T-Cell Lines and Adult T-Cell Leukemia Cells
Article Snippet: The cyanine 3-labeled cRNA was purified with RNeasy (Qiagen) and examined for its concentration and labeling quality by a spectrophotometer. .. After hybridization, the microarray was washed thoroughly and scanned with a microarray scanner (Agilent).

Article Title: Comparative gene expression analysis after exposure to 123I-iododeoxyuridine, γ- and α-radiation—potential biomarkers for the discrimination of radiation qualities
Article Snippet: Of the total RNA, 400 ng was transcribed into cDNA with an oligo-dT primer, followed by transcription into cRNA labeled with cyanine 3-CTP (Quick-Amp Labeling Kit, One-color, Agilent). cRNA purification was performed with the RNeasy Mini Kit (Qiagen). cRNA yields and the dye incorporation were measured with the NanoDrop-1000 spectrophotometer. .. After hybridization and washing, DNA microarrays were scanned with the Microarray Scanner (G2505 B, Agilent) as recommended by Agilent.

Article Title: Biological outcome and mapping of total factor cascades in response to HIF induction during regenerative angiogenesis
Article Snippet: The labeled targets were purified using the RNeasy® Mini Kit (Qiagen) and their quality and quantity were confirmed by spectrophotometry and the Bioanalyzer 2100 technology (Agilent Technologies, USA). .. After washing, the slides were scanned using the Microarray Scanner (Agilent Technologies, USA) at 5-μm resolution and at high and low photomultiplier voltages to optimize the dynamic range of image quantification.

Microarray:

Article Title: Expression of MicroRNAs in the Stem Cell Niche of the Adult Mouse Incisor
Article Snippet: .. Arrays were scanned using a microarray scanner and raw signal intensities were extracted with Feature Extraction v10.3 software (Agilent). ..

Article Title: Transcriptomics in lung tissue upon respiratory syncytial virus infection reveals aging as important modulator of immune activation and matrix maintenance
Article Snippet: .. After washing (NimbleGen Arrays User’s Guide – Gene Expression Arrays Version 5.0), slides were scanned in an ozone-free room with a microarray scanner (Agilent DNA microarray scanner G2565CA, Agilent Technologies). .. Feature extraction was performed with NimbleScan v2.5 (Roche NimbleGen) resulting in a table containing individual probe signal intensities for both dyes.

Article Title: Overexpression of CtCHS1 Increases Accumulation of Quinochalcone in Safflower
Article Snippet: .. Then the microarrays were scanned with the Microarray Scanner (Agilent). gProcessed Signal were the value of transcript abundancy. .. The expression analysis of unigenes in two lines were performed by DESeq (V1.14.0) ( ).

Article Title: Highly Enhanced Expression of CD70 on Human T-Lymphotropic Virus Type 1-Carrying T-Cell Lines and Adult T-Cell Leukemia Cells
Article Snippet: .. After hybridization, the microarray was washed thoroughly and scanned with a microarray scanner (Agilent). .. The microarray scan data were processed with Future Extraction software (version 9.5.1; Agilent), according to its manual.

Article Title: Aptamer-Based Multiplexed Proteomic Technology for Biomarker DiscoveryUnlocking Biomarker Discovery: Large Scale Application of Aptamer Proteomic Technology for Early Detection of Lung Cancer
Article Snippet: .. Microarray Imaging The microarray slides were imaged with a microarray scanner (Agilent G2565CA Microarray Scanner System, Agilent Technologies) in the Cy3-channel at 5 µm resolution at 100% PMT setting and the XRD option enabled at 0.05. .. The resulting tiff images were processed using Agilent feature extraction software version 10.5.1.1 with the GE1_105_Dec08 protocol.

Article Title: HOXA7, HOXA9, and HOXA10 are differentially expressed in clival and sacral chordomas
Article Snippet: .. The signals were captured by a Microarray Scanner (G2565, Agilent Technologies, Santa Clara, USA). .. The generated data was analysed using the software Genespring 12.1 (Agilent Technologies) and Ingenuity Pathway Analysis (IPA; Qiagen).

Article Title: Analysis of Differential Expression Patterns of mRNA and Protein During Cold-acclimation and De-acclimation in Arabidopsis *
Article Snippet: .. Arrays were scanned with a microarray scanner (G2505B, Agilent Technologies) and analyzed using GeneSpring Ver.7 (Agilent Technologies). ..

