rna arna  (Qiagen)


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    Structured Review

    Qiagen rna arna
    Minimal input <t>RNA</t> mass for optimal T7SL IVT. a Graph showing the correlation between the input total RNA mass (X axis) and the <t>aRNA</t> yield (Y axis). b aRNA length distribution obtained with different input RNA mass. Note that below 6.25 ng input, the aRNA lose the typical smooth length distribution. For all samples, the same RNA mass were applied on a BioAnalyzer chip. c RNA-Seq scatterplot with different RNA inputs (from 100 to 3 ng) for T7SL IVT. Pearson correlation is depicted, based on log normalized read counts. Note that even when 3 ng of mass input is used for RNA amplification, the transcriptome quantification is very similar across all expression levels. “Sort” sample correspond to 10 5 epimastigotes sorted directly to RNA extraction buffer, which roughly corresponds to 68 ng of total RNA (Additional file 4 , Table S2)
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    Images

    1) Product Images from "Trypanosoma cruzi specific mRNA amplification by in vitro transcription improves parasite transcriptomics in host-parasite RNA mixtures"

    Article Title: Trypanosoma cruzi specific mRNA amplification by in vitro transcription improves parasite transcriptomics in host-parasite RNA mixtures

    Journal: BMC Genomics

    doi: 10.1186/s12864-017-4163-y

    Minimal input RNA mass for optimal T7SL IVT. a Graph showing the correlation between the input total RNA mass (X axis) and the aRNA yield (Y axis). b aRNA length distribution obtained with different input RNA mass. Note that below 6.25 ng input, the aRNA lose the typical smooth length distribution. For all samples, the same RNA mass were applied on a BioAnalyzer chip. c RNA-Seq scatterplot with different RNA inputs (from 100 to 3 ng) for T7SL IVT. Pearson correlation is depicted, based on log normalized read counts. Note that even when 3 ng of mass input is used for RNA amplification, the transcriptome quantification is very similar across all expression levels. “Sort” sample correspond to 10 5 epimastigotes sorted directly to RNA extraction buffer, which roughly corresponds to 68 ng of total RNA (Additional file 4 , Table S2)
    Figure Legend Snippet: Minimal input RNA mass for optimal T7SL IVT. a Graph showing the correlation between the input total RNA mass (X axis) and the aRNA yield (Y axis). b aRNA length distribution obtained with different input RNA mass. Note that below 6.25 ng input, the aRNA lose the typical smooth length distribution. For all samples, the same RNA mass were applied on a BioAnalyzer chip. c RNA-Seq scatterplot with different RNA inputs (from 100 to 3 ng) for T7SL IVT. Pearson correlation is depicted, based on log normalized read counts. Note that even when 3 ng of mass input is used for RNA amplification, the transcriptome quantification is very similar across all expression levels. “Sort” sample correspond to 10 5 epimastigotes sorted directly to RNA extraction buffer, which roughly corresponds to 68 ng of total RNA (Additional file 4 , Table S2)

    Techniques Used: Chromatin Immunoprecipitation, RNA Sequencing Assay, Amplification, Expressing, RNA Extraction

    T7SL IVT method. a Comparison between T7oligo(dT) (left) and T7SL IVT (right) methods. In the Eberwine method, the reverse transcription reaction is performed using a T7oligo(dT) primer, resulting in a first-strand cDNA containing the T7 promoter. The T7 RNA polymerase is added for in vitro transcription of the purified cDNA and antisense aRNA is obtained. For the second method (T7SL IVT), the reverse transcription reaction is performed using random primers and the second-strand cDNA is obtained by a DNA polymerase reaction with the T7SL primer, which also contains the T7 promoter. After cDNA purification, in vitro transcription with the T7 RNA polymerase is performed, producing sense aRNA. b Distribution of RNA lengths from IVT samples and poly(A) + RNA (control), quantified by the BioAnalyzer 2100 equipment (Agilent). c Median length of poly(A) + RNA and aRNAs from the IVT samples. d aRNA yield obtained from the two IVT methods
    Figure Legend Snippet: T7SL IVT method. a Comparison between T7oligo(dT) (left) and T7SL IVT (right) methods. In the Eberwine method, the reverse transcription reaction is performed using a T7oligo(dT) primer, resulting in a first-strand cDNA containing the T7 promoter. The T7 RNA polymerase is added for in vitro transcription of the purified cDNA and antisense aRNA is obtained. For the second method (T7SL IVT), the reverse transcription reaction is performed using random primers and the second-strand cDNA is obtained by a DNA polymerase reaction with the T7SL primer, which also contains the T7 promoter. After cDNA purification, in vitro transcription with the T7 RNA polymerase is performed, producing sense aRNA. b Distribution of RNA lengths from IVT samples and poly(A) + RNA (control), quantified by the BioAnalyzer 2100 equipment (Agilent). c Median length of poly(A) + RNA and aRNAs from the IVT samples. d aRNA yield obtained from the two IVT methods

    Techniques Used: In Vitro, Purification

    aRNA-Seq results. a RNA-Seq coverage along annotated genes. To plot all genes in the same graph, all coding sequences were split in 100 bins (percentiles) and the number of reads aligned to each percentile were summed and plotted as a ratio against the bin with higher number of aligned reads. Dotted lines are standard deviation. b IGV genome browser visualization of RNA-Seq reads alignment along a 3 kb gene for all three methods used (specified in left). Coverage were plotted in log scale. c correlation between the technical replicates (same RNA input for different amplification reactions) of T7SL IVT and T7oligo(dT) IVT methods. d correlation between biological replicates (RNA from separate epimastigote populations) of T7SL IVT and T7oligo(dT) IVT. For all scatter plots, scales are log 2 of normalized read counts and values inside the graphs represent Pearson correlation
    Figure Legend Snippet: aRNA-Seq results. a RNA-Seq coverage along annotated genes. To plot all genes in the same graph, all coding sequences were split in 100 bins (percentiles) and the number of reads aligned to each percentile were summed and plotted as a ratio against the bin with higher number of aligned reads. Dotted lines are standard deviation. b IGV genome browser visualization of RNA-Seq reads alignment along a 3 kb gene for all three methods used (specified in left). Coverage were plotted in log scale. c correlation between the technical replicates (same RNA input for different amplification reactions) of T7SL IVT and T7oligo(dT) IVT methods. d correlation between biological replicates (RNA from separate epimastigote populations) of T7SL IVT and T7oligo(dT) IVT. For all scatter plots, scales are log 2 of normalized read counts and values inside the graphs represent Pearson correlation

    Techniques Used: RNA Sequencing Assay, Standard Deviation, Amplification

    Performance of T7SL IVT on RNA mixtures. a Length distribution profiles for aRNA produced from pure samples ( T. cruzi epimastigote and HeLa), mixture of T. cruzi (epimastigote) and HeLa and blank samples (no RNA for amplification reaction). Percentage are relative mass of Epi:HeLa on RNA mixture used for T7SL IVT. b After T7SL IVT and RNA-Seq of mixture samples, reads were aligned to T. cruzi and human genomes. The percentage of aligned reads with best match on parasite or human genome were retrieved and plotted. The input mass (in ng) used in each mixture is specified at the bottom. c Scatterplot comparing T7SL Pfx IVT and mixtures of HeLA-Epi RNAs, or PolyA+ RNA against HeLA-Epi RNAs. d Scatter plots of epimastigote to trypomastigote fold changes when comparing PolyA(+) transcriptome quantification to T7SL using T.cruzi /HeLa RNA mixtures
    Figure Legend Snippet: Performance of T7SL IVT on RNA mixtures. a Length distribution profiles for aRNA produced from pure samples ( T. cruzi epimastigote and HeLa), mixture of T. cruzi (epimastigote) and HeLa and blank samples (no RNA for amplification reaction). Percentage are relative mass of Epi:HeLa on RNA mixture used for T7SL IVT. b After T7SL IVT and RNA-Seq of mixture samples, reads were aligned to T. cruzi and human genomes. The percentage of aligned reads with best match on parasite or human genome were retrieved and plotted. The input mass (in ng) used in each mixture is specified at the bottom. c Scatterplot comparing T7SL Pfx IVT and mixtures of HeLA-Epi RNAs, or PolyA+ RNA against HeLA-Epi RNAs. d Scatter plots of epimastigote to trypomastigote fold changes when comparing PolyA(+) transcriptome quantification to T7SL using T.cruzi /HeLa RNA mixtures

    Techniques Used: Produced, Amplification, RNA Sequencing Assay

    2) Product Images from "Potent monoclonal antibodies against Clostridium difficile toxin A elicited by DNA immunization"

    Article Title: Potent monoclonal antibodies against Clostridium difficile toxin A elicited by DNA immunization

    Journal: Human Vaccines & Immunotherapeutics

    doi: 10.4161/hv.25656

    Figure 2. Immunological testing of TcdA-specific hybridoma clones generated from TcdA-C DNA vaccine immunized mice. ( A ) ELISA of culture supernatants (1:100 dilution) from selected hybridoma clones against TcdA-C. ( B ) Western blot analysis of
    Figure Legend Snippet: Figure 2. Immunological testing of TcdA-specific hybridoma clones generated from TcdA-C DNA vaccine immunized mice. ( A ) ELISA of culture supernatants (1:100 dilution) from selected hybridoma clones against TcdA-C. ( B ) Western blot analysis of

    Techniques Used: Clone Assay, Generated, Mouse Assay, Enzyme-linked Immunosorbent Assay, Western Blot

    Figure 8. Comparison of TcdA toxin binding activities for purified mAb 5D8 ( A ) or 2C7 ( B ) produced either from hybridoma culture or from supernatant of 293T cells co-transfected with paired Ig gamma and kappa chain clones. ELISA curves labeled
    Figure Legend Snippet: Figure 8. Comparison of TcdA toxin binding activities for purified mAb 5D8 ( A ) or 2C7 ( B ) produced either from hybridoma culture or from supernatant of 293T cells co-transfected with paired Ig gamma and kappa chain clones. ELISA curves labeled

