Structured Review

Thermo Fisher rnaseq
Expression value distributions of different quantification methods for the same 258 samples. For each method, each gene's expression value was represented by the median value from the 258 samples. a) <t>Affymetrix</t> microarray analysis followed by RMA normalization method. b) Agilent microarray analysis followed by RMA normalization method. c) <t>RNAseq</t> analysis followed by the RPKM normalization method, the last bar represents genes with RPKM over 100. d) RNAseq analysis followed by the RSEM normalization method, the last bar represents genes with RSEM over 3000.
Rnaseq, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/rnaseq/product/Thermo Fisher
Average 99 stars, based on 5 article reviews
Price from $9.99 to $1999.99
rnaseq - by Bioz Stars, 2020-01
99/100 stars

Images

1) Product Images from "Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data"

Article Title: Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data

Journal: PLoS ONE

doi: 10.1371/journal.pone.0071462

Expression value distributions of different quantification methods for the same 258 samples. For each method, each gene's expression value was represented by the median value from the 258 samples. a) Affymetrix microarray analysis followed by RMA normalization method. b) Agilent microarray analysis followed by RMA normalization method. c) RNAseq analysis followed by the RPKM normalization method, the last bar represents genes with RPKM over 100. d) RNAseq analysis followed by the RSEM normalization method, the last bar represents genes with RSEM over 3000.
Figure Legend Snippet: Expression value distributions of different quantification methods for the same 258 samples. For each method, each gene's expression value was represented by the median value from the 258 samples. a) Affymetrix microarray analysis followed by RMA normalization method. b) Agilent microarray analysis followed by RMA normalization method. c) RNAseq analysis followed by the RPKM normalization method, the last bar represents genes with RPKM over 100. d) RNAseq analysis followed by the RSEM normalization method, the last bar represents genes with RSEM over 3000.

Techniques Used: Expressing, Microarray

Spearman correlation coefficient analysis between different quantification methods. For each comparison, the samples from the tumor dataset that were analyzed by the corresponding methods were extracted. For each sample, the Spearman correlation coefficient of the expression values from those methods was calculated. a) The comparison between the RPKM method and the RSEM method. The Spearman correlation coefficients were as high as around 0.94. b) The comparison between the Affymetrix method and the RPKM/RSEM method. The Spearman correlation coefficients were around 0.8. c) The comparison between the Agilent method and the RPKM/RSEM method. Since the Agilent method generated a ratio value for each gene but the RNAseq methods generated an absolute expression value for each gene, the Spearman correlation coefficients between the Agilent method and the RNAseq methods were as low as ∼0.2. d) The comparison between the Agilent method and the Affymetrix method. Since the Affymetrix method also generated an absolute expression value for each gene, the Spearman correlations were also as low as ∼0.2.
Figure Legend Snippet: Spearman correlation coefficient analysis between different quantification methods. For each comparison, the samples from the tumor dataset that were analyzed by the corresponding methods were extracted. For each sample, the Spearman correlation coefficient of the expression values from those methods was calculated. a) The comparison between the RPKM method and the RSEM method. The Spearman correlation coefficients were as high as around 0.94. b) The comparison between the Affymetrix method and the RPKM/RSEM method. The Spearman correlation coefficients were around 0.8. c) The comparison between the Agilent method and the RPKM/RSEM method. Since the Agilent method generated a ratio value for each gene but the RNAseq methods generated an absolute expression value for each gene, the Spearman correlation coefficients between the Agilent method and the RNAseq methods were as low as ∼0.2. d) The comparison between the Agilent method and the Affymetrix method. Since the Affymetrix method also generated an absolute expression value for each gene, the Spearman correlations were also as low as ∼0.2.

Techniques Used: Expressing, Generated

Fold-change consistency between the Agilent method and the RPKM method from 53 paired tumor-normal breast cancer samples. The common genes were divided into four groups based on their RNAseq expression value, and linear regression was performed to evaluate the fold-change consistency for each group. This indicates that the fold-change derived from genes with higher RNAseq expression was more concordant with the fold-change derived from microarray expression than the fold-change derived from genes with lower RNAseq expression.
Figure Legend Snippet: Fold-change consistency between the Agilent method and the RPKM method from 53 paired tumor-normal breast cancer samples. The common genes were divided into four groups based on their RNAseq expression value, and linear regression was performed to evaluate the fold-change consistency for each group. This indicates that the fold-change derived from genes with higher RNAseq expression was more concordant with the fold-change derived from microarray expression than the fold-change derived from genes with lower RNAseq expression.

Techniques Used: Expressing, Derivative Assay, Microarray

Differentially expressed gene concordance analysis using 53 paired tumor-normal breast cancer samples. a) The Spearman correlation coefficients of tumor/normal ratios between the Agilent method, the RPKM method and the RSEM method. b) Venn diagram summarizing the overlap between genes called as significantly differentially expressed (adjusted FDR less than 0.01 and fold-change larger than 2). The differentially expressed genes in Figure 3b were computed using commonly measured genes between microarray and RNAseq. c) Scatter plot of fold-change per gene as measured by the Agilent method and the RNAseq RPKM method. Genes identified as differentially expressed with consistent fold-change direction by both methods are plotted in green. Genes identified as differentially expressed with inconsistent fold change direction by both methods are plotted in red. Genes identified as differentially expressed by either RNAseq method or Agilent method are plotted in blue and yellow, respectively. Genes not identified as differentially expressed by either method are plotted in black. Only 1.2% genes identified as differentially expressed genes by both methods were inconsistent on the fold-change direction (red data).
Figure Legend Snippet: Differentially expressed gene concordance analysis using 53 paired tumor-normal breast cancer samples. a) The Spearman correlation coefficients of tumor/normal ratios between the Agilent method, the RPKM method and the RSEM method. b) Venn diagram summarizing the overlap between genes called as significantly differentially expressed (adjusted FDR less than 0.01 and fold-change larger than 2). The differentially expressed genes in Figure 3b were computed using commonly measured genes between microarray and RNAseq. c) Scatter plot of fold-change per gene as measured by the Agilent method and the RNAseq RPKM method. Genes identified as differentially expressed with consistent fold-change direction by both methods are plotted in green. Genes identified as differentially expressed with inconsistent fold change direction by both methods are plotted in red. Genes identified as differentially expressed by either RNAseq method or Agilent method are plotted in blue and yellow, respectively. Genes not identified as differentially expressed by either method are plotted in black. Only 1.2% genes identified as differentially expressed genes by both methods were inconsistent on the fold-change direction (red data).