Article Title: Whole transcriptome characterization of the effects of dehydration and rehydration on Cladonia rangiferina, the grey reindeer lichen
Article Snippet: .. Data analysis The oligonucleotide probe identifiers and signal intensities from the scanned microarray image files were determined using software running on the microarray scanner (Feature Extraction, v 10.5.1.1, Agilent). ..

Article Title: Comparative gene expression analysis after exposure to 123I-iododeoxyuridine, γ- and α-radiation—potential biomarkers for the discrimination of radiation qualities
Article Snippet: .. After hybridization and washing, DNA microarrays were scanned with the Microarray Scanner (G2505 B, Agilent) as recommended by Agilent. .. Analysis of DNA microarray data The images of the scanned microarrays were processed with the Agilent Feature Extraction software.

Article Title: Increased Expression of Matrix Extracellular Phosphoglycoprotein (MEPE) in Cortical Bone of the Rat Tibia after Mechanical Loading: Identification by Oligonucleotide Microarray
Article Snippet: .. Slides were dried by centrifugation at 200 g for 3 min. After drying, the slides were scanned at 10 µm resolution for Cy3 and Cy5 intensities using the microarray scanner (Agilent Technologies) operated by Agilent Scan Control software and Feature Extraction software. ..

Article Title: Biological outcome and mapping of total factor cascades in response to HIF induction during regenerative angiogenesis
Article Snippet: .. After washing, the slides were scanned using the Microarray Scanner (Agilent Technologies, USA) at 5-μm resolution and at high and low photomultiplier voltages to optimize the dynamic range of image quantification. .. The data were extracted from these images using the Agilent Feature Extraction v.9.5.3 software.

Article Title: Genome-wide analysis of aberrantly expressed lncRNAs and miRNAs with associated co-expression and ceRNA networks in β-thalassemia and hereditary persistence of fetal hemoglobin
Article Snippet: .. The arrays were washed and immediately scanned using a microarray scanner (Axon, USA). .. Finally, the scanned images were imported into GenePix software (Axon, USA) for grid alignment and data extraction.

Derivative Assay:

Article Title: Biological outcome and mapping of total factor cascades in response to HIF induction during regenerative angiogenesis
Article Snippet: Internal standards were derived from the Two-Color RNA Spike-in Kit (Agilent Technologies, USA). .. After washing, the slides were scanned using the Microarray Scanner (Agilent Technologies, USA) at 5-μm resolution and at high and low photomultiplier voltages to optimize the dynamic range of image quantification.

Hybridization:

Article Title: Transcriptomics in lung tissue upon respiratory syncytial virus infection reveals aging as important modulator of immune activation and matrix maintenance
Article Snippet: Hybridization was performed with a NimbleGen Hybridization System 4 (Roche NimbleGen) for 20 hours at 42 °C. .. After washing (NimbleGen Arrays User’s Guide – Gene Expression Arrays Version 5.0), slides were scanned in an ozone-free room with a microarray scanner (Agilent DNA microarray scanner G2565CA, Agilent Technologies).

Article Title: Overexpression of CtCHS1 Increases Accumulation of Quinochalcone in Safflower
Article Snippet: Hybridization of the RNA was performed using the gene expression hybridization kit (Agilent). .. Then the microarrays were scanned with the Microarray Scanner (Agilent). gProcessed Signal were the value of transcript abundancy.

Article Title: Highly Enhanced Expression of CD70 on Human T-Lymphotropic Virus Type 1-Carrying T-Cell Lines and Adult T-Cell Leukemia Cells
Article Snippet: .. After hybridization, the microarray was washed thoroughly and scanned with a microarray scanner (Agilent). .. The microarray scan data were processed with Future Extraction software (version 9.5.1; Agilent), according to its manual.

Article Title: Comparative gene expression analysis after exposure to 123I-iododeoxyuridine, γ- and α-radiation—potential biomarkers for the discrimination of radiation qualities
Article Snippet: .. After hybridization and washing, DNA microarrays were scanned with the Microarray Scanner (G2505 B, Agilent) as recommended by Agilent. .. Analysis of DNA microarray data The images of the scanned microarrays were processed with the Agilent Feature Extraction software.