    Techniques Used: Binding Assay, Purification, Produced, Transfection, Clone Assay, Enzyme-linked Immunosorbent Assay, Labeling

    3) Product Images from "Organic Solute Transporter α-β Protects Ileal Enterocytes From Bile Acid–Induced Injury"

    Article Title: Organic Solute Transporter α-β Protects Ileal Enterocytes From Bile Acid–Induced Injury

    Journal: Cellular and Molecular Gastroenterology and Hepatology

    doi: 10.1016/j.jcmgh.2018.01.006

    Ileal expression of Nrf2 ARE target genes. ( A ) Microarray analysis of ileum in adult male WT and Ostα -/- mice. Differentially expressed genes whose expression was induced (2-fold change; P
    Figure Legend Snippet: Ileal expression of Nrf2 ARE target genes. ( A ) Microarray analysis of ileum in adult male WT and Ostα -/- mice. Differentially expressed genes whose expression was induced (2-fold change; P

    Techniques Used: Expressing, Microarray, Mouse Assay

    4) Product Images from "MBD4 Facilitates Immunoglobulin Class Switch Recombination"

    Article Title: MBD4 Facilitates Immunoglobulin Class Switch Recombination

    Journal: Molecular and Cellular Biology

    doi: 10.1128/MCB.00316-16

    CSR is impaired in Mbd4 KO cells. Control (Ctrl) CH12 cells and Mbd4 -deficient cells were treated with CIT for 24 h (A, C, and D) or as indicated (B). (A) Ctrl (+/+), Mbd4 HET (1A-12 N/+ , 1A-12 Δ/+ , M19 N/+ ), and KO (1A-12 Δ/Δ ) cells
    Figure Legend Snippet: CSR is impaired in Mbd4 KO cells. Control (Ctrl) CH12 cells and Mbd4 -deficient cells were treated with CIT for 24 h (A, C, and D) or as indicated (B). (A) Ctrl (+/+), Mbd4 HET (1A-12 N/+ , 1A-12 Δ/+ , M19 N/+ ), and KO (1A-12 Δ/Δ ) cells

    Techniques Used:

    Expression of truncated MBD4 has no deleterious effects on CSR. (A) Diagram of the Mbd4
    Figure Legend Snippet: Expression of truncated MBD4 has no deleterious effects on CSR. (A) Diagram of the Mbd4

    Techniques Used: Expressing

    Similar DSB distributions in Mbd4 KO and Msh2 -deficient B cells. CH12 control (Ctrl) and Mbd4 KO cells were treated with CIT for 12 h and were then analyzed by LM-PCR. Control ( n = 52) and Mbd4 KO ( n = 39) LM-PCR products were subjected to DNA sequence
    Figure Legend Snippet: Similar DSB distributions in Mbd4 KO and Msh2 -deficient B cells. CH12 control (Ctrl) and Mbd4 KO cells were treated with CIT for 12 h and were then analyzed by LM-PCR. Control ( n = 52) and Mbd4 KO ( n = 39) LM-PCR products were subjected to DNA sequence

    Techniques Used: Polymerase Chain Reaction, Sequencing

    Complementation of impaired CSR in Mbd4 -deficient cell lines. (A) The gRNA with protospacer adjacent motif (PAM) used to target Mbd4 by CRISPR-Cas9 is aligned to the genomic map of the Mbd4 gene exons (rectangles) and introns (lines). (B) The gRNA and
    Figure Legend Snippet: Complementation of impaired CSR in Mbd4 -deficient cell lines. (A) The gRNA with protospacer adjacent motif (PAM) used to target Mbd4 by CRISPR-Cas9 is aligned to the genomic map of the Mbd4 gene exons (rectangles) and introns (lines). (B) The gRNA and

    Techniques Used: CRISPR

    Expression of MBD4 full-length and short isoforms is lost in Mbd4 -deficient CH12 cells. (A) NCBI browser screenshot of the genomic Mbd4 locus and a segment of the Ift122 gene. Mbd4 transcripts are indicated with exons (dark green boxes), untranslated
    Figure Legend Snippet: Expression of MBD4 full-length and short isoforms is lost in Mbd4 -deficient CH12 cells. (A) NCBI browser screenshot of the genomic Mbd4 locus and a segment of the Ift122 gene. Mbd4 transcripts are indicated with exons (dark green boxes), untranslated

    Techniques Used: Expressing

    Increased microhomology in Sμ-Sα junctions from Mbd4 KO cells. Sμ-Sα junctions were amplified from genomic DNA prepared from CH12 control (Ctrl) ( n = 34) and Mbd4 KO ( n = 24) cells stimulated with CIT for 24 h, and the
    Figure Legend Snippet: Increased microhomology in Sμ-Sα junctions from Mbd4 KO cells. Sμ-Sα junctions were amplified from genomic DNA prepared from CH12 control (Ctrl) ( n = 34) and Mbd4 KO ( n = 24) cells stimulated with CIT for 24 h, and the

    Techniques Used: Amplification

    Sμ DSB formation is reduced in Mbd4 -deficient cells. (A) Diagrammatic summary of AID- and BER-induced DSB formation. (a) AID deaminates dC to produce uracil (U) residues. An AID hot spot motif (DGYW/WRCH [D stands for G, A, or T; H stands for
    Figure Legend Snippet: Sμ DSB formation is reduced in Mbd4 -deficient cells. (A) Diagrammatic summary of AID- and BER-induced DSB formation. (a) AID deaminates dC to produce uracil (U) residues. An AID hot spot motif (DGYW/WRCH [D stands for G, A, or T; H stands for

    Techniques Used:

    5) Product Images from "Smooth muscle FGF/ TGFβ cross talk regulates atherosclerosis progression"

    Article Title: Smooth muscle FGF/ TGFβ cross talk regulates atherosclerosis progression

    Journal: EMBO Molecular Medicine

    doi: 10.15252/emmm.201506181

    FRS 2α knockdown increases smooth muscle marker gene expression via the TGF β pathway in primary human aortic smooth muscle cells ( HASMC s) Left: Immunoblot analysis of smooth muscle marker gene expression in control and FRS 2α‐knockdown HASMC s. Blots are representative of four independent experiments. Right: Band intensities of SM α‐actin, SM 22α, and SM ‐calponin were normalized to β‐tubulin and expressed as a fraction of a control value. qRT – PCR analysis of SMC transcription factor gene expression in control and FRS 2α‐knockdown HASMC s. β‐actin was used for sample loading normalization. Histogram of qRT‐PCR results is representative of three independent experiments. Collagen gel contraction assays were used to determine the contractile ability of control or FRS 2α‐knockdown HASMC s. Histogram of collagen gel contraction assays is representative of three independent experiments. Upper panels: Immunoblots of smooth muscle markers, phosphorylated Smad2 (p‐Smad2), and TGF βR1 expression in control and FRS 2α‐knockdown HASMC s treated with SB 431542 (10 μM), TGF βR2, or Smad2 sh RNA lentiviruses. Blots are representative of three independent experiments. Bottom panels: Band intensities of SM ‐calponin and p‐Smad2 were normalized to β‐tubulin, HSP 90, or Smad2 and expressed as a fraction of a control value. Data information: Results are expressed as means ± SD (* P
    Figure Legend Snippet: FRS 2α knockdown increases smooth muscle marker gene expression via the TGF β pathway in primary human aortic smooth muscle cells ( HASMC s) Left: Immunoblot analysis of smooth muscle marker gene expression in control and FRS 2α‐knockdown HASMC s. Blots are representative of four independent experiments. Right: Band intensities of SM α‐actin, SM 22α, and SM ‐calponin were normalized to β‐tubulin and expressed as a fraction of a control value. qRT – PCR analysis of SMC transcription factor gene expression in control and FRS 2α‐knockdown HASMC s. β‐actin was used for sample loading normalization. Histogram of qRT‐PCR results is representative of three independent experiments. Collagen gel contraction assays were used to determine the contractile ability of control or FRS 2α‐knockdown HASMC s. Histogram of collagen gel contraction assays is representative of three independent experiments. Upper panels: Immunoblots of smooth muscle markers, phosphorylated Smad2 (p‐Smad2), and TGF βR1 expression in control and FRS 2α‐knockdown HASMC s treated with SB 431542 (10 μM), TGF βR2, or Smad2 sh RNA lentiviruses. Blots are representative of three independent experiments. Bottom panels: Band intensities of SM ‐calponin and p‐Smad2 were normalized to β‐tubulin, HSP 90, or Smad2 and expressed as a fraction of a control value. Data information: Results are expressed as means ± SD (* P

    Techniques Used: Marker, Expressing, Quantitative RT-PCR, Western Blot

    6) Product Images from "Promoter-proximal pausing mediated by the exon junction complex regulates splicing"

    Article Title: Promoter-proximal pausing mediated by the exon junction complex regulates splicing

