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Agilent technologies rna
Analysis of IL-6 mRNA levels within synovial tissue from rheumatoid arthritis (RA) as compared with that from osteoarthritis (OA) patients. Upper panels: quality control of total <t>RNA</t> preparations. Aliquots (300 ng) of total RNA extracted from synovial tissue from RA and OA patients were plotted on a RNA 6000 Nano-LabChip. Quality of RNA was scanned using a <t>2100</t> bioanalyzer. RNA gel electropherograms show the presence of 28S and 18S ribosomal units, indicating intact RNA of the investigated samples. Lower panels: differential IL-6 mRNA levels were determined by semiquantitative reverse transcription polymerase chain reaction (PCR). The figure shows a representative analysis of eight cDNA samples derived from patients with RA and of eight cDNA samples from patients with OA. cDNA samples were adjusted to equal glyceraldehyde-3-phosphate dehydrogenase (G3PDH) levels, performed by competitive PCR using an internal standard (see Materials and methods). Numbered lanes correspond to individual patients within Table 1 .
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1) Product Images from "High CXCR3 expression in synovial mast cells associated with CXCL9 and CXCL10 expression in inflammatory synovial tissues of patients with rheumatoid arthritis"

Article Title: High CXCR3 expression in synovial mast cells associated with CXCL9 and CXCL10 expression in inflammatory synovial tissues of patients with rheumatoid arthritis

Journal: Arthritis Research & Therapy

doi:

Analysis of IL-6 mRNA levels within synovial tissue from rheumatoid arthritis (RA) as compared with that from osteoarthritis (OA) patients. Upper panels: quality control of total RNA preparations. Aliquots (300 ng) of total RNA extracted from synovial tissue from RA and OA patients were plotted on a RNA 6000 Nano-LabChip. Quality of RNA was scanned using a 2100 bioanalyzer. RNA gel electropherograms show the presence of 28S and 18S ribosomal units, indicating intact RNA of the investigated samples. Lower panels: differential IL-6 mRNA levels were determined by semiquantitative reverse transcription polymerase chain reaction (PCR). The figure shows a representative analysis of eight cDNA samples derived from patients with RA and of eight cDNA samples from patients with OA. cDNA samples were adjusted to equal glyceraldehyde-3-phosphate dehydrogenase (G3PDH) levels, performed by competitive PCR using an internal standard (see Materials and methods). Numbered lanes correspond to individual patients within Table 1 .
Figure Legend Snippet: Analysis of IL-6 mRNA levels within synovial tissue from rheumatoid arthritis (RA) as compared with that from osteoarthritis (OA) patients. Upper panels: quality control of total RNA preparations. Aliquots (300 ng) of total RNA extracted from synovial tissue from RA and OA patients were plotted on a RNA 6000 Nano-LabChip. Quality of RNA was scanned using a 2100 bioanalyzer. RNA gel electropherograms show the presence of 28S and 18S ribosomal units, indicating intact RNA of the investigated samples. Lower panels: differential IL-6 mRNA levels were determined by semiquantitative reverse transcription polymerase chain reaction (PCR). The figure shows a representative analysis of eight cDNA samples derived from patients with RA and of eight cDNA samples from patients with OA. cDNA samples were adjusted to equal glyceraldehyde-3-phosphate dehydrogenase (G3PDH) levels, performed by competitive PCR using an internal standard (see Materials and methods). Numbered lanes correspond to individual patients within Table 1 .

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Derivative Assay

2) Product Images from "Blood Transcriptional Signatures for Disease Progression in a Rat Model of Osteoarthritis"

Article Title: Blood Transcriptional Signatures for Disease Progression in a Rat Model of Osteoarthritis

Journal: International Journal of Genomics

doi: 10.1155/2017/1746426

Gene expression patterns in blood associated with OA progression in the rat model of the knee joint arthritis. Hierarchical clustering of MIA-induced transcriptional alterations in whole blood. Microarray results are shown as a heat map and include 41 transcripts with significantly different levels of transcript abundance. Colored rectangles represent transcript abundance 2, 14, 21, and 28 days after the intra-articular injection of the MIA of the gene labeled on the right. The intensity of the color is proportional to the standardized values (between −3 and 3) from each microarray, as indicated on the bar below the heat map image. Hierarchical clustering was performed with the dChip software using Euclidean distance and average linkage method. Major MIA-induced gene transcription patterns are arbitrarily described as A–C. The regulated genes from gene clusters A–C were labeled on the right.
Figure Legend Snippet: Gene expression patterns in blood associated with OA progression in the rat model of the knee joint arthritis. Hierarchical clustering of MIA-induced transcriptional alterations in whole blood. Microarray results are shown as a heat map and include 41 transcripts with significantly different levels of transcript abundance. Colored rectangles represent transcript abundance 2, 14, 21, and 28 days after the intra-articular injection of the MIA of the gene labeled on the right. The intensity of the color is proportional to the standardized values (between −3 and 3) from each microarray, as indicated on the bar below the heat map image. Hierarchical clustering was performed with the dChip software using Euclidean distance and average linkage method. Major MIA-induced gene transcription patterns are arbitrarily described as A–C. The regulated genes from gene clusters A–C were labeled on the right.

Techniques Used: Expressing, Microarray, Injection, Labeling, Software

Gene expression profiles of three genes regulated in both animal model and human blood samples. (a) Clustering of the OA patients based on the expression of three genes commonly regulated in the blood of rats and humans. mRNA abundance levels measured by the microarrays were obtained from the GARP study [ 11 ]. The dataset consists of blood gene expression profiles of 106 OA patients and 33 controls (OA samples were indicated by green while controls by violet colors). The intensity of the color is proportional to the standardized values (between −3 and 3) from each microarray, as indicated on the bar below the heat map image. Hierarchical clustering was performed with the dChip software using correlation distance metric and centroid linkage method. (b) Time course of gene expression alterations in rat blood of the selected genes. The profiles of individual animals are presented ( n = 5).
Figure Legend Snippet: Gene expression profiles of three genes regulated in both animal model and human blood samples. (a) Clustering of the OA patients based on the expression of three genes commonly regulated in the blood of rats and humans. mRNA abundance levels measured by the microarrays were obtained from the GARP study [ 11 ]. The dataset consists of blood gene expression profiles of 106 OA patients and 33 controls (OA samples were indicated by green while controls by violet colors). The intensity of the color is proportional to the standardized values (between −3 and 3) from each microarray, as indicated on the bar below the heat map image. Hierarchical clustering was performed with the dChip software using correlation distance metric and centroid linkage method. (b) Time course of gene expression alterations in rat blood of the selected genes. The profiles of individual animals are presented ( n = 5).