Techniques Used: Microarray

2) Product Images from "Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data"

Article Title: Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data

Journal: PLoS ONE

doi: 10.1371/journal.pone.0071462

Expression value distributions of different quantification methods for the same 258 samples. For each method, each gene's expression value was represented by the median value from the 258 samples. a) Affymetrix microarray analysis followed by RMA normalization method. b) Agilent microarray analysis followed by RMA normalization method. c) RNAseq analysis followed by the RPKM normalization method, the last bar represents genes with RPKM over 100. d) RNAseq analysis followed by the RSEM normalization method, the last bar represents genes with RSEM over 3000.
Figure Legend Snippet: Expression value distributions of different quantification methods for the same 258 samples. For each method, each gene's expression value was represented by the median value from the 258 samples. a) Affymetrix microarray analysis followed by RMA normalization method. b) Agilent microarray analysis followed by RMA normalization method. c) RNAseq analysis followed by the RPKM normalization method, the last bar represents genes with RPKM over 100. d) RNAseq analysis followed by the RSEM normalization method, the last bar represents genes with RSEM over 3000.

Techniques Used: Expressing, Microarray

Spearman correlation coefficient analysis between different quantification methods. For each comparison, the samples from the tumor dataset that were analyzed by the corresponding methods were extracted. For each sample, the Spearman correlation coefficient of the expression values from those methods was calculated. a) The comparison between the RPKM method and the RSEM method. The Spearman correlation coefficients were as high as around 0.94. b) The comparison between the Affymetrix method and the RPKM/RSEM method. The Spearman correlation coefficients were around 0.8. c) The comparison between the Agilent method and the RPKM/RSEM method. Since the Agilent method generated a ratio value for each gene but the RNAseq methods generated an absolute expression value for each gene, the Spearman correlation coefficients between the Agilent method and the RNAseq methods were as low as ∼0.2. d) The comparison between the Agilent method and the Affymetrix method. Since the Affymetrix method also generated an absolute expression value for each gene, the Spearman correlations were also as low as ∼0.2.
Figure Legend Snippet: Spearman correlation coefficient analysis between different quantification methods. For each comparison, the samples from the tumor dataset that were analyzed by the corresponding methods were extracted. For each sample, the Spearman correlation coefficient of the expression values from those methods was calculated. a) The comparison between the RPKM method and the RSEM method. The Spearman correlation coefficients were as high as around 0.94. b) The comparison between the Affymetrix method and the RPKM/RSEM method. The Spearman correlation coefficients were around 0.8. c) The comparison between the Agilent method and the RPKM/RSEM method. Since the Agilent method generated a ratio value for each gene but the RNAseq methods generated an absolute expression value for each gene, the Spearman correlation coefficients between the Agilent method and the RNAseq methods were as low as ∼0.2. d) The comparison between the Agilent method and the Affymetrix method. Since the Affymetrix method also generated an absolute expression value for each gene, the Spearman correlations were also as low as ∼0.2.

Techniques Used: Expressing, Generated

Fold-change consistency between the Agilent method and the RPKM method from 53 paired tumor-normal breast cancer samples. The common genes were divided into four groups based on their RNAseq expression value, and linear regression was performed to evaluate the fold-change consistency for each group. This indicates that the fold-change derived from genes with higher RNAseq expression was more concordant with the fold-change derived from microarray expression than the fold-change derived from genes with lower RNAseq expression.
Figure Legend Snippet: Fold-change consistency between the Agilent method and the RPKM method from 53 paired tumor-normal breast cancer samples. The common genes were divided into four groups based on their RNAseq expression value, and linear regression was performed to evaluate the fold-change consistency for each group. This indicates that the fold-change derived from genes with higher RNAseq expression was more concordant with the fold-change derived from microarray expression than the fold-change derived from genes with lower RNAseq expression.

Techniques Used: Expressing, Derivative Assay, Microarray

Differentially expressed gene concordance analysis using 53 paired tumor-normal breast cancer samples. a) The Spearman correlation coefficients of tumor/normal ratios between the Agilent method, the RPKM method and the RSEM method. b) Venn diagram summarizing the overlap between genes called as significantly differentially expressed (adjusted FDR less than 0.01 and fold-change larger than 2). The differentially expressed genes in Figure 3b were computed using commonly measured genes between microarray and RNAseq. c) Scatter plot of fold-change per gene as measured by the Agilent method and the RNAseq RPKM method. Genes identified as differentially expressed with consistent fold-change direction by both methods are plotted in green. Genes identified as differentially expressed with inconsistent fold change direction by both methods are plotted in red. Genes identified as differentially expressed by either RNAseq method or Agilent method are plotted in blue and yellow, respectively. Genes not identified as differentially expressed by either method are plotted in black. Only 1.2% genes identified as differentially expressed genes by both methods were inconsistent on the fold-change direction (red data).
Figure Legend Snippet: Differentially expressed gene concordance analysis using 53 paired tumor-normal breast cancer samples. a) The Spearman correlation coefficients of tumor/normal ratios between the Agilent method, the RPKM method and the RSEM method. b) Venn diagram summarizing the overlap between genes called as significantly differentially expressed (adjusted FDR less than 0.01 and fold-change larger than 2). The differentially expressed genes in Figure 3b were computed using commonly measured genes between microarray and RNAseq. c) Scatter plot of fold-change per gene as measured by the Agilent method and the RNAseq RPKM method. Genes identified as differentially expressed with consistent fold-change direction by both methods are plotted in green. Genes identified as differentially expressed with inconsistent fold change direction by both methods are plotted in red. Genes identified as differentially expressed by either RNAseq method or Agilent method are plotted in blue and yellow, respectively. Genes not identified as differentially expressed by either method are plotted in black. Only 1.2% genes identified as differentially expressed genes by both methods were inconsistent on the fold-change direction (red data).