    Journal: Nature Communications

    doi: 10.1038/s41467-019-08381-0

    Mago prevents premature release into transcription elongation. a ChIP-qPCR analysis of Pol II and Ser2P occupancies at MAPK locus. The tested regions for enrichment are shown in the scheme. Error bars indicate the standard deviation of three biological replicates. b Track examples of total Pol II and Ser2P ChIP-Seq from S2R+ cells extracts, after either control or Mago knockdown. The tracks are average of two independent biological replicates after input and “spike-in” normalization. Shown here are the profiles on MAPK , a well-described pre-EJC target gene. c , d Metagene profiles of averaged total Pol II occupancies from two independent biological replicates after “spike-in” normalization in control and Mago-depleted cells along with standard error of mean for all the expressed genes, −600 bp upstream of transcription start sites (TSS) and +600 bp downstream of transcription end sites (TES) ( c ); or centered at the TSS in a ±1 Kb window ( d ). Log2 fold changes against input control are shown on Y -axis, while X -axis depicts genomic coordinates. e Metagene profiles of averaged Ser2P occupancies in control and Mago-depleted cells of two independent biological replicates also displaying standard error of mean for all expressed genes. Log2 fold changes against input control are shown on Y -axis, while X -axis depicts scaled genomic coordinates. f Schematic representation of the calculation of the Pol II release ratio (PRR). The promoter is defined as 250 bp upstream and downstream of TSS, while the gene body is 500 bp downstream of TSS to 500 bp upstream of transcription end site (TES). g The empirical cumulative distribution function (ECDF) plot of computed PRR in control and Mago knockdown conditions, after “spike-in” normalization. p -value is derived from two-sample Kolmogorov-Smirnov test. h Box plots showing changes in PRRs upon Mago depletion when compared to control, separated into different PRR quartiles. The quartiles were generated for genes that are Pol II bound in both control and Mago knockdown conditions. i Schematic depiction of the DRB-4sU-Seq approach. j Metagene profile of nascent RNA from non-DRB treated 4sU-Seq data in control and Mago-depleted cells, with standard error of mean for all the expressed genes. Averaged read counts per million of mapped reads of two independent biological replicates from 4sU-Seq are shown on Y -axis while X -axis depicts scaled genomic coordinates. k Metagene profile of nascent RNA from non-DRB treated 4sU-Seq data in control and Mago-depleted cells with standard error of mean for all the expressed genes based on the average of two independent biological replicates, centered at the TSS in a ±1 Kb window. Nascent RNA was fragmented to ≤100 bp during enrichment. Averaged read counts per million of mapped reads of two independent biological replicates from 4sU-Seq are shown on Y -axis while X -axis depicts genomic coordinates
    Figure Legend Snippet: Mago prevents premature release into transcription elongation. a ChIP-qPCR analysis of Pol II and Ser2P occupancies at MAPK locus. The tested regions for enrichment are shown in the scheme. Error bars indicate the standard deviation of three biological replicates. b Track examples of total Pol II and Ser2P ChIP-Seq from S2R+ cells extracts, after either control or Mago knockdown. The tracks are average of two independent biological replicates after input and “spike-in” normalization. Shown here are the profiles on MAPK , a well-described pre-EJC target gene. c , d Metagene profiles of averaged total Pol II occupancies from two independent biological replicates after “spike-in” normalization in control and Mago-depleted cells along with standard error of mean for all the expressed genes, −600 bp upstream of transcription start sites (TSS) and +600 bp downstream of transcription end sites (TES) ( c ); or centered at the TSS in a ±1 Kb window ( d ). Log2 fold changes against input control are shown on Y -axis, while X -axis depicts genomic coordinates. e Metagene profiles of averaged Ser2P occupancies in control and Mago-depleted cells of two independent biological replicates also displaying standard error of mean for all expressed genes. Log2 fold changes against input control are shown on Y -axis, while X -axis depicts scaled genomic coordinates. f Schematic representation of the calculation of the Pol II release ratio (PRR). The promoter is defined as 250 bp upstream and downstream of TSS, while the gene body is 500 bp downstream of TSS to 500 bp upstream of transcription end site (TES). g The empirical cumulative distribution function (ECDF) plot of computed PRR in control and Mago knockdown conditions, after “spike-in” normalization. p -value is derived from two-sample Kolmogorov-Smirnov test. h Box plots showing changes in PRRs upon Mago depletion when compared to control, separated into different PRR quartiles. The quartiles were generated for genes that are Pol II bound in both control and Mago knockdown conditions. i Schematic depiction of the DRB-4sU-Seq approach. j Metagene profile of nascent RNA from non-DRB treated 4sU-Seq data in control and Mago-depleted cells, with standard error of mean for all the expressed genes. Averaged read counts per million of mapped reads of two independent biological replicates from 4sU-Seq are shown on Y -axis while X -axis depicts scaled genomic coordinates. k Metagene profile of nascent RNA from non-DRB treated 4sU-Seq data in control and Mago-depleted cells with standard error of mean for all the expressed genes based on the average of two independent biological replicates, centered at the TSS in a ±1 Kb window. Nascent RNA was fragmented to ≤100 bp during enrichment. Averaged read counts per million of mapped reads of two independent biological replicates from 4sU-Seq are shown on Y -axis while X -axis depicts genomic coordinates

    Techniques Used: Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Standard Deviation, Derivative Assay, Generated

    7) Product Images from "miR-590-5p, miR-219-5p, miR-15b and miR-628-5p are commonly regulated by IL-3, GM-CSF and G-CSF in acute myeloid leukemia"

    Article Title: miR-590-5p, miR-219-5p, miR-15b and miR-628-5p are commonly regulated by IL-3, GM-CSF and G-CSF in acute myeloid leukemia

    Journal: Leukemia Research

    doi: 10.1016/j.leukres.2011.09.027

    Profiling outcomes of IL-3, GM-CSF, and G-CSF regulated miRNA in AML-193 cells
    Figure Legend Snippet: Profiling outcomes of IL-3, GM-CSF, and G-CSF regulated miRNA in AML-193 cells

    Techniques Used:

    AML-193 as a model system for testing IL-3, GM-CSF, and G-CSF induced miRNA profiling via potential JAK2-STAT5 pathway
    Figure Legend Snippet: AML-193 as a model system for testing IL-3, GM-CSF, and G-CSF induced miRNA profiling via potential JAK2-STAT5 pathway

    Techniques Used:

    Specific miRNAs independently regulated by IL-3, GM-CSF, and G-CSF in AML-193 cells
    Figure Legend Snippet: Specific miRNAs independently regulated by IL-3, GM-CSF, and G-CSF in AML-193 cells

    Techniques Used:

    IL-3, GM-CSF, and G-CSF directionally regulate specific miRNAs in AML-193 cells
    Figure Legend Snippet: IL-3, GM-CSF, and G-CSF directionally regulate specific miRNAs in AML-193 cells

    Techniques Used:

    8) Product Images from "miR-590-5p, miR-219-5p, miR-15b and miR-628-5p are commonly regulated by IL-3, GM-CSF and G-CSF in acute myeloid leukemia"

    Article Title: miR-590-5p, miR-219-5p, miR-15b and miR-628-5p are commonly regulated by IL-3, GM-CSF and G-CSF in acute myeloid leukemia

    Journal: Leukemia Research

    doi: 10.1016/j.leukres.2011.09.027

    Profiling outcomes of IL-3, GM-CSF, and G-CSF regulated miRNA in AML-193 cells
    Figure Legend Snippet: Profiling outcomes of IL-3, GM-CSF, and G-CSF regulated miRNA in AML-193 cells

    Techniques Used:

    AML-193 as a model system for testing IL-3, GM-CSF, and G-CSF induced miRNA profiling via potential JAK2-STAT5 pathway
    Figure Legend Snippet: AML-193 as a model system for testing IL-3, GM-CSF, and G-CSF induced miRNA profiling via potential JAK2-STAT5 pathway

    Techniques Used:

    Specific miRNAs independently regulated by IL-3, GM-CSF, and G-CSF in AML-193 cells
    Figure Legend Snippet: Specific miRNAs independently regulated by IL-3, GM-CSF, and G-CSF in AML-193 cells

    Techniques Used:

    IL-3, GM-CSF, and G-CSF directionally regulate specific miRNAs in AML-193 cells
    Figure Legend Snippet: IL-3, GM-CSF, and G-CSF directionally regulate specific miRNAs in AML-193 cells

    Techniques Used:

    9) Product Images from "Promoter-proximal pausing mediated by the exon junction complex regulates splicing"

    Article Title: Promoter-proximal pausing mediated by the exon junction complex regulates splicing