Techniques Used: Expressing, Animal Model, Microarray, Software

3) Product Images from "Autism-Associated Gene Expression in Peripheral Leucocytes Commonly Observed between Subjects with Autism and Healthy Women Having Autistic Children"

Article Title: Autism-Associated Gene Expression in Peripheral Leucocytes Commonly Observed between Subjects with Autism and Healthy Women Having Autistic Children

Journal: PLoS ONE

doi: 10.1371/journal.pone.0024723

Similarity in gene expression profiling between the ASD and asdMO group. Venn diagram of differentially expressed genes for the ASD group compared with the Control group and the asdMO group compared with the ctrlMO group ( > 2-fold change) (A). RNA was prepared from each group and subjected to microarray analysis. Differentially expressed 19 and 57 genes by > 2-fold in ASD group and asdMO group, respectively. Three genes were overlapped. The mean of expression values of the 19 genes (B) and the 57 genes (C) changed in a parallel direction between the ASD and asdMO group. The normalized intensity value of genes, which was up-regulated or down-regulated by 2-fold, is shown in red or green, respectively, compared with control or ctrlMO. Venn diagram of differentially expressed 496 and 1126 genes by > 1.5-fold in ASD group and asdMO group (D). 399 genes were overlapped. The mean of expression values of the overlapped 399 genes was similar direction between the ASD and asdMO group (E). The normalized intensity value of genes, which was up-regulated or down-regulated by 1.5-fold, is shown in red or green, compared with control.
Figure Legend Snippet: Similarity in gene expression profiling between the ASD and asdMO group. Venn diagram of differentially expressed genes for the ASD group compared with the Control group and the asdMO group compared with the ctrlMO group ( > 2-fold change) (A). RNA was prepared from each group and subjected to microarray analysis. Differentially expressed 19 and 57 genes by > 2-fold in ASD group and asdMO group, respectively. Three genes were overlapped. The mean of expression values of the 19 genes (B) and the 57 genes (C) changed in a parallel direction between the ASD and asdMO group. The normalized intensity value of genes, which was up-regulated or down-regulated by 2-fold, is shown in red or green, respectively, compared with control or ctrlMO. Venn diagram of differentially expressed 496 and 1126 genes by > 1.5-fold in ASD group and asdMO group (D). 399 genes were overlapped. The mean of expression values of the overlapped 399 genes was similar direction between the ASD and asdMO group (E). The normalized intensity value of genes, which was up-regulated or down-regulated by 1.5-fold, is shown in red or green, compared with control.

Techniques Used: Expressing, Microarray

4) Product Images from "Adaptation of aphid stylectomy for analyses of proteins and mRNAs in barley phloem sap"

Article Title: Adaptation of aphid stylectomy for analyses of proteins and mRNAs in barley phloem sap

Journal: Journal of Experimental Botany

doi: 10.1093/jxb/ern181

Determination of RNase activity in stylectomy exudate of barley plants. RNase activity was tested with barley leaf total RNA. Samples were separated and visualized using an Agilent Bioanalyzer 2100. Phloem sap (green), leaf extract (blue), water (red), or 1.6 ng ml −1 (light blue), 8 ng ml −1 (pink), or 40 ng ml −1 (orange) RNase A standards were added to total RNA. RNase activity caused a decrease in the amount of high molecular weight rRNA—visible as four peaks between 1000 and 3600 nucleotides (nt)—and an accumulation of low molecular weight RNA fragments between 25 and 900 nt. Note that the peak maxima for the 1.6 ng ml −1 RNase A standard (light blue arrowheads) are consistently lower than the peak maxima for the phloem sample (green arrowheads) and the water control (red curve), whereas the light blue curve runs on top of the red and green (less pronounced) curves in the low molecular weight range. RNA concentration is depicted in arbitrary units and plotted versus the molecular weight in nucleotides determined by an internal RNA size marker.
Figure Legend Snippet: Determination of RNase activity in stylectomy exudate of barley plants. RNase activity was tested with barley leaf total RNA. Samples were separated and visualized using an Agilent Bioanalyzer 2100. Phloem sap (green), leaf extract (blue), water (red), or 1.6 ng ml −1 (light blue), 8 ng ml −1 (pink), or 40 ng ml −1 (orange) RNase A standards were added to total RNA. RNase activity caused a decrease in the amount of high molecular weight rRNA—visible as four peaks between 1000 and 3600 nucleotides (nt)—and an accumulation of low molecular weight RNA fragments between 25 and 900 nt. Note that the peak maxima for the 1.6 ng ml −1 RNase A standard (light blue arrowheads) are consistently lower than the peak maxima for the phloem sample (green arrowheads) and the water control (red curve), whereas the light blue curve runs on top of the red and green (less pronounced) curves in the low molecular weight range. RNA concentration is depicted in arbitrary units and plotted versus the molecular weight in nucleotides determined by an internal RNA size marker.

Techniques Used: Activity Assay, Molecular Weight, Concentration Assay, Marker

5) Product Images from "Adaptation of aphid stylectomy for analyses of proteins and mRNAs in barley phloem sap"

Article Title: Adaptation of aphid stylectomy for analyses of proteins and mRNAs in barley phloem sap

Journal: Journal of Experimental Botany

doi: 10.1093/jxb/ern181

Determination of RNase activity in stylectomy exudate of barley plants. RNase activity was tested with barley leaf total RNA. Samples were separated and visualized using an Agilent Bioanalyzer 2100. Phloem sap (green), leaf extract (blue), water (red), or 1.6 ng ml −1 (light blue), 8 ng ml −1 (pink), or 40 ng ml −1 (orange) RNase A standards were added to total RNA. RNase activity caused a decrease in the amount of high molecular weight rRNA—visible as four peaks between 1000 and 3600 nucleotides (nt)—and an accumulation of low molecular weight RNA fragments between 25 and 900 nt. Note that the peak maxima for the 1.6 ng ml −1 RNase A standard (light blue arrowheads) are consistently lower than the peak maxima for the phloem sample (green arrowheads) and the water control (red curve), whereas the light blue curve runs on top of the red and green (less pronounced) curves in the low molecular weight range. RNA concentration is depicted in arbitrary units and plotted versus the molecular weight in nucleotides determined by an internal RNA size marker.
Figure Legend Snippet: Determination of RNase activity in stylectomy exudate of barley plants. RNase activity was tested with barley leaf total RNA. Samples were separated and visualized using an Agilent Bioanalyzer 2100. Phloem sap (green), leaf extract (blue), water (red), or 1.6 ng ml −1 (light blue), 8 ng ml −1 (pink), or 40 ng ml −1 (orange) RNase A standards were added to total RNA. RNase activity caused a decrease in the amount of high molecular weight rRNA—visible as four peaks between 1000 and 3600 nucleotides (nt)—and an accumulation of low molecular weight RNA fragments between 25 and 900 nt. Note that the peak maxima for the 1.6 ng ml −1 RNase A standard (light blue arrowheads) are consistently lower than the peak maxima for the phloem sample (green arrowheads) and the water control (red curve), whereas the light blue curve runs on top of the red and green (less pronounced) curves in the low molecular weight range. RNA concentration is depicted in arbitrary units and plotted versus the molecular weight in nucleotides determined by an internal RNA size marker.