Techniques Used: Microarray

3) Product Images from "RNAseq reveals hypervirulence-specific host responses to M. tuberculosis infection"

Article Title: RNAseq reveals hypervirulence-specific host responses to M. tuberculosis infection

Journal: Virulence

doi: 10.1080/21505594.2016.1250994

qPCR based validation and corresponding secreted proteins of differentially expressed cytokines and chemokines in BMDM after M.tb infection. A. Relative mRNA expression (fold change) of various cytokines and chemokines induced by BMDMs following infection with hypo- and hypervirulent M.tb as analyzed through qPCR (n = 3). B. Corresponding heatmap as generated by RNAseq under the same infection conditions (Red-Upregulation, Green-downregulation). C and D. Corresponding secreted cytokines and chemokines in BMDMs under the same infection conditions as measured by ELISA (n = 6). The means and standard error of a minimum of 3 independent experiments are shown, * indicates significance p
Figure Legend Snippet: qPCR based validation and corresponding secreted proteins of differentially expressed cytokines and chemokines in BMDM after M.tb infection. A. Relative mRNA expression (fold change) of various cytokines and chemokines induced by BMDMs following infection with hypo- and hypervirulent M.tb as analyzed through qPCR (n = 3). B. Corresponding heatmap as generated by RNAseq under the same infection conditions (Red-Upregulation, Green-downregulation). C and D. Corresponding secreted cytokines and chemokines in BMDMs under the same infection conditions as measured by ELISA (n = 6). The means and standard error of a minimum of 3 independent experiments are shown, * indicates significance p

Techniques Used: Real-time Polymerase Chain Reaction, Infection, Expressing, Generated, Enzyme-linked Immunosorbent Assay

Virulence-specific gene expression confirmed through qPCR and Western blot in BMDM and THP-1 macrophages infected with hypo- and hypervirulent M.tb . A. Relative mRNA expression (fold change) of selected differentially expressed genes induced by BMDMs following infection with hypervirulent M.tb after 12 h of infection as analyzed through qPCR (n = 4). B. Corresponding heatmap as generated by RNAseq under the same infection conditions in BMDMs (Red-Upregulation, Green-downregulation), Rep = Replicate. C. Relative mRNA expression (fold change) of the same virulence-specific genes induced by THP-1s following infection with hypervirulent M.tb after 12 h of infection as analyzed through qPCR (n = 4). D. Western blot of corresponding proteins expressed by BMDMs and THP-1s under the same infection conditions, GAPDH was used as a loading control (n = 4), Uninf. = Uninfected BMDM and THP-1, Hypov.= Hypovirulent infection, Hyperv. = Hypervirulent infection. *p
Figure Legend Snippet: Virulence-specific gene expression confirmed through qPCR and Western blot in BMDM and THP-1 macrophages infected with hypo- and hypervirulent M.tb . A. Relative mRNA expression (fold change) of selected differentially expressed genes induced by BMDMs following infection with hypervirulent M.tb after 12 h of infection as analyzed through qPCR (n = 4). B. Corresponding heatmap as generated by RNAseq under the same infection conditions in BMDMs (Red-Upregulation, Green-downregulation), Rep = Replicate. C. Relative mRNA expression (fold change) of the same virulence-specific genes induced by THP-1s following infection with hypervirulent M.tb after 12 h of infection as analyzed through qPCR (n = 4). D. Western blot of corresponding proteins expressed by BMDMs and THP-1s under the same infection conditions, GAPDH was used as a loading control (n = 4), Uninf. = Uninfected BMDM and THP-1, Hypov.= Hypovirulent infection, Hyperv. = Hypervirulent infection. *p

Techniques Used: Expressing, Real-time Polymerase Chain Reaction, Western Blot, Infection, Generated

4) Product Images from "Analyses of Allele-Specific Gene Expression in Highly Divergent Mouse Crosses Identifies Pervasive Allelic Imbalance"

Article Title: Analyses of Allele-Specific Gene Expression in Highly Divergent Mouse Crosses Identifies Pervasive Allelic Imbalance

Journal: Nature genetics

doi: 10.1038/ng.3222

Diallel crossing scheme and sample sizes. We selected three divergent inbred strains representative of three subspecies within the Mus musculus species group. We generated offspring from all possible pairwise crosses to form a 3×3 diallel, including age- and sex-matched biological replicates for each of the nine possible genotypic combinations. Mice were aged to 23 days, sacrificed, and total RNA extracted from whole brain, liver, kidney, and lung. Sample size shown is for RNAseq (52 female, 39 male). RNAseq was performed on RNA extracted from brain and microarrays were run on RNA extracted from brain, liver, kidney, and lung.
Figure Legend Snippet: Diallel crossing scheme and sample sizes. We selected three divergent inbred strains representative of three subspecies within the Mus musculus species group. We generated offspring from all possible pairwise crosses to form a 3×3 diallel, including age- and sex-matched biological replicates for each of the nine possible genotypic combinations. Mice were aged to 23 days, sacrificed, and total RNA extracted from whole brain, liver, kidney, and lung. Sample size shown is for RNAseq (52 female, 39 male). RNAseq was performed on RNA extracted from brain and microarrays were run on RNA extracted from brain, liver, kidney, and lung.

Techniques Used: Generated, Mouse Assay

5) Product Images from "Activation and repression by oncogenic Myc shape tumour-specific gene expression profiles"

Article Title: Activation and repression by oncogenic Myc shape tumour-specific gene expression profiles

Journal: Nature

doi: 10.1038/nature13473

Binding of Myc to chromatin and Myc-dependent changes in gene expression in U2OS cells. a. Distribution of Myc tags around the TSS of all human Pol II genes with and without induction of exogenous MYC . b. Example of Myc-binding to a promoter and an intragenic enhancer. Enhancers are identified by the presence of H3K4me1 and H3K27Ac and the absence of H3K4me3. Exons are indicated as vertical bars, the UTR shown as a thick black line. c. Heat map documenting binding of Myc to all enhancers identified in U2OS cells. Enhancer positions are centered according to Myc occupancy within a window of +/-1 kb of the centre of the enhancer region and are sorted according to the number of H3K4me1 tags. d. The diagram shows the Myc-induced change in expression (plotted as log 2 FC) versus total expression levels for all genes found in the RNAseq as determined by RNA-sequencing. Red colour indicates significantly regulated genes (q
Figure Legend Snippet: Binding of Myc to chromatin and Myc-dependent changes in gene expression in U2OS cells. a. Distribution of Myc tags around the TSS of all human Pol II genes with and without induction of exogenous MYC . b. Example of Myc-binding to a promoter and an intragenic enhancer. Enhancers are identified by the presence of H3K4me1 and H3K27Ac and the absence of H3K4me3. Exons are indicated as vertical bars, the UTR shown as a thick black line. c. Heat map documenting binding of Myc to all enhancers identified in U2OS cells. Enhancer positions are centered according to Myc occupancy within a window of +/-1 kb of the centre of the enhancer region and are sorted according to the number of H3K4me1 tags. d. The diagram shows the Myc-induced change in expression (plotted as log 2 FC) versus total expression levels for all genes found in the RNAseq as determined by RNA-sequencing. Red colour indicates significantly regulated genes (q