    Journal: Nature Communications

    doi: 10.1038/s41467-019-08381-0

    Mago prevents premature release into transcription elongation. a ChIP-qPCR analysis of Pol II and Ser2P occupancies at MAPK locus. The tested regions for enrichment are shown in the scheme. Error bars indicate the standard deviation of three biological replicates. b Track examples of total Pol II and Ser2P ChIP-Seq from S2R+ cells extracts, after either control or Mago knockdown. The tracks are average of two independent biological replicates after input and “spike-in” normalization. Shown here are the profiles on MAPK , a well-described pre-EJC target gene. c , d Metagene profiles of averaged total Pol II occupancies from two independent biological replicates after “spike-in” normalization in control and Mago-depleted cells along with standard error of mean for all the expressed genes, −600 bp upstream of transcription start sites (TSS) and +600 bp downstream of transcription end sites (TES) ( c ); or centered at the TSS in a ±1 Kb window ( d ). Log2 fold changes against input control are shown on Y -axis, while X -axis depicts genomic coordinates. e Metagene profiles of averaged Ser2P occupancies in control and Mago-depleted cells of two independent biological replicates also displaying standard error of mean for all expressed genes. Log2 fold changes against input control are shown on Y -axis, while X -axis depicts scaled genomic coordinates. f Schematic representation of the calculation of the Pol II release ratio (PRR). The promoter is defined as 250 bp upstream and downstream of TSS, while the gene body is 500 bp downstream of TSS to 500 bp upstream of transcription end site (TES). g The empirical cumulative distribution function (ECDF) plot of computed PRR in control and Mago knockdown conditions, after “spike-in” normalization. p -value is derived from two-sample Kolmogorov-Smirnov test. h Box plots showing changes in PRRs upon Mago depletion when compared to control, separated into different PRR quartiles. The quartiles were generated for genes that are Pol II bound in both control and Mago knockdown conditions. i Schematic depiction of the DRB-4sU-Seq approach. j Metagene profile of nascent RNA from non-DRB treated 4sU-Seq data in control and Mago-depleted cells, with standard error of mean for all the expressed genes. Averaged read counts per million of mapped reads of two independent biological replicates from 4sU-Seq are shown on Y -axis while X -axis depicts scaled genomic coordinates. k Metagene profile of nascent RNA from non-DRB treated 4sU-Seq data in control and Mago-depleted cells with standard error of mean for all the expressed genes based on the average of two independent biological replicates, centered at the TSS in a ±1 Kb window. Nascent RNA was fragmented to ≤100 bp during enrichment. Averaged read counts per million of mapped reads of two independent biological replicates from 4sU-Seq are shown on Y -axis while X -axis depicts genomic coordinates
    Figure Legend Snippet: Mago prevents premature release into transcription elongation. a ChIP-qPCR analysis of Pol II and Ser2P occupancies at MAPK locus. The tested regions for enrichment are shown in the scheme. Error bars indicate the standard deviation of three biological replicates. b Track examples of total Pol II and Ser2P ChIP-Seq from S2R+ cells extracts, after either control or Mago knockdown. The tracks are average of two independent biological replicates after input and “spike-in” normalization. Shown here are the profiles on MAPK , a well-described pre-EJC target gene. c , d Metagene profiles of averaged total Pol II occupancies from two independent biological replicates after “spike-in” normalization in control and Mago-depleted cells along with standard error of mean for all the expressed genes, −600 bp upstream of transcription start sites (TSS) and +600 bp downstream of transcription end sites (TES) ( c ); or centered at the TSS in a ±1 Kb window ( d ). Log2 fold changes against input control are shown on Y -axis, while X -axis depicts genomic coordinates. e Metagene profiles of averaged Ser2P occupancies in control and Mago-depleted cells of two independent biological replicates also displaying standard error of mean for all expressed genes. Log2 fold changes against input control are shown on Y -axis, while X -axis depicts scaled genomic coordinates. f Schematic representation of the calculation of the Pol II release ratio (PRR). The promoter is defined as 250 bp upstream and downstream of TSS, while the gene body is 500 bp downstream of TSS to 500 bp upstream of transcription end site (TES). g The empirical cumulative distribution function (ECDF) plot of computed PRR in control and Mago knockdown conditions, after “spike-in” normalization. p -value is derived from two-sample Kolmogorov-Smirnov test. h Box plots showing changes in PRRs upon Mago depletion when compared to control, separated into different PRR quartiles. The quartiles were generated for genes that are Pol II bound in both control and Mago knockdown conditions. i Schematic depiction of the DRB-4sU-Seq approach. j Metagene profile of nascent RNA from non-DRB treated 4sU-Seq data in control and Mago-depleted cells, with standard error of mean for all the expressed genes. Averaged read counts per million of mapped reads of two independent biological replicates from 4sU-Seq are shown on Y -axis while X -axis depicts scaled genomic coordinates. k Metagene profile of nascent RNA from non-DRB treated 4sU-Seq data in control and Mago-depleted cells with standard error of mean for all the expressed genes based on the average of two independent biological replicates, centered at the TSS in a ±1 Kb window. Nascent RNA was fragmented to ≤100 bp during enrichment. Averaged read counts per million of mapped reads of two independent biological replicates from 4sU-Seq are shown on Y -axis while X -axis depicts genomic coordinates

    Techniques Used: Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Standard Deviation, Derivative Assay, Generated

    10) Product Images from "Functional features of cancer stem cells in melanoma cell lines"

    Article Title: Functional features of cancer stem cells in melanoma cell lines

    Journal: Cancer Cell International

    doi: 10.1186/1475-2867-13-78

    Tumorigenicity of D10 cells. A : The Change in tumor volume over a period of 12 weeks is shown in the graph. (*) = p ≤ 0.05. Bars represent SD. Tumor progression of CD133+ D10 cells significantly (p ≤ 0.05) differs from unsorted D10 tumors. B : Injection of CD133+ D10 cells into the right flank (R) leads to tumor formation (white arrows) while CD133- D10 cells are not capable of inducing tumor growth. Bilateral injection of unsorted D10 cells is followed by bilateral tumor formation.
    Figure Legend Snippet: Tumorigenicity of D10 cells. A : The Change in tumor volume over a period of 12 weeks is shown in the graph. (*) = p ≤ 0.05. Bars represent SD. Tumor progression of CD133+ D10 cells significantly (p ≤ 0.05) differs from unsorted D10 tumors. B : Injection of CD133+ D10 cells into the right flank (R) leads to tumor formation (white arrows) while CD133- D10 cells are not capable of inducing tumor growth. Bilateral injection of unsorted D10 cells is followed by bilateral tumor formation.

    Techniques Used: Injection

    Categorization of differentially expressed genes, detected in CD133+ D10 cells. Number of genes encompassed with a specific A : molecular function and B : biological process. Black columns: upregulated genes. Gray columns: downregulated genes.
    Figure Legend Snippet: Categorization of differentially expressed genes, detected in CD133+ D10 cells. Number of genes encompassed with a specific A : molecular function and B : biological process. Black columns: upregulated genes. Gray columns: downregulated genes.

    Techniques Used:

    Limiting dilution analysis and clonogenic assay. A : Limiting dilution analysis. Percentage of positive wells (positive well = 1 cell colony/well) at different cell concentrations of CD133+ and CD133- D10 cells for calculating Poisson’s distribution (Figure 4 B). B : Clonogenic capacity of D10 cells. Results of Poisson’s distribution with the frequency of proliferating cells in CD133+ (black column) and CD133- (white column) D10 cells, results expressed as mean percentages ± SD; ( * ) = p ≤ 0.001.
    Figure Legend Snippet: Limiting dilution analysis and clonogenic assay. A : Limiting dilution analysis. Percentage of positive wells (positive well = 1 cell colony/well) at different cell concentrations of CD133+ and CD133- D10 cells for calculating Poisson’s distribution (Figure 4 B). B : Clonogenic capacity of D10 cells. Results of Poisson’s distribution with the frequency of proliferating cells in CD133+ (black column) and CD133- (white column) D10 cells, results expressed as mean percentages ± SD; ( * ) = p ≤ 0.001.

    Techniques Used: Clonogenic Assay

    Immunohistochemistry of xenografts and patient samples. CD133 expression (brown spots, black arrows) in different tissue samples: A : normal skin section showing a few brown spots. B : primary melanoma tissue section, C : melanoma lymph node metastasis and D : xenograft induced by CD133+ D10 cells, all showing intense positivity for CD133. E : xenograft induced by unsorted D10 cells with less intense CD133+ staining. Scale bar 100 μm.
    Figure Legend Snippet: Immunohistochemistry of xenografts and patient samples. CD133 expression (brown spots, black arrows) in different tissue samples: A : normal skin section showing a few brown spots. B : primary melanoma tissue section, C : melanoma lymph node metastasis and D : xenograft induced by CD133+ D10 cells, all showing intense positivity for CD133. E : xenograft induced by unsorted D10 cells with less intense CD133+ staining. Scale bar 100 μm.

    Techniques Used: Immunohistochemistry, Expressing, Staining

    Expression of CD133 and CD117 in melanoma cell lines. Cell lines were stained with APC-and PE-conjugated monoclonal antibodies against the CD133 and CD117 epitope. The figure shows the dotplots of A : D10, B : Me39, C : RE, D : Na8, E : Me59 and F : HBL. Corresponding statistics are shown in Table 3 .
    Figure Legend Snippet: Expression of CD133 and CD117 in melanoma cell lines. Cell lines were stained with APC-and PE-conjugated monoclonal antibodies against the CD133 and CD117 epitope. The figure shows the dotplots of A : D10, B : Me39, C : RE, D : Na8, E : Me59 and F : HBL. Corresponding statistics are shown in Table 3 .

    Techniques Used: Expressing, Staining

    11) Product Images from "Organic Solute Transporter α-β Protects Ileal Enterocytes From Bile Acid–Induced Injury"

    Article Title: Organic Solute Transporter α-β Protects Ileal Enterocytes From Bile Acid–Induced Injury

    Journal: Cellular and Molecular Gastroenterology and Hepatology

    doi: 10.1016/j.jcmgh.2018.01.006

    Ileal expression of Nrf2 ARE target genes. ( A ) Microarray analysis of ileum in adult male WT and Ostα -/- mice. Differentially expressed genes whose expression was induced (2-fold change; P
    Figure Legend Snippet: Ileal expression of Nrf2 ARE target genes. ( A ) Microarray analysis of ileum in adult male WT and Ostα -/- mice. Differentially expressed genes whose expression was induced (2-fold change; P

    Techniques Used: Expressing, Microarray, Mouse Assay

    12) Product Images from "Promoter-proximal pausing mediated by the exon junction complex regulates splicing"

    Article Title: Promoter-proximal pausing mediated by the exon junction complex regulates splicing