Techniques Used: Activity Assay, Molecular Weight, Concentration Assay, Marker

6) Product Images from "Ribosome quality control is a central protection mechanism for yeast exposed to deoxynivalenol and trichothecin"

Article Title: Ribosome quality control is a central protection mechanism for yeast exposed to deoxynivalenol and trichothecin

Journal: BMC Genomics

doi: 10.1186/s12864-016-2718-y

Microarray analysis of DON treated cells reveals both induced and repressed mitochondrial related genes and induced amino acid biosynthesis genes. Genes with the largest increase of transcript level (differences) are connected to cytoplasmic translation and ribosome synthesis whereas glycolysis and amino acid biosynthesis genes are repressed. Clustering of normalized and filtered expression values including enriched GO terms is indicated. a fold change values and b expression level differences. c Expression differences and fold change of 120 ribosomal protein genes
Figure Legend Snippet: Microarray analysis of DON treated cells reveals both induced and repressed mitochondrial related genes and induced amino acid biosynthesis genes. Genes with the largest increase of transcript level (differences) are connected to cytoplasmic translation and ribosome synthesis whereas glycolysis and amino acid biosynthesis genes are repressed. Clustering of normalized and filtered expression values including enriched GO terms is indicated. a fold change values and b expression level differences. c Expression differences and fold change of 120 ribosomal protein genes

Techniques Used: Microarray, Expressing

Comparative transcription pattern analysis. a The Microarray expression pattern of DON and TTC sensitive mutants highlights a slow growth expression pattern in many strains. b DON treated cells have an initial dose dependent slow growth expression pattern (Type A: blue bars) which is inverted (Type B: orange bars) at later time points. Expression values of the genes of the DON treatment are sorted in parallel to the heat map of the microarray compendium depicted below. Expression values were obtained from http://deleteome.holstegelab.nl/
Figure Legend Snippet: Comparative transcription pattern analysis. a The Microarray expression pattern of DON and TTC sensitive mutants highlights a slow growth expression pattern in many strains. b DON treated cells have an initial dose dependent slow growth expression pattern (Type A: blue bars) which is inverted (Type B: orange bars) at later time points. Expression values of the genes of the DON treatment are sorted in parallel to the heat map of the microarray compendium depicted below. Expression values were obtained from http://deleteome.holstegelab.nl/

Techniques Used: Microarray, Expressing

7) Product Images from "High CXCR3 expression in synovial mast cells associated with CXCL9 and CXCL10 expression in inflammatory synovial tissues of patients with rheumatoid arthritis"

Article Title: High CXCR3 expression in synovial mast cells associated with CXCL9 and CXCL10 expression in inflammatory synovial tissues of patients with rheumatoid arthritis

Journal: Arthritis Research & Therapy

doi:

Analysis of IL-6 mRNA levels within synovial tissue from rheumatoid arthritis (RA) as compared with that from osteoarthritis (OA) patients. Upper panels: quality control of total RNA preparations. Aliquots (300 ng) of total RNA extracted from synovial tissue from RA and OA patients were plotted on a RNA 6000 Nano-LabChip. Quality of RNA was scanned using a 2100 bioanalyzer. RNA gel electropherograms show the presence of 28S and 18S ribosomal units, indicating intact RNA of the investigated samples. Lower panels: differential IL-6 mRNA levels were determined by semiquantitative reverse transcription polymerase chain reaction (PCR). The figure shows a representative analysis of eight cDNA samples derived from patients with RA and of eight cDNA samples from patients with OA. cDNA samples were adjusted to equal glyceraldehyde-3-phosphate dehydrogenase (G3PDH) levels, performed by competitive PCR using an internal standard (see Materials and methods). Numbered lanes correspond to individual patients within Table 1 .
Figure Legend Snippet: Analysis of IL-6 mRNA levels within synovial tissue from rheumatoid arthritis (RA) as compared with that from osteoarthritis (OA) patients. Upper panels: quality control of total RNA preparations. Aliquots (300 ng) of total RNA extracted from synovial tissue from RA and OA patients were plotted on a RNA 6000 Nano-LabChip. Quality of RNA was scanned using a 2100 bioanalyzer. RNA gel electropherograms show the presence of 28S and 18S ribosomal units, indicating intact RNA of the investigated samples. Lower panels: differential IL-6 mRNA levels were determined by semiquantitative reverse transcription polymerase chain reaction (PCR). The figure shows a representative analysis of eight cDNA samples derived from patients with RA and of eight cDNA samples from patients with OA. cDNA samples were adjusted to equal glyceraldehyde-3-phosphate dehydrogenase (G3PDH) levels, performed by competitive PCR using an internal standard (see Materials and methods). Numbered lanes correspond to individual patients within Table 1 .

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Derivative Assay

8) Product Images from "Characterization of mouse serum exosomal small RNA content: The origins and their roles in modulating inflammatory response"

Article Title: Characterization of mouse serum exosomal small RNA content: The origins and their roles in modulating inflammatory response

Journal: Oncotarget

doi: 10.18632/oncotarget.17448

Characterization of exosomes isolated from mouse serum by Exoquick precipitation ( A ) The TEM image depicts the spherical morphology of the isolated particles, bar = 200 nm. ( B ) The NTA analysis plot illustrates the size distribution and concentration of the isolated particles. The indicated concentration is the value for samples that were diluted 1,000-fold. ( C ) NTA analysis image corresponding to the data in (B). ( D ) The expression of TSG101 and CD63 in the isolated particles as determined by Western blotting. Lanes 1 to 3 are serum, exosomes-depleted serum and serum exosomes, respectively. The size distribution of mSEs RNAs as detected by Bioanalyzer and RNA chip ( E ) and small RNA chip ( F ). The images are the representatives of three or more independent experiments.
Figure Legend Snippet: Characterization of exosomes isolated from mouse serum by Exoquick precipitation ( A ) The TEM image depicts the spherical morphology of the isolated particles, bar = 200 nm. ( B ) The NTA analysis plot illustrates the size distribution and concentration of the isolated particles. The indicated concentration is the value for samples that were diluted 1,000-fold. ( C ) NTA analysis image corresponding to the data in (B). ( D ) The expression of TSG101 and CD63 in the isolated particles as determined by Western blotting. Lanes 1 to 3 are serum, exosomes-depleted serum and serum exosomes, respectively. The size distribution of mSEs RNAs as detected by Bioanalyzer and RNA chip ( E ) and small RNA chip ( F ). The images are the representatives of three or more independent experiments.