Techniques Used: Binding Assay, Expressing, RNA Sequencing Assay

6) Product Images from "Evidence for Direct Control of Virulence and Defense Gene Circuits by the Pseudomonas aeruginosa Quorum Sensing Regulator, MvfR"

Article Title: Evidence for Direct Control of Virulence and Defense Gene Circuits by the Pseudomonas aeruginosa Quorum Sensing Regulator, MvfR

Journal: Scientific Reports

doi: 10.1038/srep34083

MvfR generates a positive feedback loop by binding to and inducing the small RNA PhrS. ( a ) ChIPseq analysis reveals that MvfR binds to phrS region. The black bar above the binding intensity plots represents the peak identified using SPP peak caller. ( b ) RNAseq analysis indicates that MvfR induces the expression of phrS . Light blue bar = mvfR mutant at OD 600nm 2, dark blue bar = mvfR mutant at OD 600nm 3. ( c ) qRTPCR analysis validates that MvfR induces the expression of phrS . Faint blue bar = mvfR mutant at OD 600nm 1, light blue bar = mvfR mutant at OD 600nm 2. Data show the average +/− SEM of 3 independent replicates. Statistical significance was assessed using one way ANOVA + Dunnett’s post-test.
Figure Legend Snippet: MvfR generates a positive feedback loop by binding to and inducing the small RNA PhrS. ( a ) ChIPseq analysis reveals that MvfR binds to phrS region. The black bar above the binding intensity plots represents the peak identified using SPP peak caller. ( b ) RNAseq analysis indicates that MvfR induces the expression of phrS . Light blue bar = mvfR mutant at OD 600nm 2, dark blue bar = mvfR mutant at OD 600nm 3. ( c ) qRTPCR analysis validates that MvfR induces the expression of phrS . Faint blue bar = mvfR mutant at OD 600nm 1, light blue bar = mvfR mutant at OD 600nm 2. Data show the average +/− SEM of 3 independent replicates. Statistical significance was assessed using one way ANOVA + Dunnett’s post-test.

Techniques Used: Binding Assay, Expressing, Mutagenesis

7) Product Images from "NT5E/CD73 as Correlative Factor of Patient Survival and Natural Killer Cell Infiltration in Glioblastoma"

Article Title: NT5E/CD73 as Correlative Factor of Patient Survival and Natural Killer Cell Infiltration in Glioblastoma

Journal: Journal of Clinical Medicine

doi: 10.3390/jcm8101526

Survival analysis in the context of NT5E and natural killer (NK) gene signature expression. ( A ) Expression of NT5E in GBM patient samples plotted on the basis of patient vital status. Analysis was done in R2 ( n = 540). ( B ) Disease-free survival of GBM patients on the basis of NT5E expression level from TCGA RNASeq V2 RSEM data ( p = 0.0039; z = 2; left ; n = 166); NK gene signatures comprising 13 NK-specific genes from U133 Affymetrix gene expression data ( p = 0.0285; middle panel ); and both NT5E and NK gene signatures from U133 Affymetrix gene expression data ( p = 0.0109; right ). Kaplan–Meier plots were generated in cBioPortal ( n = 533). ( C ) Overall survival of GBM patients with the mesenchymal subtype based on NT5E expression. Analysis was done in GEPIA2 ( n = 163). ( D ) Overall survival stratified by risk group for patients expressing NT5E and ADORA2A . Analysis was done in R2.
Figure Legend Snippet: Survival analysis in the context of NT5E and natural killer (NK) gene signature expression. ( A ) Expression of NT5E in GBM patient samples plotted on the basis of patient vital status. Analysis was done in R2 ( n = 540). ( B ) Disease-free survival of GBM patients on the basis of NT5E expression level from TCGA RNASeq V2 RSEM data ( p = 0.0039; z = 2; left ; n = 166); NK gene signatures comprising 13 NK-specific genes from U133 Affymetrix gene expression data ( p = 0.0285; middle panel ); and both NT5E and NK gene signatures from U133 Affymetrix gene expression data ( p = 0.0109; right ). Kaplan–Meier plots were generated in cBioPortal ( n = 533). ( C ) Overall survival of GBM patients with the mesenchymal subtype based on NT5E expression. Analysis was done in GEPIA2 ( n = 163). ( D ) Overall survival stratified by risk group for patients expressing NT5E and ADORA2A . Analysis was done in R2.

Techniques Used: Expressing, Generated

8) Product Images from "Reductions in hypothalamic Gfap expression, glial cells and α-tanycytes in lean and hypermetabolic Gnasxl-deficient mice"

Article Title: Reductions in hypothalamic Gfap expression, glial cells and α-tanycytes in lean and hypermetabolic Gnasxl-deficient mice

Journal: Molecular Brain

doi: 10.1186/s13041-016-0219-1

Reduced Gfap RNA expression levels in Gnasxl m+/p- hypothalami. A similar 2-fold down-regulation of Gfap RNA levels was found by RNAseq and qRT-PCR in Gnasxl knock-out hypothalami (*** p
Figure Legend Snippet: Reduced Gfap RNA expression levels in Gnasxl m+/p- hypothalami. A similar 2-fold down-regulation of Gfap RNA levels was found by RNAseq and qRT-PCR in Gnasxl knock-out hypothalami (*** p

Techniques Used: RNA Expression, Quantitative RT-PCR, Knock-Out

Related Articles

Amplification:

Article Title: Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant
Article Snippet: Ribosomal RNA was twice subtracted from total RNA with the RiboMinus Plant Kit for RNAseq (Invitrogen, Carlsbad, CA, USA). .. A cDNA library template was constructed, fragmented, and gel-purified, and the resulting 250 bp average fragments were amplified, according to Illumina (San Diego, CA, USA) protocols.

Article Title: Activation and repression by oncogenic Myc shape tumour-specific gene expression profiles
Article Snippet: For RNAseq in U2OS cells, PolyA+ -RNA was isolated from total with Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific). .. First and second strand synthesis was performed and the resulting cDNA was end-repaired, ligated to NEBnext Adaptor, size selected (250bps) and purified with Qiagen gel extraction kit. cDNA was then amplified with 15 cycle of PCR and the resulting library was subjected to Illumina GAIIx sequencing according to the manufacturer instructions.