    Journal: Nature Communications

    doi: 10.1038/s41467-019-08381-0

    Mago prevents premature release into transcription elongation. a ChIP-qPCR analysis of Pol II and Ser2P occupancies at MAPK locus. The tested regions for enrichment are shown in the scheme. Error bars indicate the standard deviation of three biological replicates. b Track examples of total Pol II and Ser2P ChIP-Seq from S2R+ cells extracts, after either control or Mago knockdown. The tracks are average of two independent biological replicates after input and “spike-in” normalization. Shown here are the profiles on MAPK , a well-described pre-EJC target gene. c , d Metagene profiles of averaged total Pol II occupancies from two independent biological replicates after “spike-in” normalization in control and Mago-depleted cells along with standard error of mean for all the expressed genes, −600 bp upstream of transcription start sites (TSS) and +600 bp downstream of transcription end sites (TES) ( c ); or centered at the TSS in a ±1 Kb window ( d ). Log2 fold changes against input control are shown on Y -axis, while X -axis depicts genomic coordinates. e Metagene profiles of averaged Ser2P occupancies in control and Mago-depleted cells of two independent biological replicates also displaying standard error of mean for all expressed genes. Log2 fold changes against input control are shown on Y -axis, while X -axis depicts scaled genomic coordinates. f Schematic representation of the calculation of the Pol II release ratio (PRR). The promoter is defined as 250 bp upstream and downstream of TSS, while the gene body is 500 bp downstream of TSS to 500 bp upstream of transcription end site (TES). g The empirical cumulative distribution function (ECDF) plot of computed PRR in control and Mago knockdown conditions, after “spike-in” normalization. p -value is derived from two-sample Kolmogorov-Smirnov test. h Box plots showing changes in PRRs upon Mago depletion when compared to control, separated into different PRR quartiles. The quartiles were generated for genes that are Pol II bound in both control and Mago knockdown conditions. i Schematic depiction of the DRB-4sU-Seq approach. j Metagene profile of nascent RNA from non-DRB treated 4sU-Seq data in control and Mago-depleted cells, with standard error of mean for all the expressed genes. Averaged read counts per million of mapped reads of two independent biological replicates from 4sU-Seq are shown on Y -axis while X -axis depicts scaled genomic coordinates. k Metagene profile of nascent RNA from non-DRB treated 4sU-Seq data in control and Mago-depleted cells with standard error of mean for all the expressed genes based on the average of two independent biological replicates, centered at the TSS in a ±1 Kb window. Nascent RNA was fragmented to ≤100 bp during enrichment. Averaged read counts per million of mapped reads of two independent biological replicates from 4sU-Seq are shown on Y -axis while X -axis depicts genomic coordinates
    Figure Legend Snippet: Mago prevents premature release into transcription elongation. a ChIP-qPCR analysis of Pol II and Ser2P occupancies at MAPK locus. The tested regions for enrichment are shown in the scheme. Error bars indicate the standard deviation of three biological replicates. b Track examples of total Pol II and Ser2P ChIP-Seq from S2R+ cells extracts, after either control or Mago knockdown. The tracks are average of two independent biological replicates after input and “spike-in” normalization. Shown here are the profiles on MAPK , a well-described pre-EJC target gene. c , d Metagene profiles of averaged total Pol II occupancies from two independent biological replicates after “spike-in” normalization in control and Mago-depleted cells along with standard error of mean for all the expressed genes, −600 bp upstream of transcription start sites (TSS) and +600 bp downstream of transcription end sites (TES) ( c ); or centered at the TSS in a ±1 Kb window ( d ). Log2 fold changes against input control are shown on Y -axis, while X -axis depicts genomic coordinates. e Metagene profiles of averaged Ser2P occupancies in control and Mago-depleted cells of two independent biological replicates also displaying standard error of mean for all expressed genes. Log2 fold changes against input control are shown on Y -axis, while X -axis depicts scaled genomic coordinates. f Schematic representation of the calculation of the Pol II release ratio (PRR). The promoter is defined as 250 bp upstream and downstream of TSS, while the gene body is 500 bp downstream of TSS to 500 bp upstream of transcription end site (TES). g The empirical cumulative distribution function (ECDF) plot of computed PRR in control and Mago knockdown conditions, after “spike-in” normalization. p -value is derived from two-sample Kolmogorov-Smirnov test. h Box plots showing changes in PRRs upon Mago depletion when compared to control, separated into different PRR quartiles. The quartiles were generated for genes that are Pol II bound in both control and Mago knockdown conditions. i Schematic depiction of the DRB-4sU-Seq approach. j Metagene profile of nascent RNA from non-DRB treated 4sU-Seq data in control and Mago-depleted cells, with standard error of mean for all the expressed genes. Averaged read counts per million of mapped reads of two independent biological replicates from 4sU-Seq are shown on Y -axis while X -axis depicts scaled genomic coordinates. k Metagene profile of nascent RNA from non-DRB treated 4sU-Seq data in control and Mago-depleted cells with standard error of mean for all the expressed genes based on the average of two independent biological replicates, centered at the TSS in a ±1 Kb window. Nascent RNA was fragmented to ≤100 bp during enrichment. Averaged read counts per million of mapped reads of two independent biological replicates from 4sU-Seq are shown on Y -axis while X -axis depicts genomic coordinates

    Techniques Used: Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Standard Deviation, Derivative Assay, Generated

    13) Product Images from "Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers"

    Article Title: Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers

    Journal: Viruses

    doi: 10.3390/v8020053

    Lowest p -values of clusters established by the pipeline. The p -values are arranged by feature of the strongest significant association of each of the 6165 clusters. The 50 features involved as strongest associations have been coloured by type: biological (red), methodological (green), and technical (blue). The boxes span the first and third quartiles. The dark band inside each box represents the median. The whiskers of the boxes extend to the lowest and highest values within a distance of 1.5 times the interquartile range. As can be seen, most p -values were above 1e-24, but a few methodological features have associated clusters with very low p -values, such as f056, f068, f069, f076, f079, and f084. The library preparation kit ScriptSeq v2 RNA-Seq, Illumina (f084) displays strongly associated clusters with p -values as low as 3.04e-89 that mapped as species Avian myeloblastosis-associated virus . Clusters that were annotated as NCBI species Parvovirus NIH/CQV were associated to laboratory-kit RNeasy MinElute, Qiagen (f076) with minimal p -value 5.48e-38. Finally, a cluster annotated as Acanthocystis turfacea chlorella virus MN0810.1 (ATCV) was associated to DNase/RNase: Promega DNase stop solution (f069) with p -value = 4.19e-12.
    Figure Legend Snippet: Lowest p -values of clusters established by the pipeline. The p -values are arranged by feature of the strongest significant association of each of the 6165 clusters. The 50 features involved as strongest associations have been coloured by type: biological (red), methodological (green), and technical (blue). The boxes span the first and third quartiles. The dark band inside each box represents the median. The whiskers of the boxes extend to the lowest and highest values within a distance of 1.5 times the interquartile range. As can be seen, most p -values were above 1e-24, but a few methodological features have associated clusters with very low p -values, such as f056, f068, f069, f076, f079, and f084. The library preparation kit ScriptSeq v2 RNA-Seq, Illumina (f084) displays strongly associated clusters with p -values as low as 3.04e-89 that mapped as species Avian myeloblastosis-associated virus . Clusters that were annotated as NCBI species Parvovirus NIH/CQV were associated to laboratory-kit RNeasy MinElute, Qiagen (f076) with minimal p -value 5.48e-38. Finally, a cluster annotated as Acanthocystis turfacea chlorella virus MN0810.1 (ATCV) was associated to DNase/RNase: Promega DNase stop solution (f069) with p -value = 4.19e-12.

    Techniques Used: RNA Sequencing Assay

    14) Product Images from "Promoter-proximal pausing mediated by the exon junction complex regulates splicing"

    Article Title: Promoter-proximal pausing mediated by the exon junction complex regulates splicing

    Journal: Nature Communications

    doi: 10.1038/s41467-019-08381-0

    Mago prevents premature release into transcription elongation. a ChIP-qPCR analysis of Pol II and Ser2P occupancies at MAPK locus. The tested regions for enrichment are shown in the scheme. Error bars indicate the standard deviation of three biological replicates. b Track examples of total Pol II and Ser2P ChIP-Seq from S2R+ cells extracts, after either control or Mago knockdown. The tracks are average of two independent biological replicates after input and “spike-in” normalization. Shown here are the profiles on MAPK , a well-described pre-EJC target gene. c , d Metagene profiles of averaged total Pol II occupancies from two independent biological replicates after “spike-in” normalization in control and Mago-depleted cells along with standard error of mean for all the expressed genes, −600 bp upstream of transcription start sites (TSS) and +600 bp downstream of transcription end sites (TES) ( c ); or centered at the TSS in a ±1 Kb window ( d ). Log2 fold changes against input control are shown on Y -axis, while X -axis depicts genomic coordinates. e Metagene profiles of averaged Ser2P occupancies in control and Mago-depleted cells of two independent biological replicates also displaying standard error of mean for all expressed genes. Log2 fold changes against input control are shown on Y -axis, while X -axis depicts scaled genomic coordinates. f Schematic representation of the calculation of the Pol II release ratio (PRR). The promoter is defined as 250 bp upstream and downstream of TSS, while the gene body is 500 bp downstream of TSS to 500 bp upstream of transcription end site (TES). g The empirical cumulative distribution function (ECDF) plot of computed PRR in control and Mago knockdown conditions, after “spike-in” normalization. p -value is derived from two-sample Kolmogorov-Smirnov test. h Box plots showing changes in PRRs upon Mago depletion when compared to control, separated into different PRR quartiles. The quartiles were generated for genes that are Pol II bound in both control and Mago knockdown conditions. i Schematic depiction of the DRB-4sU-Seq approach. j Metagene profile of nascent RNA from non-DRB treated 4sU-Seq data in control and Mago-depleted cells, with standard error of mean for all the expressed genes. Averaged read counts per million of mapped reads of two independent biological replicates from 4sU-Seq are shown on Y -axis while X -axis depicts scaled genomic coordinates. k Metagene profile of nascent RNA from non-DRB treated 4sU-Seq data in control and Mago-depleted cells with standard error of mean for all the expressed genes based on the average of two independent biological replicates, centered at the TSS in a ±1 Kb window. Nascent RNA was fragmented to ≤100 bp during enrichment. Averaged read counts per million of mapped reads of two independent biological replicates from 4sU-Seq are shown on Y -axis while X -axis depicts genomic coordinates
    Figure Legend Snippet: Mago prevents premature release into transcription elongation. a ChIP-qPCR analysis of Pol II and Ser2P occupancies at MAPK locus. The tested regions for enrichment are shown in the scheme. Error bars indicate the standard deviation of three biological replicates. b Track examples of total Pol II and Ser2P ChIP-Seq from S2R+ cells extracts, after either control or Mago knockdown. The tracks are average of two independent biological replicates after input and “spike-in” normalization. Shown here are the profiles on MAPK , a well-described pre-EJC target gene. c , d Metagene profiles of averaged total Pol II occupancies from two independent biological replicates after “spike-in” normalization in control and Mago-depleted cells along with standard error of mean for all the expressed genes, −600 bp upstream of transcription start sites (TSS) and +600 bp downstream of transcription end sites (TES) ( c ); or centered at the TSS in a ±1 Kb window ( d ). Log2 fold changes against input control are shown on Y -axis, while X -axis depicts genomic coordinates. e Metagene profiles of averaged Ser2P occupancies in control and Mago-depleted cells of two independent biological replicates also displaying standard error of mean for all expressed genes. Log2 fold changes against input control are shown on Y -axis, while X -axis depicts scaled genomic coordinates. f Schematic representation of the calculation of the Pol II release ratio (PRR). The promoter is defined as 250 bp upstream and downstream of TSS, while the gene body is 500 bp downstream of TSS to 500 bp upstream of transcription end site (TES). g The empirical cumulative distribution function (ECDF) plot of computed PRR in control and Mago knockdown conditions, after “spike-in” normalization. p -value is derived from two-sample Kolmogorov-Smirnov test. h Box plots showing changes in PRRs upon Mago depletion when compared to control, separated into different PRR quartiles. The quartiles were generated for genes that are Pol II bound in both control and Mago knockdown conditions. i Schematic depiction of the DRB-4sU-Seq approach. j Metagene profile of nascent RNA from non-DRB treated 4sU-Seq data in control and Mago-depleted cells, with standard error of mean for all the expressed genes. Averaged read counts per million of mapped reads of two independent biological replicates from 4sU-Seq are shown on Y -axis while X -axis depicts scaled genomic coordinates. k Metagene profile of nascent RNA from non-DRB treated 4sU-Seq data in control and Mago-depleted cells with standard error of mean for all the expressed genes based on the average of two independent biological replicates, centered at the TSS in a ±1 Kb window. Nascent RNA was fragmented to ≤100 bp during enrichment. Averaged read counts per million of mapped reads of two independent biological replicates from 4sU-Seq are shown on Y -axis while X -axis depicts genomic coordinates