Techniques Used: Isolation, Transmission Electron Microscopy, Concentration Assay, Expressing, Western Blot, Chromatin Immunoprecipitation

9) Product Images from "Adaptation of aphid stylectomy for analyses of proteins and mRNAs in barley phloem sap"

Article Title: Adaptation of aphid stylectomy for analyses of proteins and mRNAs in barley phloem sap

Journal: Journal of Experimental Botany

doi: 10.1093/jxb/ern181

Determination of RNase activity in stylectomy exudate of barley plants. RNase activity was tested with barley leaf total RNA. Samples were separated and visualized using an Agilent Bioanalyzer 2100. Phloem sap (green), leaf extract (blue), water (red), or 1.6 ng ml −1 (light blue), 8 ng ml −1 (pink), or 40 ng ml −1 (orange) RNase A standards were added to total RNA. RNase activity caused a decrease in the amount of high molecular weight rRNA—visible as four peaks between 1000 and 3600 nucleotides (nt)—and an accumulation of low molecular weight RNA fragments between 25 and 900 nt. Note that the peak maxima for the 1.6 ng ml −1 RNase A standard (light blue arrowheads) are consistently lower than the peak maxima for the phloem sample (green arrowheads) and the water control (red curve), whereas the light blue curve runs on top of the red and green (less pronounced) curves in the low molecular weight range. RNA concentration is depicted in arbitrary units and plotted versus the molecular weight in nucleotides determined by an internal RNA size marker.
Figure Legend Snippet: Determination of RNase activity in stylectomy exudate of barley plants. RNase activity was tested with barley leaf total RNA. Samples were separated and visualized using an Agilent Bioanalyzer 2100. Phloem sap (green), leaf extract (blue), water (red), or 1.6 ng ml −1 (light blue), 8 ng ml −1 (pink), or 40 ng ml −1 (orange) RNase A standards were added to total RNA. RNase activity caused a decrease in the amount of high molecular weight rRNA—visible as four peaks between 1000 and 3600 nucleotides (nt)—and an accumulation of low molecular weight RNA fragments between 25 and 900 nt. Note that the peak maxima for the 1.6 ng ml −1 RNase A standard (light blue arrowheads) are consistently lower than the peak maxima for the phloem sample (green arrowheads) and the water control (red curve), whereas the light blue curve runs on top of the red and green (less pronounced) curves in the low molecular weight range. RNA concentration is depicted in arbitrary units and plotted versus the molecular weight in nucleotides determined by an internal RNA size marker.

Techniques Used: Activity Assay, Molecular Weight, Concentration Assay, Marker

10) Product Images from "Genopal(TM): A Novel Hollow Fibre Array for Focused Microarray Analysis"

Article Title: Genopal(TM): A Novel Hollow Fibre Array for Focused Microarray Analysis

Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

doi: 10.1093/dnares/dsq025

Structure of Genopal™ and its mass production application via slicing of the Genopal™ block. (A) Schematic representation of the Genopal™ microarray, which is composed of plastic hollow fibres. Oligonucleotide DNA capture probes were attached to a hydrophilic gel within the three-dimensional space of each hollow fibre. (B) The chemical structure of the comb polymers containing polymer-forming functional groups on their side chains. These polymers were inserted into the hollow fibres. (C) Comb polymers with poly HEMA added to their side chains firmly adhered to the inner walls of the hollow fibres. (D) Schematic representation of a Genopal™ block: the hollow fibres were bundled in an orderly arrangement, hardened with resin to form a Genopal™ block and sliced into thin microarrays.
Figure Legend Snippet: Structure of Genopal™ and its mass production application via slicing of the Genopal™ block. (A) Schematic representation of the Genopal™ microarray, which is composed of plastic hollow fibres. Oligonucleotide DNA capture probes were attached to a hydrophilic gel within the three-dimensional space of each hollow fibre. (B) The chemical structure of the comb polymers containing polymer-forming functional groups on their side chains. These polymers were inserted into the hollow fibres. (C) Comb polymers with poly HEMA added to their side chains firmly adhered to the inner walls of the hollow fibres. (D) Schematic representation of a Genopal™ block: the hollow fibres were bundled in an orderly arrangement, hardened with resin to form a Genopal™ block and sliced into thin microarrays.

Techniques Used: Blocking Assay, Microarray, Functional Assay

The aGp array provides sufficient sensitivity for diagnostic application. (A) A scatter plot of the log of signal intensity of the HV pool versus patient TA8 is plotted along the horizontal and vertical axes, respectively. DEFA3, IL-4 and IL-10 genes are indicated by orange arrows. The attached colour bar indicates a relative intensity scale. (B) The correlation coefficients of the Genopal™ autoimmunity array and Agilent's microarray against qPCR are shown. The correlation coefficient of DEFA3 for both Genopal™ and Agilent's arrays was high. On the other hand, because the signal intensities of IL-4 and IL-10 were within two orders of magnitude, as shown in the columns on the right, the correlation coefficient of IL-4 or IL-10 is lower than DEFA3.
Figure Legend Snippet: The aGp array provides sufficient sensitivity for diagnostic application. (A) A scatter plot of the log of signal intensity of the HV pool versus patient TA8 is plotted along the horizontal and vertical axes, respectively. DEFA3, IL-4 and IL-10 genes are indicated by orange arrows. The attached colour bar indicates a relative intensity scale. (B) The correlation coefficients of the Genopal™ autoimmunity array and Agilent's microarray against qPCR are shown. The correlation coefficient of DEFA3 for both Genopal™ and Agilent's arrays was high. On the other hand, because the signal intensities of IL-4 and IL-10 were within two orders of magnitude, as shown in the columns on the right, the correlation coefficient of IL-4 or IL-10 is lower than DEFA3.

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

Comparison of the mRNA expression levels ( y -axis) of 25 selected genes ( x -axis) in PBMCs of patient TA8 using nCounter™ (blue bars), aGp array (Genopal™; red bars) or Agilent's microarray (green bars). Yellow arrows indicate genes that had similar expression levels in the three methods. Turquoise or pink arrows indicate the genes used by nCounter™ to favour aGp or Agilent in terms of their expression levels. Purple arrows indicate the genes that exhibited different expression levels among the three methods.
Figure Legend Snippet: Comparison of the mRNA expression levels ( y -axis) of 25 selected genes ( x -axis) in PBMCs of patient TA8 using nCounter™ (blue bars), aGp array (Genopal™; red bars) or Agilent's microarray (green bars). Yellow arrows indicate genes that had similar expression levels in the three methods. Turquoise or pink arrows indicate the genes used by nCounter™ to favour aGp or Agilent in terms of their expression levels. Purple arrows indicate the genes that exhibited different expression levels among the three methods.