Article Title: Increased Expression of Matrix Extracellular Phosphoglycoprotein (MEPE) in Cortical Bone of the Rat Tibia after Mechanical Loading: Identification by Oligonucleotide Microarray
Article Snippet: Paragraph title: Microarray, probe generation, hybridization and washing ... Slides were dried by centrifugation at 200 g for 3 min. After drying, the slides were scanned at 10 µm resolution for Cy3 and Cy5 intensities using the microarray scanner (Agilent Technologies) operated by Agilent Scan Control software and Feature Extraction software.

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    Agilent technologies agilent scanner
    CXCR4 RNA and protein expression is increased in anoikis-resistant cells Gene expression of the anoikis-resistant fraction versus monolayer cells of 2 normal (MCF10a and 226L) and 3 malignant (SKBR3, MCF7 and T47D) breast cell lines were analysed using an <t>Agilent</t> custom microarray. 12 genes increased > 2-fold expression in the anoikis-resistant population versus monolayer cells while 3 genes significantly decreased > 2-fold expression averaging expression across all cell lines (A). Quantitative RT-PCR and FACS confirmed increased gene and cell surface expression of CXCR4 in 4 out of the 5 cell lines analysed compared with monolayer cells (B and C). CXCR4 transcript levels were also found to be significantly higher in CD44+/CD24− flow sorted cells from Creighton et al. 2009 [ 28 ] (D). Pearson correlation was used for hierarchical clustering of gene expression (rows), red = high and blue = low relative to mean (white), grey = no expression. Mono – monolayer cells, AR – 12 hour anoikis-resistant cells, n.d. – not detectable. FACS plots representative of 3 independent experiments, (D) n = 14, error bars ± S.E.M., ** p
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    CXCR4 RNA and protein expression is increased in anoikis-resistant cells Gene expression of the anoikis-resistant fraction versus monolayer cells of 2 normal (MCF10a and 226L) and 3 malignant (SKBR3, MCF7 and T47D) breast cell lines were analysed using an Agilent custom microarray. 12 genes increased > 2-fold expression in the anoikis-resistant population versus monolayer cells while 3 genes significantly decreased > 2-fold expression averaging expression across all cell lines (A). Quantitative RT-PCR and FACS confirmed increased gene and cell surface expression of CXCR4 in 4 out of the 5 cell lines analysed compared with monolayer cells (B and C). CXCR4 transcript levels were also found to be significantly higher in CD44+/CD24− flow sorted cells from Creighton et al. 2009 [ 28 ] (D). Pearson correlation was used for hierarchical clustering of gene expression (rows), red = high and blue = low relative to mean (white), grey = no expression. Mono – monolayer cells, AR – 12 hour anoikis-resistant cells, n.d. – not detectable. FACS plots representative of 3 independent experiments, (D) n = 14, error bars ± S.E.M., ** p

    Journal: Oncotarget

    Article Title: A differential role for CXCR4 in the regulation of normal versus malignant breast stem cell activity

    doi:

    Figure Lengend Snippet: CXCR4 RNA and protein expression is increased in anoikis-resistant cells Gene expression of the anoikis-resistant fraction versus monolayer cells of 2 normal (MCF10a and 226L) and 3 malignant (SKBR3, MCF7 and T47D) breast cell lines were analysed using an Agilent custom microarray. 12 genes increased > 2-fold expression in the anoikis-resistant population versus monolayer cells while 3 genes significantly decreased > 2-fold expression averaging expression across all cell lines (A). Quantitative RT-PCR and FACS confirmed increased gene and cell surface expression of CXCR4 in 4 out of the 5 cell lines analysed compared with monolayer cells (B and C). CXCR4 transcript levels were also found to be significantly higher in CD44+/CD24− flow sorted cells from Creighton et al. 2009 [ 28 ] (D). Pearson correlation was used for hierarchical clustering of gene expression (rows), red = high and blue = low relative to mean (white), grey = no expression. Mono – monolayer cells, AR – 12 hour anoikis-resistant cells, n.d. – not detectable. FACS plots representative of 3 independent experiments, (D) n = 14, error bars ± S.E.M., ** p

    Article Snippet: The chips were scanned using an Agilent scanner.

    Techniques: Expressing, Microarray, Quantitative RT-PCR, FACS, Flow Cytometry

    Hierarchical cluster plot generated from miRNA expression profiling of a repertoire of a variety of CNS cell lineages (neuronal, microglia, astrocytes). A microglia specific cluster of miRNAs is indicated. Red indicates high levels of miRNA expression, green low levels and gray indicates expression that was undetected by the microarray used.