Synthesized:

Article Title: The extracellular matrix proteoglycan lumican improves survival and counteracts cardiac dilatation and failure in mice subjected to pressure overload
Article Snippet: Gene expression analysis Total RNA was extracted, cDNA synthesized and Fast Real Time PCR System or dd-PCR was performed. .. RNAseq was performed as described , on total RNA extracted from LV tissue using Trizol (Thermo Scientific).

Construct:

Article Title: Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant
Article Snippet: Ribosomal RNA was twice subtracted from total RNA with the RiboMinus Plant Kit for RNAseq (Invitrogen, Carlsbad, CA, USA). .. A cDNA library template was constructed, fragmented, and gel-purified, and the resulting 250 bp average fragments were amplified, according to Illumina (San Diego, CA, USA) protocols.

SYBR Green Assay:

Article Title: Evidence for Direct Control of Virulence and Defense Gene Circuits by the Pseudomonas aeruginosa Quorum Sensing Regulator, MvfR
Article Snippet: qRT-PCR RNA samples were prepared as described above for RNAseq. cDNA was generated by RT-PCR using Superscript III First-Strand kit (Invitrogen) according to manufacturer’s instructions. .. Quantitative PCR was performed using Brilliant II SYBR Green QPCR Master Mix (Stratagene) as in with a Mx3005P qPCR machine (Stratagene).

Article Title: Reductions in hypothalamic Gfap expression, glial cells and α-tanycytes in lean and hypermetabolic Gnasxl-deficient mice
Article Snippet: .. qRT-PCR Quantitative RT-PCR was carried out on the same three pooled WT and three pooled Gnasxl m+/p- total RNA samples that had been used for the RNAseq experiments. cDNA was synthesised using MMLV Reverse Transcriptase (Life Technologies) and real-time PCR was performed using the Brilliant II SYBR Green QPCR Master Mix with Low Rox (Agilent Technologies) on an Applied Biosystems 7500 Fast Real‐Time PCR System. .. Relative quantification was calculated through normalisation to two housekeeping genes, β-Actin (Actb) and Cyclophilin A (Ppia ), using the Applied Biosystems 7500 software.

Microarray:

Article Title: Analyses of Allele-Specific Gene Expression in Highly Divergent Mouse Crosses Identifies Pervasive Allelic Imbalance
Article Snippet: .. Microarray: processing and QC Brain, liver, kidney and lung RNA from the same mice used for RNAseq were hybridized to Affymetrix Mouse Gene 1.1 ST 96-Array Plate arrays using a GeneTitan instrument from Affymetrix according to the manufacturer’s protocols. .. We used robust multiarray average method (RMA) implemented in the Affymetrix gene expression console with default settings (median polish and sketch-quantile normalization) to estimate normalized expression levels of transcripts.

Article Title: NT5E/CD73 as Correlative Factor of Patient Survival and Natural Killer Cell Infiltration in Glioblastoma
Article Snippet: .. A z-value threshold was set to 2 in cBioportal for RNASeq (V2, RSEM) data and 1 for U133 Affymetrix microarray data. .. Determination of Tumor-Infiltrating Natural Killer Cells Level 3 TCGA RNAseq data, mapped to the human genome and collected from the Affymetrix HT Human Genome U133a microarray platform, were extracted.

Article Title: Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data
Article Snippet: The overlap between Agilent and Affymetrix arrays was 1134 samples, the overlap between the Agilent array and RNAseq was 1662 samples, and the overlap between Affymetrix array and RNAseq was 699 samples. describes the detailed sample distributions between technologies and cancer types. .. Level 3 released gene level expression data for microarray, gene and exon level expression data for RNAseq were downloaded for 14 cancers from TCGA.

Article Title: Whole-transcriptome brain expression and exon-usage profiling in major depression and suicide: evidence for altered glial, endothelial and ATPase activity
Article Snippet: Paragraph title: Confirmation of differential expression results using available microarray data and qPCR ... There were 23 total genes identified by RNAseq , all having greater expression in CON vs. MDD-S, that were also included on the Affymetrix U133A platform.

Quantitation Assay:

Article Title: Comparative sequence analysis reveals regulation of genes in developing schistosomula of Schistosoma mansoni exposed to host portal serum
Article Snippet: The rRNA was depleted using RiboMinus Eukaryote Kit for RNAseq (Invitrogen, cat10837-08). .. Quantitation of mRNA was assessed by using a Qubit 2.0 Fluorometer (Life Technologies catQ32866) and a Qubit RNA Assay Kit (Invitrogen catQ32852) for RNA samples, according to the protocol recommended by the manufacturer.

Expressing:

Article Title: Analyses of Allele-Specific Gene Expression in Highly Divergent Mouse Crosses Identifies Pervasive Allelic Imbalance
Article Snippet: Microarray: processing and QC Brain, liver, kidney and lung RNA from the same mice used for RNAseq were hybridized to Affymetrix Mouse Gene 1.1 ST 96-Array Plate arrays using a GeneTitan instrument from Affymetrix according to the manufacturer’s protocols. .. We used robust multiarray average method (RMA) implemented in the Affymetrix gene expression console with default settings (median polish and sketch-quantile normalization) to estimate normalized expression levels of transcripts.

Article Title: Genomic signatures defining responsiveness to allopurinol and combination therapy for lung cancer identified by systems therapeutics analyses
Article Snippet: .. Then, among models with highest sensitivity score and positive for RAS mutation, we selected a model for validation as an allopurinol‐sensitive model using RNAseq and Affymetrix hg10st gene expression data (TM0153 model and TM00206 model, respectively). .. Among models with highest resistance score and negative for RAS mutation, we selected a model for validation as an allopurinol‐resistant model using Affymetrix hg10st gene expression data (TM00188).

Article Title: NT5E/CD73 as Correlative Factor of Patient Survival and Natural Killer Cell Infiltration in Glioblastoma
Article Snippet: Paragraph title: 2.3. Survival Analysis Based on Gene Expression Data ... A z-value threshold was set to 2 in cBioportal for RNASeq (V2, RSEM) data and 1 for U133 Affymetrix microarray data.

Article Title: Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data
Article Snippet: Out of 4747 samples, 2250 were expression profiled using Agilent G450A_07 arrays, 1269 were expression profiled using Affymetrix HT_U133 arrays, and 4064 were expression profiled using RNAseq. .. The overlap between Agilent and Affymetrix arrays was 1134 samples, the overlap between the Agilent array and RNAseq was 1662 samples, and the overlap between Affymetrix array and RNAseq was 699 samples. describes the detailed sample distributions between technologies and cancer types.