Techniques Used: Expressing, Microarray

Expression profiles of DEFA3 (A), IL-4 (Bi) and IL-10 (Bii) in the 13 TA patients. The vertical axis indicates the log 2 ratio measured by qPCR–GAPDH (blue), aGp array (green) and Agilent's microarray (purple). The horizontal axis indicates the patient number. (A) The comparison of the values of peaks and valleys for DEFA3 revealed that these three methods yielded very similar expression profiles. (Bi and ii) The expression profiles of the IL-4 and IL-10 genes for the 13 TA patients were different between qPCR–GAPDH (blue), aGp array (green) and Agilent's microarray (purple).
Figure Legend Snippet: Expression profiles of DEFA3 (A), IL-4 (Bi) and IL-10 (Bii) in the 13 TA patients. The vertical axis indicates the log 2 ratio measured by qPCR–GAPDH (blue), aGp array (green) and Agilent's microarray (purple). The horizontal axis indicates the patient number. (A) The comparison of the values of peaks and valleys for DEFA3 revealed that these three methods yielded very similar expression profiles. (Bi and ii) The expression profiles of the IL-4 and IL-10 genes for the 13 TA patients were different between qPCR–GAPDH (blue), aGp array (green) and Agilent's microarray (purple).

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

11) Product Images from "CAWS administration increases the expression of interferon ? and complement factors that lead to severe vasculitis in DBA/2 mice"

Article Title: CAWS administration increases the expression of interferon ? and complement factors that lead to severe vasculitis in DBA/2 mice

Journal: BMC Immunology

doi: 10.1186/1471-2172-14-44

Expression profiling of the microarray data for genes involved in interferon-related signal transduction pathways following administration of CAWS to B6 and DBA/2 mice. Mosaic tiles and hierarchical clustering of microarray data are shown for the genes involved in interferon signaling (A) , the role of protein kinase R (Pkr) in interferon induction and antiviral response (B) , acute phase response signaling (C) , and acute myeloid leukemia signaling (D) . B6 and DBA/2 samples were clustered using a hierarchical clustering program (Spearman) to discover gene-to-gene relationships. Irf1, Eif2ak2, Trl, Lbp, Cebpb, Sfpil1, and Csf1r are highlighted by black arrows, Cfb and C3 by turquoise, Ifng by red and Irf9 by green arrows. (E) Intensity gradients indicate the mean value of the expression level (log2 ratio): blue (down-regulation) and crimson (upregulation) are shown compared to the average value at 0 w after CAWS administration (gray). (F) Scatter plots of the highlighted genes in log of signal intensity at 2 w (left panel) or 4 w (right panel) versus 0 w following CAWS administration in DBA/2 mice; data are plotted along the vertical and horizontal axes (arbitrary unit: a.u.), respectively. Highlighted genes are Ifng (red font), C3 (turquoise font), Cfb (turquoise font), and Irf9 (green font).
Figure Legend Snippet: Expression profiling of the microarray data for genes involved in interferon-related signal transduction pathways following administration of CAWS to B6 and DBA/2 mice. Mosaic tiles and hierarchical clustering of microarray data are shown for the genes involved in interferon signaling (A) , the role of protein kinase R (Pkr) in interferon induction and antiviral response (B) , acute phase response signaling (C) , and acute myeloid leukemia signaling (D) . B6 and DBA/2 samples were clustered using a hierarchical clustering program (Spearman) to discover gene-to-gene relationships. Irf1, Eif2ak2, Trl, Lbp, Cebpb, Sfpil1, and Csf1r are highlighted by black arrows, Cfb and C3 by turquoise, Ifng by red and Irf9 by green arrows. (E) Intensity gradients indicate the mean value of the expression level (log2 ratio): blue (down-regulation) and crimson (upregulation) are shown compared to the average value at 0 w after CAWS administration (gray). (F) Scatter plots of the highlighted genes in log of signal intensity at 2 w (left panel) or 4 w (right panel) versus 0 w following CAWS administration in DBA/2 mice; data are plotted along the vertical and horizontal axes (arbitrary unit: a.u.), respectively. Highlighted genes are Ifng (red font), C3 (turquoise font), Cfb (turquoise font), and Irf9 (green font).

Techniques Used: Expressing, Microarray, Transduction, Mouse Assay

Expression profiling of microarray data for complement system genes following administration of CAWS to B6 and DBA/2 mice. (A) Mosaic tile representation of genes involved in the complement system. B6 and DBA/2 samples were clustered using a hierarchical clustering program (Spearman) to identify gene-to-gene relationships. Intensity gradients indicate the mean value of the expression level (log2 ratio): blue (down-regulation) and crimson (upregulation) are shown compared to the average value at week 0 (0 w) after CAWS administration (gray). C3ar1, Fcna, C4, Cfb, Cfh, and C3 genes are highlighted by turquoise arrows. (B) Scatter plots of the log of signal intensity at 2 w (top panel) or 4 w (bottom panel) versus 0 w of CAWS administration in DBA/2 mice. Data are plotted over the entire signal intensity range to demonstrate that these expression arrays provide a high-resolution platform. C3ar1, Fcna, C4, Cfb, Cfh, and C3 genes are highlighted in red font.
Figure Legend Snippet: Expression profiling of microarray data for complement system genes following administration of CAWS to B6 and DBA/2 mice. (A) Mosaic tile representation of genes involved in the complement system. B6 and DBA/2 samples were clustered using a hierarchical clustering program (Spearman) to identify gene-to-gene relationships. Intensity gradients indicate the mean value of the expression level (log2 ratio): blue (down-regulation) and crimson (upregulation) are shown compared to the average value at week 0 (0 w) after CAWS administration (gray). C3ar1, Fcna, C4, Cfb, Cfh, and C3 genes are highlighted by turquoise arrows. (B) Scatter plots of the log of signal intensity at 2 w (top panel) or 4 w (bottom panel) versus 0 w of CAWS administration in DBA/2 mice. Data are plotted over the entire signal intensity range to demonstrate that these expression arrays provide a high-resolution platform. C3ar1, Fcna, C4, Cfb, Cfh, and C3 genes are highlighted in red font.