    Journal: PLoS ONE

    Article Title: MicroRNA 146a (miR-146a) Is Over-Expressed during Prion Disease and Modulates the Innate Immune Response and the Microglial Activation State

    doi: 10.1371/journal.pone.0030832

    Figure Lengend Snippet: Hierarchical cluster plot generated from miRNA expression profiling of a repertoire of a variety of CNS cell lineages (neuronal, microglia, astrocytes). A microglia specific cluster of miRNAs is indicated. Red indicates high levels of miRNA expression, green low levels and gray indicates expression that was undetected by the microarray used.

    Article Snippet: Microarray slide washing and scanning The slides were washed according to Agilent's manufacturer's protocol for 4×44K arrays and scanned with the Agilent Microarray Scanner system with surescan technology (v.6.3) using the scanner settings for the 4×44K array format according to Agilent technologies manufacturer's instructions.

    Techniques: Generated, Expressing, Microarray

    EOC 13.31 cells were stimulated with 100 ng/ml semi-pure LPS and temporal changes in cytokine gene expression relative to mock-treated control were measured by microarray analysis. MiR-146a expression relative to mock-treated control was measured by TaqMan® qRT-PCR and expression is shown as grey bars.

    Journal: PLoS ONE

    Article Title: MicroRNA 146a (miR-146a) Is Over-Expressed during Prion Disease and Modulates the Innate Immune Response and the Microglial Activation State

    doi: 10.1371/journal.pone.0030832

    Figure Lengend Snippet: EOC 13.31 cells were stimulated with 100 ng/ml semi-pure LPS and temporal changes in cytokine gene expression relative to mock-treated control were measured by microarray analysis. MiR-146a expression relative to mock-treated control was measured by TaqMan® qRT-PCR and expression is shown as grey bars.

    Article Snippet: Microarray slide washing and scanning The slides were washed according to Agilent's manufacturer's protocol for 4×44K arrays and scanned with the Agilent Microarray Scanner system with surescan technology (v.6.3) using the scanner settings for the 4×44K array format according to Agilent technologies manufacturer's instructions.

    Techniques: Expressing, Microarray, Quantitative RT-PCR

    High expressed miRNAs in normal human placenta ( A ) HeatMap representing the top 30 high expressed miRNAs in normal human placenta. ( B ) Boxplot presenting normalized level of expression of the 866 miRNAs evaluated in normal human placenta using microarray miRNA expression profile. The bold line indicates de median of signal intensity of all miRNAs; the top edge represents the 75th percentile and the bottom edge the 25th percentile. Vertical bars indicate the upper and inferior limits and circles represent outlier points/samples (points 1.5 IQR above the 3rd quartile of the boxplot).

    Journal: Oncotarget

    Article Title: Highly expressed placental miRNAs control key biological processes in human cancer cell lines

    doi: 10.18632/oncotarget.25264

    Figure Lengend Snippet: High expressed miRNAs in normal human placenta ( A ) HeatMap representing the top 30 high expressed miRNAs in normal human placenta. ( B ) Boxplot presenting normalized level of expression of the 866 miRNAs evaluated in normal human placenta using microarray miRNA expression profile. The bold line indicates de median of signal intensity of all miRNAs; the top edge represents the 75th percentile and the bottom edge the 25th percentile. Vertical bars indicate the upper and inferior limits and circles represent outlier points/samples (points 1.5 IQR above the 3rd quartile of the boxplot).

    Article Snippet: Microarray slides were scanned using the High-Resolution Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA).

    Techniques: Expressing, Microarray

    Custom DNA and RNA pool generation from microarray. A) Agilent microarrays contain ssDNA probes that have variable designed sequences (multicoloured) and a T7 promoter sequence (orange lines). A Cy3 (green circle) labeled T7 promoter primer (orange line) is annealed to ssDNA microarray probes which are subsequently double-stranded by enzymatic primer extension using T4 DNA polymerase (blue dotted line). A dsDNA linker (purple lines), labeled with Cy5 (red circle), is ligated to the dsDNA microarray probes using T4 DNA ligase. Cy3 and Cy5 signals are detected on microarrays by scanning at 532 and 635 nm, respectively, to verify efficient T7 primer annealing and linker ligation. Scanned Cy3 and Cy5 microarray images are shown (enclosed by dotted blue circles). B) PCR amplification of the dsDNA pool using ssDNA pool purified from the microarray as template. ssDNA pool (PCR template) dilutions as well as bands corresponding to an 80 bp DNA ladder and a 80–91 bp dsDNA pool are indicated on the ethidium bromide stained agarose gel image. C) Linker cleavage is mediated by a Type IIS restriction enzymes, BspQI. Representative bands corresponding to undigested PCR amplified dsDNA pool (enclosed by yellow box), BspQI digested dsDNA template (enclosed by pink box), and cleaved dsDNA linker (enclosed by blue box) are indicated. D) The non-random RNA pool (multicoloured lines and high intensity band in the agarose gel image) is generated via T7 RNA polymerase mediated transcription reactions, using gel purified dsDNA templates (shown in panel 2C ).