Article Title: RNAi screens in mice identify physiological regulators of oncogenic growth
Article Snippet: RNAseq and IPA network analyses Epidermal progenitors were FACS sorted into TrizolLS (Invitrogen) and RNA was purified using Direct-zol RNA MiniPrep kit (Zymo Research) per manufacturer’s instructions. .. Reads were mapped to mm9 build of the mouse genome using TopHat, and transcript assembly and differential expression were determined using Cufflinks .

Article Title: Activation and repression by oncogenic Myc shape tumour-specific gene expression profiles
Article Snippet: Paragraph title: Q-PCRs (RT und ChIP) and global gene expression analysis ... For RNAseq in U2OS cells, PolyA+ -RNA was isolated from total with Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific).

Article Title: Evidence for Direct Control of Virulence and Defense Gene Circuits by the Pseudomonas aeruginosa Quorum Sensing Regulator, MvfR
Article Snippet: qRT-PCR RNA samples were prepared as described above for RNAseq. cDNA was generated by RT-PCR using Superscript III First-Strand kit (Invitrogen) according to manufacturer’s instructions. .. RpoD expression was used as a reference gene as described in .

Article Title: Whole-transcriptome brain expression and exon-usage profiling in major depression and suicide: evidence for altered glial, endothelial and ATPase activity
Article Snippet: .. There were 23 total genes identified by RNAseq , all having greater expression in CON vs. MDD-S, that were also included on the Affymetrix U133A platform. ..

Article Title: Identification of 19 new risk loci and potential regulatory mechanisms influencing susceptibility to testicular germ cell tumor
Article Snippet: .. We investigated for evidence of association between the SNPs at each locus and tissue specific changes in gene expression using two publically available resources: (i) RNAseq and Affymetrix 6.0 SNP data for 150 TGCT patients from The Cancer Genome Atlas and (ii) normal testicular tissue data from GTEx from 157 samples . ..

Article Title: The extracellular matrix proteoglycan lumican improves survival and counteracts cardiac dilatation and failure in mice subjected to pressure overload
Article Snippet: Paragraph title: Gene expression analysis ... RNAseq was performed as described , on total RNA extracted from LV tissue using Trizol (Thermo Scientific).

Infection:

Article Title: RNAseq reveals hypervirulence-specific host responses to M. tuberculosis infection
Article Snippet: RNA extraction and mRNA enrichment Total RNA from BMDM and THP-1 cells were extracted using the RNeasy® Plus Mini Kit (Cat. No. 74134, Qiagen, Limburg, Netherlands) according to the manufacturer's instructions immediately following the 12 h infection period. .. Only RNA with a RNA integrity Number (RIN) above 9.0 were used for RNAseq and qPCR experiments. mRNA enrichment was achieved using the Dynabeads® mRNA DIRECT™ Kit (Cat. No. 61012, Ambion, Life Technologies, Oslo, Norway) according to the manufacturer's instructions.

Reverse Transcription Polymerase Chain Reaction:

Article Title: Evidence for Direct Control of Virulence and Defense Gene Circuits by the Pseudomonas aeruginosa Quorum Sensing Regulator, MvfR
Article Snippet: .. qRT-PCR RNA samples were prepared as described above for RNAseq. cDNA was generated by RT-PCR using Superscript III First-Strand kit (Invitrogen) according to manufacturer’s instructions. ..

Indirect Immunoperoxidase Assay:

Article Title: RNAi screens in mice identify physiological regulators of oncogenic growth
Article Snippet: .. RNAseq and IPA network analyses Epidermal progenitors were FACS sorted into TrizolLS (Invitrogen) and RNA was purified using Direct-zol RNA MiniPrep kit (Zymo Research) per manufacturer’s instructions. .. Quality of the RNA was determined using Agilent 2100 Bioanalyzer, with all samples passing the quality threshold of RNA integrity numbers (RIN) > 8.

Generated:

Article Title: NT5E/CD73 as Correlative Factor of Patient Survival and Natural Killer Cell Infiltration in Glioblastoma
Article Snippet: Kaplan–Meier curves were generated with a median survival cutoff. .. A z-value threshold was set to 2 in cBioportal for RNASeq (V2, RSEM) data and 1 for U133 Affymetrix microarray data.

Article Title: Activation and repression by oncogenic Myc shape tumour-specific gene expression profiles
Article Snippet: Raw data were generated using the Feature Extraction software v10.1.1.1 from Agilent. .. For RNAseq in U2OS cells, PolyA+ -RNA was isolated from total with Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific).

Article Title: Evidence for Direct Control of Virulence and Defense Gene Circuits by the Pseudomonas aeruginosa Quorum Sensing Regulator, MvfR
Article Snippet: .. qRT-PCR RNA samples were prepared as described above for RNAseq. cDNA was generated by RT-PCR using Superscript III First-Strand kit (Invitrogen) according to manufacturer’s instructions. ..

Sequencing:

Article Title: Activation and repression by oncogenic Myc shape tumour-specific gene expression profiles
Article Snippet: For RNAseq in U2OS cells, PolyA+ -RNA was isolated from total with Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific). .. First and second strand synthesis was performed and the resulting cDNA was end-repaired, ligated to NEBnext Adaptor, size selected (250bps) and purified with Qiagen gel extraction kit. cDNA was then amplified with 15 cycle of PCR and the resulting library was subjected to Illumina GAIIx sequencing according to the manufacturer instructions.

Hi-C:

Article Title: Identification of 19 new risk loci and potential regulatory mechanisms influencing susceptibility to testicular germ cell tumor
Article Snippet: We investigated for evidence of association between the SNPs at each locus and tissue specific changes in gene expression using two publically available resources: (i) RNAseq and Affymetrix 6.0 SNP data for 150 TGCT patients from The Cancer Genome Atlas and (ii) normal testicular tissue data from GTEx from 157 samples . .. To reduce multiple testing, association tests were only performed between SNP and gene pairs where either: (i) a direct promoter variant was observed (as per column six of ) or (ii) a Hi-C contact to a gene promoter was observed (as per column nine of ), together with functionally active chromatin (as per column seven of ).

RNA Sequencing Assay:

Article Title: Whole-transcriptome brain expression and exon-usage profiling in major depression and suicide: evidence for altered glial, endothelial and ATPase activity
Article Snippet: There were 23 total genes identified by RNAseq , all having greater expression in CON vs. MDD-S, that were also included on the Affymetrix U133A platform. .. Consistent with our RNA-seq findings, the majority of genes (17/23) had greater mean expression in the CON vs. MDD-S group (sign-test p=0.03, see ).