Techniques Used: Expressing, Microarray, Mouse Assay

Comparison of the mRNA expression levels. The mRNA expression levels of C3 (A) , C4 (B) , Cfb (C) , Cfh (D) , FcnA (E) , and Ifng (F) were as assessed by qRT-PCR and DNA microarray of PBMCs obtained from B6 and DBA/2 mice at 2 w, 4 w, 8 w, and 9 w following CAWS administration. The vertical axis indicates the mRNA level (arbitrary unit: a.u.) relative to that at 0 w, which was fixed at 1.0 a.u.
Figure Legend Snippet: Comparison of the mRNA expression levels. The mRNA expression levels of C3 (A) , C4 (B) , Cfb (C) , Cfh (D) , FcnA (E) , and Ifng (F) were as assessed by qRT-PCR and DNA microarray of PBMCs obtained from B6 and DBA/2 mice at 2 w, 4 w, 8 w, and 9 w following CAWS administration. The vertical axis indicates the mRNA level (arbitrary unit: a.u.) relative to that at 0 w, which was fixed at 1.0 a.u.

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

Expression profiling of the microarray data for transcription factor genes following administration of CAWS to B6 and DBA/2 mice. (A) Mosaic tiles and hierarchical clustering of microarray data are shown. B6 and DBA/2 samples were clustered using a hierarchical clustering program (Spearman) to identify gene-to-gene relationships. Genes upregulated predominantly in DBA/2 mice following administration of CAWS are highlighted by colored and black arrows. (B) Intensity gradients indicate the mean value of the expression level (log2 ratio): blue (down-regulation) and crimson (upregulation) are shown compared to the average value at 0 w after CAWS administration (gray). (C) Scatter plots of highlighted genes in the log of signal intensity at 2 w (left panel) or 4 w (right panel) versus 0 w following CAWS administration in DBA/2 mice; data are plotted along the vertical and horizontal axes (arbitrary unit: a.u.), respectively.
Figure Legend Snippet: Expression profiling of the microarray data for transcription factor genes following administration of CAWS to B6 and DBA/2 mice. (A) Mosaic tiles and hierarchical clustering of microarray data are shown. B6 and DBA/2 samples were clustered using a hierarchical clustering program (Spearman) to identify gene-to-gene relationships. Genes upregulated predominantly in DBA/2 mice following administration of CAWS are highlighted by colored and black arrows. (B) Intensity gradients indicate the mean value of the expression level (log2 ratio): blue (down-regulation) and crimson (upregulation) are shown compared to the average value at 0 w after CAWS administration (gray). (C) Scatter plots of highlighted genes in the log of signal intensity at 2 w (left panel) or 4 w (right panel) versus 0 w following CAWS administration in DBA/2 mice; data are plotted along the vertical and horizontal axes (arbitrary unit: a.u.), respectively.

Techniques Used: Expressing, Microarray, Mouse Assay

12) Product Images from "High CXCR3 expression in synovial mast cells associated with CXCL9 and CXCL10 expression in inflammatory synovial tissues of patients with rheumatoid arthritis"

Article Title: High CXCR3 expression in synovial mast cells associated with CXCL9 and CXCL10 expression in inflammatory synovial tissues of patients with rheumatoid arthritis

Journal: Arthritis Research & Therapy

doi:

Analysis of IL-6 mRNA levels within synovial tissue from rheumatoid arthritis (RA) as compared with that from osteoarthritis (OA) patients. Upper panels: quality control of total RNA preparations. Aliquots (300 ng) of total RNA extracted from synovial tissue from RA and OA patients were plotted on a RNA 6000 Nano-LabChip. Quality of RNA was scanned using a 2100 bioanalyzer. RNA gel electropherograms show the presence of 28S and 18S ribosomal units, indicating intact RNA of the investigated samples. Lower panels: differential IL-6 mRNA levels were determined by semiquantitative reverse transcription polymerase chain reaction (PCR). The figure shows a representative analysis of eight cDNA samples derived from patients with RA and of eight cDNA samples from patients with OA. cDNA samples were adjusted to equal glyceraldehyde-3-phosphate dehydrogenase (G3PDH) levels, performed by competitive PCR using an internal standard (see Materials and methods). Numbered lanes correspond to individual patients within Table 1 .
Figure Legend Snippet: Analysis of IL-6 mRNA levels within synovial tissue from rheumatoid arthritis (RA) as compared with that from osteoarthritis (OA) patients. Upper panels: quality control of total RNA preparations. Aliquots (300 ng) of total RNA extracted from synovial tissue from RA and OA patients were plotted on a RNA 6000 Nano-LabChip. Quality of RNA was scanned using a 2100 bioanalyzer. RNA gel electropherograms show the presence of 28S and 18S ribosomal units, indicating intact RNA of the investigated samples. Lower panels: differential IL-6 mRNA levels were determined by semiquantitative reverse transcription polymerase chain reaction (PCR). The figure shows a representative analysis of eight cDNA samples derived from patients with RA and of eight cDNA samples from patients with OA. cDNA samples were adjusted to equal glyceraldehyde-3-phosphate dehydrogenase (G3PDH) levels, performed by competitive PCR using an internal standard (see Materials and methods). Numbered lanes correspond to individual patients within Table 1 .

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Derivative Assay

13) Product Images from "Changes in Gene Expression Profiles in Response to Selenium Supplementation among Individuals with Arsenic-induced Pre-malignant Skin Lesions"

Article Title: Changes in Gene Expression Profiles in Response to Selenium Supplementation among Individuals with Arsenic-induced Pre-malignant Skin Lesions

Journal: Toxicology letters

doi: 10.1016/j.toxlet.2007.01.006

(A) Agilent 2100 BioAnalyzer electropherogram of 10 RNA samples overlaid on ladder marker peaks (shown in red). After the initial spike, the ladder peaks correspond to 200 bp, 500 bp, 1000 bp, 2000 bp and 4000 bp respectively. The two distinct sharp peaks
Figure Legend Snippet: (A) Agilent 2100 BioAnalyzer electropherogram of 10 RNA samples overlaid on ladder marker peaks (shown in red). After the initial spike, the ladder peaks correspond to 200 bp, 500 bp, 1000 bp, 2000 bp and 4000 bp respectively. The two distinct sharp peaks

Techniques Used: Marker

14) Product Images from "IFI27 Is a Useful Genetic Marker for Diagnosis of Immunoglobulin A Nephropathy and Membranous Nephropathy Using Peripheral Blood"

Article Title: IFI27 Is a Useful Genetic Marker for Diagnosis of Immunoglobulin A Nephropathy and Membranous Nephropathy Using Peripheral Blood

Journal: PLoS ONE

doi: 10.1371/journal.pone.0153252

Comparison of DNA microarray and qRT-PCR data. (A, B) Relative IFI27 mRNA levels for individual IgAN and MN patients determined by DNA microarray (A) or qRT-PCR (B) are shown by box graphs. Vertical axis indicates the mRNA level (arbitrary units: a.u.) relative to the value in HVs, which was fixed at 1.0 a.u.
Figure Legend Snippet: Comparison of DNA microarray and qRT-PCR data. (A, B) Relative IFI27 mRNA levels for individual IgAN and MN patients determined by DNA microarray (A) or qRT-PCR (B) are shown by box graphs. Vertical axis indicates the mRNA level (arbitrary units: a.u.) relative to the value in HVs, which was fixed at 1.0 a.u.