    Techniques Used: Chromatin Immunoprecipitation, Real-time Polymerase Chain Reaction, Standard Deviation, Derivative Assay, Generated

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    Article Snippet: Standard procedures including total RNA isolation, cDNA synthesis, cRNA labeling, microarray hybridization and image acquisition were done as described in the manufacturer’s protocol and our previous publications [ , ]. .. Briefly, total RNA samples were isolated with TRIzol reagent (Invitrogen) then purified with RNeasy MinElute Cleanup Kit (Qiagen) following the manufacturer’s protocol.

    Article Title: Cytosine arabinoside induces ectoderm and inhibits mesoderm expression in human embryonic stem cells during multilineage differentiation
    Article Snippet: Paragraph title: Microarray hybridization ... The total RNA was purified using RNeasy minelute cleanup kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

    Article Title: Identification and Functional Annotation of Genes Differentially Expressed in the Reproductive Tissues of the Olive Tree (Olea europaea L.) through the Generation of Subtractive Libraries
    Article Snippet: .. Construction of the suppression subtractive hybridization (SSH) libraries Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen) from samples of the different years, and the contaminating genomic DNA was removed by DNAase I (Qiagen) treatment followed by a clean-up with the RNeasy MinElute Cleanup kit (Qiagen). cDNA was then synthesized from pistil, leaf, and mature pollen total RNA using the SMART PCR cDNA Synthesis kit (Clontech). .. The subtracted libraries were constructed with the PCR-Select cDNA Subtraction Kit (Clontech).

    Countercurrent Chromatography:

    Article Title: Rett syndrome astrocytes are abnormal and spread MeCP2 deficiency through gap junctions
    Article Snippet: The following reverse primer was used to pair with both forward primers: 5'- CCA CCC TCC AGT TTG GTT TA -3'. .. Because these primer sets may also amplify the chromosomal DNA, the DNA content of the samples was further minimized by purifying RNA using the RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA) according to manufacturer’s instruction.

    Sequencing:

    Article Title: The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan
    Article Snippet: Paragraph title: mRNA sequencing ... The fragmented mRNA was immediately purified with RNeasy MinElute Cleanup Kit (74204, Qiagen) to stop the reaction and to remove small RNA fragments ( < 100 bases).

    Article Title: Rett syndrome astrocytes are abnormal and spread MeCP2 deficiency through gap junctions
    Article Snippet: The forward primer sequence for Wt transcript was 5'- GAC CCC TTG GGA CTG AAG TT -3' and that for mutant transcript was 5'- CCA TGC GAT AAG CTT GAT GA -3'. .. Because these primer sets may also amplify the chromosomal DNA, the DNA content of the samples was further minimized by purifying RNA using the RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA) according to manufacturer’s instruction.

    Ligation:

    Article Title: The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan
    Article Snippet: The fragmented mRNA was immediately purified with RNeasy MinElute Cleanup Kit (74204, Qiagen) to stop the reaction and to remove small RNA fragments ( < 100 bases). .. Ligation of RNA 3′ adapter (RA3, part # 15013207, Illumina) was done using T4 RNA Ligase 2, truncated K227Q (M0351L, New England Biolabs Inc) according to the Illumina protocol.

    Article Title: Protein-driven RNA nanostructured devices that function in vitro and control mammalian cell fate
    Article Snippet: Cy3- and Cy5-labelling of RNA Cy3- and Cy5-labelled RNAs were prepared by ligation using T4 RNA ligase (Ambion), pCp-Cy3 (Jena Bioscience) and pCp-Cy5 (Jena Bioscience). .. Cy3- and Cy5-labelling was performed with 150 pmol RNA using 10 U T4 RNA ligase, 3 nmol pCp-Cy3 or pCp-Cy5 and 10% (v/v) dimethyl sulfoxide in 10 µl at 16 °C for 36–48 h. The Cy3- and Cy5-labelled RNAs were purified using an RNeasy MinElute Cleanup Kit (Qiagen).

    Cell Culture:

    Article Title: PGC-Enriched miRNAs Control Germ Cell Development
    Article Snippet: miRNA microarray analysis Total RNAs were extracted from the cultured cells using Trizol reagent (Invitrogen, USA). .. For preparation of cellular miRNAs, small-sized RNAs containing miRNAs were isolated from total RNA using the RNeasy MinElute Cleanup kit (Qiagen, USA) according to the manufacturer’s protocol.

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Detection of Viable Cryptosporidium parvum in Soil by Reverse Transcription-Real-Time PCR Targeting hsp70 mRNA ▿
    Article Snippet: .. For samples that did not show successful amplification, an additional purification using RNeasy MinElute cleanup kit was performed before RT-PCR. .. For method 2, the garnet bead in the lysis tube was replaced by a bead mixture of various diameters (2 mm, 0.4 g; 1 mm, 0.4 g; 0.5 mm, 0.4 g) before extraction to ensure higher (m)RNA yield.

    Article Title: Differential Regulation of Orthologous Chitinase Genes in Mycoparasitic Trichoderma Species ▿ Species ▿ †
    Article Snippet: Paragraph title: RNA isolation and RT-PCR. ... All isolated RNAs were treated with DNase I (Fermentas, St Leon-Rot, Germany) and purified using the RNeasy MinElute cleanup kit (Qiagen, Hilden, Germany).

    RNA Sequencing Assay:

    Article Title: Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers
    Article Snippet: In the methodological associations, we correctly detected the strong known association (p -value: 3.04e-89) of avian myeloblastosis-associated virus (accession L10922.1) used in the manufacture of the ScriptSeq v2 RNA-Seq library preparation kit (f089). .. The associated feature with lowest p -value to the parvovirus clusters suggested a contamination from the RNeasy MinElute purification kit (f076) manufactured by Qiagen (p -value: 5.48e-38).

    Mutagenesis:

    Article Title: Rett syndrome astrocytes are abnormal and spread MeCP2 deficiency through gap junctions
    Article Snippet: The forward primer sequence for Wt transcript was 5'- GAC CCC TTG GGA CTG AAG TT -3' and that for mutant transcript was 5'- CCA TGC GAT AAG CTT GAT GA -3'. .. Because these primer sets may also amplify the chromosomal DNA, the DNA content of the samples was further minimized by purifying RNA using the RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA) according to manufacturer’s instruction.

    Isolation:

    Article Title: PGC-Enriched miRNAs Control Germ Cell Development
    Article Snippet: .. For preparation of cellular miRNAs, small-sized RNAs containing miRNAs were isolated from total RNA using the RNeasy MinElute Cleanup kit (Qiagen, USA) according to the manufacturer’s protocol. .. The isolated small-sized RNAs (∼1 μg) were subjected to direct labeling with a fluorescent dye using the Platinum Bright 647 Infrared nucleic acid labeling kit (KREATECH, Netherland) according to the manufacturer’s instruction.

    Article Title: The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan
    Article Snippet: In brief, after isolation, 50 ng of mRNA was chemically fragmented by incubating the mRNA solution with twice the volume of alkaline hydrolysis buffer (50 mM sodium carbonate [NaHCO3 /Na2 CO3 ] pH 9.2, 1 mM EDTA) at 95 °C for 5 min to obtain fragments of ~200–300 bases. .. The fragmented mRNA was immediately purified with RNeasy MinElute Cleanup Kit (74204, Qiagen) to stop the reaction and to remove small RNA fragments ( < 100 bases).

    Article Title: Functional evidence implicating chromosome 7q22 haploinsufficiency in myelodysplastic syndrome pathogenesis
    Article Snippet: Paragraph title: RNA isolation and expression ... The RNA was then treated with DNAse 1 (Ambion, Austin, TX, United States) and purified with the RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA, United States).

    Article Title: Molecular signatures of differential responses to exercise trainings during rehabilitation
    Article Snippet: .. Briefly, total RNA samples were isolated with TRIzol reagent (Invitrogen) then purified with RNeasy MinElute Cleanup Kit (Qiagen) following the manufacturer’s protocol. .. Two hundred nanograms of total RNA from each sample were reverse-transcribed to double-stranded cDNA followed by in vitro cRNA synthesis using one-cycle target labeling and control reagents and protocol (Affymetrix).