Mutagenesis:

Article Title: Genomic signatures defining responsiveness to allopurinol and combination therapy for lung cancer identified by systems therapeutics analyses
Article Snippet: .. Then, among models with highest sensitivity score and positive for RAS mutation, we selected a model for validation as an allopurinol‐sensitive model using RNAseq and Affymetrix hg10st gene expression data (TM0153 model and TM00206 model, respectively). .. Among models with highest resistance score and negative for RAS mutation, we selected a model for validation as an allopurinol‐resistant model using Affymetrix hg10st gene expression data (TM00188).

Isolation:

Article Title: Activation and repression by oncogenic Myc shape tumour-specific gene expression profiles
Article Snippet: .. For RNAseq in U2OS cells, PolyA+ -RNA was isolated from total with Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific). .. Library preparation was performed by using the NEBnext® mRNA Library Prep Master Mix set for Illumina (E6100S/L) following the instruction manual.

Article Title: Comparative sequence analysis reveals regulation of genes in developing schistosomula of Schistosoma mansoni exposed to host portal serum
Article Snippet: Total RNA extraction and isolation was performed with TRIzol Reagent (Invitrogen, cat15596-026) and, RNeasy (Qiagen, cat74106), with a final treatment with DNAse Turbo (Ambion, catAM1907), all according to the procedures recommended by manufactures. .. The rRNA was depleted using RiboMinus Eukaryote Kit for RNAseq (Invitrogen, cat10837-08).

Mouse Assay:

Article Title: Analyses of Allele-Specific Gene Expression in Highly Divergent Mouse Crosses Identifies Pervasive Allelic Imbalance
Article Snippet: .. Microarray: processing and QC Brain, liver, kidney and lung RNA from the same mice used for RNAseq were hybridized to Affymetrix Mouse Gene 1.1 ST 96-Array Plate arrays using a GeneTitan instrument from Affymetrix according to the manufacturer’s protocols. .. We used robust multiarray average method (RMA) implemented in the Affymetrix gene expression console with default settings (median polish and sketch-quantile normalization) to estimate normalized expression levels of transcripts.

Polymerase Chain Reaction:

Article Title: Activation and repression by oncogenic Myc shape tumour-specific gene expression profiles
Article Snippet: For RNAseq in U2OS cells, PolyA+ -RNA was isolated from total with Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific). .. First and second strand synthesis was performed and the resulting cDNA was end-repaired, ligated to NEBnext Adaptor, size selected (250bps) and purified with Qiagen gel extraction kit. cDNA was then amplified with 15 cycle of PCR and the resulting library was subjected to Illumina GAIIx sequencing according to the manufacturer instructions.

Quantitative RT-PCR:

Article Title: Evidence for Direct Control of Virulence and Defense Gene Circuits by the Pseudomonas aeruginosa Quorum Sensing Regulator, MvfR
Article Snippet: .. qRT-PCR RNA samples were prepared as described above for RNAseq. cDNA was generated by RT-PCR using Superscript III First-Strand kit (Invitrogen) according to manufacturer’s instructions. ..

Article Title: Reductions in hypothalamic Gfap expression, glial cells and α-tanycytes in lean and hypermetabolic Gnasxl-deficient mice
Article Snippet: .. qRT-PCR Quantitative RT-PCR was carried out on the same three pooled WT and three pooled Gnasxl m+/p- total RNA samples that had been used for the RNAseq experiments. cDNA was synthesised using MMLV Reverse Transcriptase (Life Technologies) and real-time PCR was performed using the Brilliant II SYBR Green QPCR Master Mix with Low Rox (Agilent Technologies) on an Applied Biosystems 7500 Fast Real‐Time PCR System. .. Relative quantification was calculated through normalisation to two housekeeping genes, β-Actin (Actb) and Cyclophilin A (Ppia ), using the Applied Biosystems 7500 software.

Gel Extraction:

Article Title: Activation and repression by oncogenic Myc shape tumour-specific gene expression profiles
Article Snippet: For RNAseq in U2OS cells, PolyA+ -RNA was isolated from total with Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific). .. First and second strand synthesis was performed and the resulting cDNA was end-repaired, ligated to NEBnext Adaptor, size selected (250bps) and purified with Qiagen gel extraction kit. cDNA was then amplified with 15 cycle of PCR and the resulting library was subjected to Illumina GAIIx sequencing according to the manufacturer instructions.

cDNA Library Assay:

Article Title: Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant
Article Snippet: Ribosomal RNA was twice subtracted from total RNA with the RiboMinus Plant Kit for RNAseq (Invitrogen, Carlsbad, CA, USA). .. A cDNA library template was constructed, fragmented, and gel-purified, and the resulting 250 bp average fragments were amplified, according to Illumina (San Diego, CA, USA) protocols.

Purification:

Article Title: RNAi screens in mice identify physiological regulators of oncogenic growth
Article Snippet: .. RNAseq and IPA network analyses Epidermal progenitors were FACS sorted into TrizolLS (Invitrogen) and RNA was purified using Direct-zol RNA MiniPrep kit (Zymo Research) per manufacturer’s instructions. .. Quality of the RNA was determined using Agilent 2100 Bioanalyzer, with all samples passing the quality threshold of RNA integrity numbers (RIN) > 8.

Article Title: Activation and repression by oncogenic Myc shape tumour-specific gene expression profiles
Article Snippet: For RNAseq in U2OS cells, PolyA+ -RNA was isolated from total with Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific). .. First and second strand synthesis was performed and the resulting cDNA was end-repaired, ligated to NEBnext Adaptor, size selected (250bps) and purified with Qiagen gel extraction kit. cDNA was then amplified with 15 cycle of PCR and the resulting library was subjected to Illumina GAIIx sequencing according to the manufacturer instructions.

Chromatin Immunoprecipitation:

Article Title: Activation and repression by oncogenic Myc shape tumour-specific gene expression profiles
Article Snippet: Paragraph title: Q-PCRs (RT und ChIP) and global gene expression analysis ... For RNAseq in U2OS cells, PolyA+ -RNA was isolated from total with Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific).

Plasmid Preparation:

Article Title: Activation and repression by oncogenic Myc shape tumour-specific gene expression profiles
Article Snippet: Microarrays were carried out in technical duplicates for shMyc and in triplicates for empty vector. .. For RNAseq in U2OS cells, PolyA+ -RNA was isolated from total with Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific).