Techniques Used: Microarray, Quantitative RT-PCR

Microarray expression profiling. Scatter plot for genes highlighted in red front in Fig 1 . DNA microarray data, expressed as log of signal intensity of IgAN/MN vs HVs, are plotted along the vertical and horizontal axes, respectively. Horizontal or vertical axis indicates the raw signal intensity of IgAN/MN or HVs (arbitrary units: a.u.), respectively. CLSTN1 , COTL , KRTAP8-1 , and IFI27 , which were subjected to qRT-PCR analysis, are highlighted in red or green font.
Figure Legend Snippet: Microarray expression profiling. Scatter plot for genes highlighted in red front in Fig 1 . DNA microarray data, expressed as log of signal intensity of IgAN/MN vs HVs, are plotted along the vertical and horizontal axes, respectively. Horizontal or vertical axis indicates the raw signal intensity of IgAN/MN or HVs (arbitrary units: a.u.), respectively. CLSTN1 , COTL , KRTAP8-1 , and IFI27 , which were subjected to qRT-PCR analysis, are highlighted in red or green font.

Techniques Used: Microarray, Expressing, Quantitative RT-PCR

15) Product Images from "Adaptation of aphid stylectomy for analyses of proteins and mRNAs in barley phloem sap"

Article Title: Adaptation of aphid stylectomy for analyses of proteins and mRNAs in barley phloem sap

Journal: Journal of Experimental Botany

doi: 10.1093/jxb/ern181

Determination of RNase activity in stylectomy exudate of barley plants. RNase activity was tested with barley leaf total RNA. Samples were separated and visualized using an Agilent Bioanalyzer 2100. Phloem sap (green), leaf extract (blue), water (red), or 1.6 ng ml −1 (light blue), 8 ng ml −1 (pink), or 40 ng ml −1 (orange) RNase A standards were added to total RNA. RNase activity caused a decrease in the amount of high molecular weight rRNA—visible as four peaks between 1000 and 3600 nucleotides (nt)—and an accumulation of low molecular weight RNA fragments between 25 and 900 nt. Note that the peak maxima for the 1.6 ng ml −1 RNase A standard (light blue arrowheads) are consistently lower than the peak maxima for the phloem sample (green arrowheads) and the water control (red curve), whereas the light blue curve runs on top of the red and green (less pronounced) curves in the low molecular weight range. RNA concentration is depicted in arbitrary units and plotted versus the molecular weight in nucleotides determined by an internal RNA size marker.
Figure Legend Snippet: Determination of RNase activity in stylectomy exudate of barley plants. RNase activity was tested with barley leaf total RNA. Samples were separated and visualized using an Agilent Bioanalyzer 2100. Phloem sap (green), leaf extract (blue), water (red), or 1.6 ng ml −1 (light blue), 8 ng ml −1 (pink), or 40 ng ml −1 (orange) RNase A standards were added to total RNA. RNase activity caused a decrease in the amount of high molecular weight rRNA—visible as four peaks between 1000 and 3600 nucleotides (nt)—and an accumulation of low molecular weight RNA fragments between 25 and 900 nt. Note that the peak maxima for the 1.6 ng ml −1 RNase A standard (light blue arrowheads) are consistently lower than the peak maxima for the phloem sample (green arrowheads) and the water control (red curve), whereas the light blue curve runs on top of the red and green (less pronounced) curves in the low molecular weight range. RNA concentration is depicted in arbitrary units and plotted versus the molecular weight in nucleotides determined by an internal RNA size marker.

Techniques Used: Activity Assay, Molecular Weight, Concentration Assay, Marker

16) Product Images from "Autism-Associated Gene Expression in Peripheral Leucocytes Commonly Observed between Subjects with Autism and Healthy Women Having Autistic Children"

Article Title: Autism-Associated Gene Expression in Peripheral Leucocytes Commonly Observed between Subjects with Autism and Healthy Women Having Autistic Children

Journal: PLoS ONE

doi: 10.1371/journal.pone.0024723

Similarity in gene expression profiling between the ASD and asdMO group. Venn diagram of differentially expressed genes for the ASD group compared with the Control group and the asdMO group compared with the ctrlMO group ( > 2-fold change) (A). RNA was prepared from each group and subjected to microarray analysis. Differentially expressed 19 and 57 genes by > 2-fold in ASD group and asdMO group, respectively. Three genes were overlapped. The mean of expression values of the 19 genes (B) and the 57 genes (C) changed in a parallel direction between the ASD and asdMO group. The normalized intensity value of genes, which was up-regulated or down-regulated by 2-fold, is shown in red or green, respectively, compared with control or ctrlMO. Venn diagram of differentially expressed 496 and 1126 genes by > 1.5-fold in ASD group and asdMO group (D). 399 genes were overlapped. The mean of expression values of the overlapped 399 genes was similar direction between the ASD and asdMO group (E). The normalized intensity value of genes, which was up-regulated or down-regulated by 1.5-fold, is shown in red or green, compared with control.
Figure Legend Snippet: Similarity in gene expression profiling between the ASD and asdMO group. Venn diagram of differentially expressed genes for the ASD group compared with the Control group and the asdMO group compared with the ctrlMO group ( > 2-fold change) (A). RNA was prepared from each group and subjected to microarray analysis. Differentially expressed 19 and 57 genes by > 2-fold in ASD group and asdMO group, respectively. Three genes were overlapped. The mean of expression values of the 19 genes (B) and the 57 genes (C) changed in a parallel direction between the ASD and asdMO group. The normalized intensity value of genes, which was up-regulated or down-regulated by 2-fold, is shown in red or green, respectively, compared with control or ctrlMO. Venn diagram of differentially expressed 496 and 1126 genes by > 1.5-fold in ASD group and asdMO group (D). 399 genes were overlapped. The mean of expression values of the overlapped 399 genes was similar direction between the ASD and asdMO group (E). The normalized intensity value of genes, which was up-regulated or down-regulated by 1.5-fold, is shown in red or green, compared with control.