    Article Title: Differential Regulation of Orthologous Chitinase Genes in Mycoparasitic Trichoderma Species ▿ Species ▿ †
    Article Snippet: .. All isolated RNAs were treated with DNase I (Fermentas, St Leon-Rot, Germany) and purified using the RNeasy MinElute cleanup kit (Qiagen, Hilden, Germany). .. Reverse transcription (RT)-PCR was performed as described previously using 25 cycles per reaction ( ) with the gene-specific primers listed in .

    Article Title: Identification and Functional Annotation of Genes Differentially Expressed in the Reproductive Tissues of the Olive Tree (Olea europaea L.) through the Generation of Subtractive Libraries
    Article Snippet: .. Construction of the suppression subtractive hybridization (SSH) libraries Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen) from samples of the different years, and the contaminating genomic DNA was removed by DNAase I (Qiagen) treatment followed by a clean-up with the RNeasy MinElute Cleanup kit (Qiagen). cDNA was then synthesized from pistil, leaf, and mature pollen total RNA using the SMART PCR cDNA Synthesis kit (Clontech). .. The subtracted libraries were constructed with the PCR-Select cDNA Subtraction Kit (Clontech).

    Labeling:

    Article Title: PGC-Enriched miRNAs Control Germ Cell Development
    Article Snippet: For preparation of cellular miRNAs, small-sized RNAs containing miRNAs were isolated from total RNA using the RNeasy MinElute Cleanup kit (Qiagen, USA) according to the manufacturer’s protocol. .. The isolated small-sized RNAs (∼1 μg) were subjected to direct labeling with a fluorescent dye using the Platinum Bright 647 Infrared nucleic acid labeling kit (KREATECH, Netherland) according to the manufacturer’s instruction.

    Article Title: Molecular signatures of differential responses to exercise trainings during rehabilitation
    Article Snippet: Standard procedures including total RNA isolation, cDNA synthesis, cRNA labeling, microarray hybridization and image acquisition were done as described in the manufacturer’s protocol and our previous publications [ , ]. .. Briefly, total RNA samples were isolated with TRIzol reagent (Invitrogen) then purified with RNeasy MinElute Cleanup Kit (Qiagen) following the manufacturer’s protocol.

    Purification:

    Article Title: PGC-Enriched miRNAs Control Germ Cell Development
    Article Snippet: For preparation of cellular miRNAs, small-sized RNAs containing miRNAs were isolated from total RNA using the RNeasy MinElute Cleanup kit (Qiagen, USA) according to the manufacturer’s protocol. .. After labeling, labeled RNAs were purified from free fluorescent substrates using KREA pure columns (KREATECH, Netherland) according to the manufacturer’s instruction, and used in hybridization.

    Article Title: The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan
    Article Snippet: .. The fragmented mRNA was immediately purified with RNeasy MinElute Cleanup Kit (74204, Qiagen) to stop the reaction and to remove small RNA fragments ( < 100 bases). .. Further, purified, fragmented mRNA was treated with thermosensitive alkaline phosphatase FastAP (EF0651, Fermentas) at 37 °C for 30 min and then at 75 °C for 5 min to inactivate FastAP.

    Article Title: Planar cell polarity-mediated induction of neural stem cell expansion during axolotl spinal cord regeneration
    Article Snippet: .. Total RNA was extracted using TRIzol (Life Technologies) and purified using RNeasy MinElute cleanup kit (QIAGEN). .. Power SYBR Green QPCR Master Mix (Life technologies) was used to carry out qPCRs in a LightCycler 480 thermal cycler (Roche).

    Article Title: Detection of Viable Cryptosporidium parvum in Soil by Reverse Transcription-Real-Time PCR Targeting hsp70 mRNA ▿
    Article Snippet: .. For samples that did not show successful amplification, an additional purification using RNeasy MinElute cleanup kit was performed before RT-PCR. .. For method 2, the garnet bead in the lysis tube was replaced by a bead mixture of various diameters (2 mm, 0.4 g; 1 mm, 0.4 g; 0.5 mm, 0.4 g) before extraction to ensure higher (m)RNA yield.

    Article Title: Functional evidence implicating chromosome 7q22 haploinsufficiency in myelodysplastic syndrome pathogenesis
    Article Snippet: .. The RNA was then treated with DNAse 1 (Ambion, Austin, TX, United States) and purified with the RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA, United States). .. For TaqMan analysis, reverse transcription was carried out using the High Capacity RNA-to-cDNA Master Mix (Life Technologies).

    Article Title: Rett syndrome astrocytes are abnormal and spread MeCP2 deficiency through gap junctions
    Article Snippet: Purified RNA was resuspended in RNase free water and stored at −70°C until use. .. Because these primer sets may also amplify the chromosomal DNA, the DNA content of the samples was further minimized by purifying RNA using the RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA) according to manufacturer’s instruction.

    Article Title: Molecular signatures of differential responses to exercise trainings during rehabilitation
    Article Snippet: .. Briefly, total RNA samples were isolated with TRIzol reagent (Invitrogen) then purified with RNeasy MinElute Cleanup Kit (Qiagen) following the manufacturer’s protocol. .. Two hundred nanograms of total RNA from each sample were reverse-transcribed to double-stranded cDNA followed by in vitro cRNA synthesis using one-cycle target labeling and control reagents and protocol (Affymetrix).

    Article Title: Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers
    Article Snippet: .. The associated feature with lowest p -value to the parvovirus clusters suggested a contamination from the RNeasy MinElute purification kit (f076) manufactured by Qiagen (p -value: 5.48e-38). .. In addition, a single cluster annotated as NCBI taxonomy species Acanthocystis turfacea Chlorella virus MN0810.1 (accession JX997174.1, taxa-id 1278272) with lowest associated p -value (p -value = 4.19e-12) to laboratory kit DNase/RNase: Promega DNase stop solution (f069).

    Article Title: Protein-driven RNA nanostructured devices that function in vitro and control mammalian cell fate
    Article Snippet: .. Cy3- and Cy5-labelling was performed with 150 pmol RNA using 10 U T4 RNA ligase, 3 nmol pCp-Cy3 or pCp-Cy5 and 10% (v/v) dimethyl sulfoxide in 10 µl at 16 °C for 36–48 h. The Cy3- and Cy5-labelled RNAs were purified using an RNeasy MinElute Cleanup Kit (Qiagen). .. After the recovery of RNAs, the RNA concentration was measured in a NanoDrop (Thermo Scientific).

    Article Title: Differential Regulation of Orthologous Chitinase Genes in Mycoparasitic Trichoderma Species ▿ Species ▿ †
    Article Snippet: .. All isolated RNAs were treated with DNase I (Fermentas, St Leon-Rot, Germany) and purified using the RNeasy MinElute cleanup kit (Qiagen, Hilden, Germany). .. Reverse transcription (RT)-PCR was performed as described previously using 25 cycles per reaction ( ) with the gene-specific primers listed in .

    Article Title: Cytosine arabinoside induces ectoderm and inhibits mesoderm expression in human embryonic stem cells during multilineage differentiation
    Article Snippet: .. The total RNA was purified using RNeasy minelute cleanup kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. .. Nanodrop (ND-1000, Thermo-Fisher, Langenselbold, Germany) was used for quantification and the quality of RNA was determined by denaturing agarose gel electrophoresis.

    Polymerase Chain Reaction:

    Article Title: Functional evidence implicating chromosome 7q22 haploinsufficiency in myelodysplastic syndrome pathogenesis
    Article Snippet: The RNA was then treated with DNAse 1 (Ambion, Austin, TX, United States) and purified with the RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA, United States). .. PCR reactions were performed on an ABI 7900HT Real-Time PCR System (Applied Biosystems, Foster City, CA, United States) with the Taqman Gene Expression Master Mix (Applied Biosystems) according to manufacturer's instructions.

    Article Title: Rett syndrome astrocytes are abnormal and spread MeCP2 deficiency through gap junctions
    Article Snippet: Because these primer sets may also amplify the chromosomal DNA, the DNA content of the samples was further minimized by purifying RNA using the RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA) according to manufacturer’s instruction. .. Using the resulting RNA samples and the above primers, PCR reactions without prior reverse transcription yielded minimal detectable products.

    Article Title: Identification and Functional Annotation of Genes Differentially Expressed in the Reproductive Tissues of the Olive Tree (Olea europaea L.) through the Generation of Subtractive Libraries
    Article Snippet: .. Construction of the suppression subtractive hybridization (SSH) libraries Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen) from samples of the different years, and the contaminating genomic DNA was removed by DNAase I (Qiagen) treatment followed by a clean-up with the RNeasy MinElute Cleanup kit (Qiagen). cDNA was then synthesized from pistil, leaf, and mature pollen total RNA using the SMART PCR cDNA Synthesis kit (Clontech). .. The subtracted libraries were constructed with the PCR-Select cDNA Subtraction Kit (Clontech).

    Construct:

    Article Title: Identification and Functional Annotation of Genes Differentially Expressed in the Reproductive Tissues of the Olive Tree (Olea europaea L.) through the Generation of Subtractive Libraries
    Article Snippet: Construction of the suppression subtractive hybridization (SSH) libraries Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen) from samples of the different years, and the contaminating genomic DNA was removed by DNAase I (Qiagen) treatment followed by a clean-up with the RNeasy MinElute Cleanup kit (Qiagen). cDNA was then synthesized from pistil, leaf, and mature pollen total RNA using the SMART PCR cDNA Synthesis kit (Clontech). .. The subtracted libraries were constructed with the PCR-Select cDNA Subtraction Kit (Clontech).

    Lysis:

    Article Title: The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan
    Article Snippet: A yeast cell pellet was resuspended in 1 ml of lysis buffer from Dynabeads mRNA DIRECT Kit (61011, Life technologies) and lysed at 4 °C with 1 volume of acid washed glass beads in a FastPrep instrument (Thermo Scientific) using 2 cycles with the following settings: 45 s at 6.5 speed with 3 min pause on ice between cycles. .. The fragmented mRNA was immediately purified with RNeasy MinElute Cleanup Kit (74204, Qiagen) to stop the reaction and to remove small RNA fragments ( < 100 bases).