    Journal: Methods (San Diego, Calif.)

    Article Title: RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins

    doi: 10.1016/j.ymeth.2016.12.003

    Figure Lengend Snippet: Custom DNA and RNA pool generation from microarray. A) Agilent microarrays contain ssDNA probes that have variable designed sequences (multicoloured) and a T7 promoter sequence (orange lines). A Cy3 (green circle) labeled T7 promoter primer (orange line) is annealed to ssDNA microarray probes which are subsequently double-stranded by enzymatic primer extension using T4 DNA polymerase (blue dotted line). A dsDNA linker (purple lines), labeled with Cy5 (red circle), is ligated to the dsDNA microarray probes using T4 DNA ligase. Cy3 and Cy5 signals are detected on microarrays by scanning at 532 and 635 nm, respectively, to verify efficient T7 primer annealing and linker ligation. Scanned Cy3 and Cy5 microarray images are shown (enclosed by dotted blue circles). B) PCR amplification of the dsDNA pool using ssDNA pool purified from the microarray as template. ssDNA pool (PCR template) dilutions as well as bands corresponding to an 80 bp DNA ladder and a 80–91 bp dsDNA pool are indicated on the ethidium bromide stained agarose gel image. C) Linker cleavage is mediated by a Type IIS restriction enzymes, BspQI. Representative bands corresponding to undigested PCR amplified dsDNA pool (enclosed by yellow box), BspQI digested dsDNA template (enclosed by pink box), and cleaved dsDNA linker (enclosed by blue box) are indicated. D) The non-random RNA pool (multicoloured lines and high intensity band in the agarose gel image) is generated via T7 RNA polymerase mediated transcription reactions, using gel purified dsDNA templates (shown in panel 2C ).

    Article Snippet: Scan microarray for Cy5 signal using Axon Genepix 4000B Microarray Scanner, or an alternative microarray scanner, (600 PMT at a wavelength of 635 nm) to confirm that all spots excluding empty Agilent controls have a high intensity Cy5 signal.

    Techniques: Microarray, Sequencing, Labeling, Ligation, Polymerase Chain Reaction, Amplification, Purification, Staining, Agarose Gel Electrophoresis, Generated

    Schematic of the RNAcompete assay. A GST-tagged RBP (RBP is orange oval, GST-tag is blue crescent), is incubated with a 75-fold excess of a non-random, custom designed RNA pool (multicoloured lines). RNA selectively bound (purple line) to an RBP during a GST-pulldown assay (GST bead is represented as a beige oval) is eluted, directly labeled with either Cy3 or Cy5 (green circles), and hybridized to a custom Agilent 244K microarray. Microarray data is analyzed computationally to generate RNA-binding motifs represented as logos.

    Journal: Methods (San Diego, Calif.)

    Article Title: RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins

    doi: 10.1016/j.ymeth.2016.12.003

    Figure Lengend Snippet: Schematic of the RNAcompete assay. A GST-tagged RBP (RBP is orange oval, GST-tag is blue crescent), is incubated with a 75-fold excess of a non-random, custom designed RNA pool (multicoloured lines). RNA selectively bound (purple line) to an RBP during a GST-pulldown assay (GST bead is represented as a beige oval) is eluted, directly labeled with either Cy3 or Cy5 (green circles), and hybridized to a custom Agilent 244K microarray. Microarray data is analyzed computationally to generate RNA-binding motifs represented as logos.

    Article Snippet: Scan microarray for Cy5 signal using Axon Genepix 4000B Microarray Scanner, or an alternative microarray scanner, (600 PMT at a wavelength of 635 nm) to confirm that all spots excluding empty Agilent controls have a high intensity Cy5 signal.

    Techniques: Incubation, GST Pulldown Assay, Labeling, Microarray, RNA Binding Assay