Techniques Used: Expressing, Microarray

17) Product Images from "High CXCR3 expression in synovial mast cells associated with CXCL9 and CXCL10 expression in inflammatory synovial tissues of patients with rheumatoid arthritis"

Article Title: High CXCR3 expression in synovial mast cells associated with CXCL9 and CXCL10 expression in inflammatory synovial tissues of patients with rheumatoid arthritis

Journal: Arthritis Research & Therapy

doi:

Analysis of IL-6 mRNA levels within synovial tissue from rheumatoid arthritis (RA) as compared with that from osteoarthritis (OA) patients. Upper panels: quality control of total RNA preparations. Aliquots (300 ng) of total RNA extracted from synovial tissue from RA and OA patients were plotted on a RNA 6000 Nano-LabChip. Quality of RNA was scanned using a 2100 bioanalyzer. RNA gel electropherograms show the presence of 28S and 18S ribosomal units, indicating intact RNA of the investigated samples. Lower panels: differential IL-6 mRNA levels were determined by semiquantitative reverse transcription polymerase chain reaction (PCR). The figure shows a representative analysis of eight cDNA samples derived from patients with RA and of eight cDNA samples from patients with OA. cDNA samples were adjusted to equal glyceraldehyde-3-phosphate dehydrogenase (G3PDH) levels, performed by competitive PCR using an internal standard (see Materials and methods). Numbered lanes correspond to individual patients within Table 1 .
Figure Legend Snippet: Analysis of IL-6 mRNA levels within synovial tissue from rheumatoid arthritis (RA) as compared with that from osteoarthritis (OA) patients. Upper panels: quality control of total RNA preparations. Aliquots (300 ng) of total RNA extracted from synovial tissue from RA and OA patients were plotted on a RNA 6000 Nano-LabChip. Quality of RNA was scanned using a 2100 bioanalyzer. RNA gel electropherograms show the presence of 28S and 18S ribosomal units, indicating intact RNA of the investigated samples. Lower panels: differential IL-6 mRNA levels were determined by semiquantitative reverse transcription polymerase chain reaction (PCR). The figure shows a representative analysis of eight cDNA samples derived from patients with RA and of eight cDNA samples from patients with OA. cDNA samples were adjusted to equal glyceraldehyde-3-phosphate dehydrogenase (G3PDH) levels, performed by competitive PCR using an internal standard (see Materials and methods). Numbered lanes correspond to individual patients within Table 1 .

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Derivative Assay

Related Articles

RNA Sequencing Assay:

Article Title: Tumour-vasculature development via endothelial-to-mesenchymal transition after radiotherapy controls CD44v6+ cancer cell and macrophage polarization
Article Snippet: .. RNA-seq analysis Total RNA was isolated from HUVECs, and RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). .. RNA-seq libraries were constructed using the SENSE mRNA-Seq Library Prep Kit (Lexogen), according to the manufacturer’s instructions, and were sequenced as 100 bp paired-end runs on the HiSeq 2000 platform (Illumina).

Isolation:

Article Title: Tumour-vasculature development via endothelial-to-mesenchymal transition after radiotherapy controls CD44v6+ cancer cell and macrophage polarization
Article Snippet: .. RNA-seq analysis Total RNA was isolated from HUVECs, and RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). .. RNA-seq libraries were constructed using the SENSE mRNA-Seq Library Prep Kit (Lexogen), according to the manufacturer’s instructions, and were sequenced as 100 bp paired-end runs on the HiSeq 2000 platform (Illumina).

Real-time Polymerase Chain Reaction:

Article Title: Silencing of Long Noncoding RNA AK139328 Attenuates Ischemia/Reperfusion Injury in Mouse Livers
Article Snippet: .. Overall, real time PCR assays validated the accuracy of LncRNA profile determined by microarray analysis. .. Silencing of AK139328 attenuated ischemia/reperfusion injury in the liver Because AK139328 is one of the most significantly upregulated LncRNAs with the highest expression level among the validated LncRNAs in the liver, its role in hepatic ischemia/reperfusion injury was further evaluated.

Microarray:

Article Title: PMA and Ionomycin Induce Glioblastoma Cell Death: Activation-Induced Cell-Death-Like Phenomena Occur in Glioma Cells
Article Snippet: .. The mRNA expression of NFAT1and Fas obtained from microarray analysis in 111 clinical samples was analyzed with cluster analysis and Pearson correlation analysis. .. The expression of NFAT1 was significantly correlated with that of Fas (R = 0.627, P < 0.01) in gliomas ( ).

Article Title: Silencing of Long Noncoding RNA AK139328 Attenuates Ischemia/Reperfusion Injury in Mouse Livers
Article Snippet: .. Overall, real time PCR assays validated the accuracy of LncRNA profile determined by microarray analysis. .. Silencing of AK139328 attenuated ischemia/reperfusion injury in the liver Because AK139328 is one of the most significantly upregulated LncRNAs with the highest expression level among the validated LncRNAs in the liver, its role in hepatic ischemia/reperfusion injury was further evaluated.

other:

Article Title: Deep sequencing and miRNA profiles in alcohol-induced neuroinflammation and the TLR4 response in mice cerebral cortex
Article Snippet: After, we measured again the sRNA profiles with small-RNA kit (Agilent Technologies, Santa Clara, CA, USA) following manufacturer’s instructions and the total RNA integrity with the RNA Nano6000 kit (Agilent Technologies, Santa Clara, CA, USA).

Formalin-fixed Paraffin-Embedded:

Article Title: Biobanking: Objectives, Requirements, and Future Challenges—Experiences from the Munich Vascular Biobank
Article Snippet: .. Analysis of RNA Quality from FFPE Biospecimens by RIN and RNA Fragmentation RNA integrity number (RIN) was determined by Agilent 2100 Bioanalyzer and the RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany) in accordance with the manufacturer’s instructions. ..

Expressing:

Article Title: PMA and Ionomycin Induce Glioblastoma Cell Death: Activation-Induced Cell-Death-Like Phenomena Occur in Glioma Cells
Article Snippet: .. The mRNA expression of NFAT1and Fas obtained from microarray analysis in 111 clinical samples was analyzed with cluster analysis and Pearson correlation analysis. .. The expression of NFAT1 was significantly correlated with that of Fas (R = 0.627, P < 0.01) in gliomas ( ).

Sequencing:

Article Title: Decreasing miRNA sequencing bias using a single adapter and circularization approach
Article Snippet: .. Using RealSeq®-AC and TruSeq®, we prepared sequencing libraries from a reference sample of total RNA (Agilent) obtained from nine different human tissues and cell lines. .. We sequenced both libraries to a coverage of ten million reads and counted the number of miRNAs identified (with ten or more reads of each) by each kit at different sequencing coverages by random subsampling (Additional file : Figure S6).

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