    Sample Prep:

    Article Title: The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan
    Article Snippet: Libraries for mRNA sequencing were prepared using the “directional mRNA-seq sample preparation” protocol from Illumina, with minor modifications. .. The fragmented mRNA was immediately purified with RNeasy MinElute Cleanup Kit (74204, Qiagen) to stop the reaction and to remove small RNA fragments ( < 100 bases).

    Activated Clotting Time Assay:

    Article Title: Rett syndrome astrocytes are abnormal and spread MeCP2 deficiency through gap junctions
    Article Snippet: Because these primer sets may also amplify the chromosomal DNA, the DNA content of the samples was further minimized by purifying RNA using the RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA) according to manufacturer’s instruction. .. The forward sequence was 5'-ATG ACC ATC CTT TTC CTT ACT ATG GT-3' and the reverse sequence was 5'-TCT TCC CCT TTT AAT GGT CAG TGT AC-3'.

    Mouse Assay:

    Article Title: Rett syndrome astrocytes are abnormal and spread MeCP2 deficiency through gap junctions
    Article Snippet: To determine the relative levels of Wt and mutant Mecp2 transcripts in mice, we used previously designed primer pairs ( ). .. Because these primer sets may also amplify the chromosomal DNA, the DNA content of the samples was further minimized by purifying RNA using the RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA) according to manufacturer’s instruction.

    Software:

    Article Title: Planar cell polarity-mediated induction of neural stem cell expansion during axolotl spinal cord regeneration
    Article Snippet: Total RNA was extracted using TRIzol (Life Technologies) and purified using RNeasy MinElute cleanup kit (QIAGEN). .. LightCycler 480 software (Roche) was used to analyze relative gene expression.

    Real-time Polymerase Chain Reaction:

    Article Title: Planar cell polarity-mediated induction of neural stem cell expansion during axolotl spinal cord regeneration
    Article Snippet: Paragraph title: Quantitative real-time PCR ... Total RNA was extracted using TRIzol (Life Technologies) and purified using RNeasy MinElute cleanup kit (QIAGEN).

    Article Title: Functional evidence implicating chromosome 7q22 haploinsufficiency in myelodysplastic syndrome pathogenesis
    Article Snippet: The RNA was then treated with DNAse 1 (Ambion, Austin, TX, United States) and purified with the RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA, United States). .. Relative quantification of gene expression was determined by performing quantitative real-time PCR using the following TaqMan Gene Expression Assays (Applied Biosystems): Armc10 (Mm03011576_g1), Mll5 (Mm01129502_g1), Napepld (Mm00724596_m1), Orc5 (Mm00457242_m1), Psmc2 (Mm00803207_m1), Dnajc2 (Mm00494389_m1 ), Pmpcb (Mm01138654_m1 ), Srpk2 (Mm00486413_m1 ), Fbxl13 (Mm00622025_m1 ), Lrrc17 (Mm01167263_m1 ), Slc26a5 (Mm00446145_m1 ), Reln (Mm00465200_m1 ), Lhfpl3 (Mm03038441_m1 ), and Gapdh (Mm99999915_g1) with the TaqMan Gene Expression Master Mix (ABI).

    Agarose Gel Electrophoresis:

    Article Title: Cytosine arabinoside induces ectoderm and inhibits mesoderm expression in human embryonic stem cells during multilineage differentiation
    Article Snippet: The total RNA was purified using RNeasy minelute cleanup kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. .. Nanodrop (ND-1000, Thermo-Fisher, Langenselbold, Germany) was used for quantification and the quality of RNA was determined by denaturing agarose gel electrophoresis.

    In Vitro:

    Article Title: Molecular signatures of differential responses to exercise trainings during rehabilitation
    Article Snippet: Briefly, total RNA samples were isolated with TRIzol reagent (Invitrogen) then purified with RNeasy MinElute Cleanup Kit (Qiagen) following the manufacturer’s protocol. .. Two hundred nanograms of total RNA from each sample were reverse-transcribed to double-stranded cDNA followed by in vitro cRNA synthesis using one-cycle target labeling and control reagents and protocol (Affymetrix).

    Article Title: Cytosine arabinoside induces ectoderm and inhibits mesoderm expression in human embryonic stem cells during multilineage differentiation
    Article Snippet: The total RNA was purified using RNeasy minelute cleanup kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. .. For in vitro transcription and cRNA labelling 100 ng of total RNA was used as template and processed using Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA) according to the manufacturer's instructions.

    Concentration Assay:

    Article Title: Protein-driven RNA nanostructured devices that function in vitro and control mammalian cell fate
    Article Snippet: Cy3- and Cy5-labelling was performed with 150 pmol RNA using 10 U T4 RNA ligase, 3 nmol pCp-Cy3 or pCp-Cy5 and 10% (v/v) dimethyl sulfoxide in 10 µl at 16 °C for 36–48 h. The Cy3- and Cy5-labelled RNAs were purified using an RNeasy MinElute Cleanup Kit (Qiagen). .. After the recovery of RNAs, the RNA concentration was measured in a NanoDrop (Thermo Scientific).

    CTG Assay:

    Article Title: Rett syndrome astrocytes are abnormal and spread MeCP2 deficiency through gap junctions
    Article Snippet: The forward primer sequence for Wt transcript was 5'- GAC CCC TTG GGA CTG AAG TT -3' and that for mutant transcript was 5'- CCA TGC GAT AAG CTT GAT GA -3'. .. Because these primer sets may also amplify the chromosomal DNA, the DNA content of the samples was further minimized by purifying RNA using the RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA) according to manufacturer’s instruction.

    Staining:

    Article Title: Molecular signatures of differential responses to exercise trainings during rehabilitation
    Article Snippet: Briefly, total RNA samples were isolated with TRIzol reagent (Invitrogen) then purified with RNeasy MinElute Cleanup Kit (Qiagen) following the manufacturer’s protocol. .. Each array was washed and stained using the Affymetrix Fluidics Station 450, and then scanned using the GeneChip® Scanner 3000.

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    Qiagen rneasy minelute purification kit
    Lowest p -values of clusters established by the pipeline. The p -values are arranged by feature of the strongest significant association of each of the 6165 clusters. The 50 features involved as strongest associations have been coloured by type: biological (red), methodological (green), and technical (blue). The boxes span the first and third quartiles. The dark band inside each box represents the median. The whiskers of the boxes extend to the lowest and highest values within a distance of 1.5 times the interquartile range. As can be seen, most p -values were above 1e-24, but a few methodological features have associated clusters with very low p -values, such as f056, f068, f069, f076, f079, and f084. The library preparation kit ScriptSeq v2 RNA-Seq, Illumina (f084) displays strongly associated clusters with p -values as low as 3.04e-89 that mapped as species Avian myeloblastosis-associated virus . Clusters that were annotated as NCBI species Parvovirus NIH/CQV were associated to laboratory-kit <t>RNeasy</t> <t>MinElute,</t> Qiagen (f076) with minimal p -value 5.48e-38. Finally, a cluster annotated as Acanthocystis turfacea chlorella virus MN0810.1 (ATCV) was associated to DNase/RNase: Promega DNase stop solution (f069) with p -value = 4.19e-12.
    Rneasy Minelute Purification Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 1043 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Lowest p -values of clusters established by the pipeline. The p -values are arranged by feature of the strongest significant association of each of the 6165 clusters. The 50 features involved as strongest associations have been coloured by type: biological (red), methodological (green), and technical (blue). The boxes span the first and third quartiles. The dark band inside each box represents the median. The whiskers of the boxes extend to the lowest and highest values within a distance of 1.5 times the interquartile range. As can be seen, most p -values were above 1e-24, but a few methodological features have associated clusters with very low p -values, such as f056, f068, f069, f076, f079, and f084. The library preparation kit ScriptSeq v2 RNA-Seq, Illumina (f084) displays strongly associated clusters with p -values as low as 3.04e-89 that mapped as species Avian myeloblastosis-associated virus . Clusters that were annotated as NCBI species Parvovirus NIH/CQV were associated to laboratory-kit RNeasy MinElute, Qiagen (f076) with minimal p -value 5.48e-38. Finally, a cluster annotated as Acanthocystis turfacea chlorella virus MN0810.1 (ATCV) was associated to DNase/RNase: Promega DNase stop solution (f069) with p -value = 4.19e-12.

    Journal: Viruses

    Article Title: Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers

    doi: 10.3390/v8020053

    Figure Lengend Snippet: Lowest p -values of clusters established by the pipeline. The p -values are arranged by feature of the strongest significant association of each of the 6165 clusters. The 50 features involved as strongest associations have been coloured by type: biological (red), methodological (green), and technical (blue). The boxes span the first and third quartiles. The dark band inside each box represents the median. The whiskers of the boxes extend to the lowest and highest values within a distance of 1.5 times the interquartile range. As can be seen, most p -values were above 1e-24, but a few methodological features have associated clusters with very low p -values, such as f056, f068, f069, f076, f079, and f084. The library preparation kit ScriptSeq v2 RNA-Seq, Illumina (f084) displays strongly associated clusters with p -values as low as 3.04e-89 that mapped as species Avian myeloblastosis-associated virus . Clusters that were annotated as NCBI species Parvovirus NIH/CQV were associated to laboratory-kit RNeasy MinElute, Qiagen (f076) with minimal p -value 5.48e-38. Finally, a cluster annotated as Acanthocystis turfacea chlorella virus MN0810.1 (ATCV) was associated to DNase/RNase: Promega DNase stop solution (f069) with p -value = 4.19e-12.

    Article Snippet: The associated feature with lowest p -value to the parvovirus clusters suggested a contamination from the RNeasy MinElute purification kit (f076) manufactured by Qiagen (p -value: 5.48e-38).

    Techniques: RNA Sequencing Assay