Software:

Article Title: Activation and repression by oncogenic Myc shape tumour-specific gene expression profiles
Article Snippet: Raw data were generated using the Feature Extraction software v10.1.1.1 from Agilent. .. For RNAseq in U2OS cells, PolyA+ -RNA was isolated from total with Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific).

Article Title: Reductions in hypothalamic Gfap expression, glial cells and α-tanycytes in lean and hypermetabolic Gnasxl-deficient mice
Article Snippet: qRT-PCR Quantitative RT-PCR was carried out on the same three pooled WT and three pooled Gnasxl m+/p- total RNA samples that had been used for the RNAseq experiments. cDNA was synthesised using MMLV Reverse Transcriptase (Life Technologies) and real-time PCR was performed using the Brilliant II SYBR Green QPCR Master Mix with Low Rox (Agilent Technologies) on an Applied Biosystems 7500 Fast Real‐Time PCR System. .. Relative quantification was calculated through normalisation to two housekeeping genes, β-Actin (Actb) and Cyclophilin A (Ppia ), using the Applied Biosystems 7500 software.

Real-time Polymerase Chain Reaction:

Article Title: RNAseq reveals hypervirulence-specific host responses to M. tuberculosis infection
Article Snippet: .. Only RNA with a RNA integrity Number (RIN) above 9.0 were used for RNAseq and qPCR experiments. mRNA enrichment was achieved using the Dynabeads® mRNA DIRECT™ Kit (Cat. No. 61012, Ambion, Life Technologies, Oslo, Norway) according to the manufacturer's instructions. ..

Article Title: Evidence for Direct Control of Virulence and Defense Gene Circuits by the Pseudomonas aeruginosa Quorum Sensing Regulator, MvfR
Article Snippet: qRT-PCR RNA samples were prepared as described above for RNAseq. cDNA was generated by RT-PCR using Superscript III First-Strand kit (Invitrogen) according to manufacturer’s instructions. .. Quantitative PCR was performed using Brilliant II SYBR Green QPCR Master Mix (Stratagene) as in with a Mx3005P qPCR machine (Stratagene).

Article Title: Reductions in hypothalamic Gfap expression, glial cells and α-tanycytes in lean and hypermetabolic Gnasxl-deficient mice
Article Snippet: .. qRT-PCR Quantitative RT-PCR was carried out on the same three pooled WT and three pooled Gnasxl m+/p- total RNA samples that had been used for the RNAseq experiments. cDNA was synthesised using MMLV Reverse Transcriptase (Life Technologies) and real-time PCR was performed using the Brilliant II SYBR Green QPCR Master Mix with Low Rox (Agilent Technologies) on an Applied Biosystems 7500 Fast Real‐Time PCR System. .. Relative quantification was calculated through normalisation to two housekeeping genes, β-Actin (Actb) and Cyclophilin A (Ppia ), using the Applied Biosystems 7500 software.

Article Title: Whole-transcriptome brain expression and exon-usage profiling in major depression and suicide: evidence for altered glial, endothelial and ATPase activity
Article Snippet: Paragraph title: Confirmation of differential expression results using available microarray data and qPCR ... There were 23 total genes identified by RNAseq , all having greater expression in CON vs. MDD-S, that were also included on the Affymetrix U133A platform.

Article Title: The extracellular matrix proteoglycan lumican improves survival and counteracts cardiac dilatation and failure in mice subjected to pressure overload
Article Snippet: Gene expression analysis Total RNA was extracted, cDNA synthesized and Fast Real Time PCR System or dd-PCR was performed. .. RNAseq was performed as described , on total RNA extracted from LV tissue using Trizol (Thermo Scientific).

RNA Extraction:

Article Title: RNAseq reveals hypervirulence-specific host responses to M. tuberculosis infection
Article Snippet: Paragraph title: RNA extraction and mRNA enrichment ... Only RNA with a RNA integrity Number (RIN) above 9.0 were used for RNAseq and qPCR experiments. mRNA enrichment was achieved using the Dynabeads® mRNA DIRECT™ Kit (Cat. No. 61012, Ambion, Life Technologies, Oslo, Norway) according to the manufacturer's instructions.

Article Title: Comparative sequence analysis reveals regulation of genes in developing schistosomula of Schistosoma mansoni exposed to host portal serum
Article Snippet: Paragraph title: RNA extraction and rRNA depletion ... The rRNA was depleted using RiboMinus Eukaryote Kit for RNAseq (Invitrogen, cat10837-08).

Sample Prep:

Article Title: RNAi screens in mice identify physiological regulators of oncogenic growth
Article Snippet: RNAseq and IPA network analyses Epidermal progenitors were FACS sorted into TrizolLS (Invitrogen) and RNA was purified using Direct-zol RNA MiniPrep kit (Zymo Research) per manufacturer’s instructions. .. Library preparation using Illumina TrueSeq mRNA sample preparation kit was performed at the Weill Cornell Medical College Genomic Core facility, and cDNA was sequenced on Illumina HiSeq 2000.

Electrophoresis:

Article Title: Comparative sequence analysis reveals regulation of genes in developing schistosomula of Schistosoma mansoni exposed to host portal serum
Article Snippet: The rRNA was depleted using RiboMinus Eukaryote Kit for RNAseq (Invitrogen, cat10837-08). .. Before rRNA depletion, mRNA quality was verified by measuring rRNA integrity through capillary electrophoresis in a Bioanalyzer 2100 (Agilent, catG2939AA), employing RNA 6000 Pico Reagents (Agilent, cat5067-1514).

FACS:

Article Title: RNAi screens in mice identify physiological regulators of oncogenic growth
Article Snippet: .. RNAseq and IPA network analyses Epidermal progenitors were FACS sorted into TrizolLS (Invitrogen) and RNA was purified using Direct-zol RNA MiniPrep kit (Zymo Research) per manufacturer’s instructions. .. Quality of the RNA was determined using Agilent 2100 Bioanalyzer, with all samples passing the quality threshold of RNA integrity numbers (RIN) > 8.

Variant Assay:

Article Title: Identification of 19 new risk loci and potential regulatory mechanisms influencing susceptibility to testicular germ cell tumor
Article Snippet: We investigated for evidence of association between the SNPs at each locus and tissue specific changes in gene expression using two publically available resources: (i) RNAseq and Affymetrix 6.0 SNP data for 150 TGCT patients from The Cancer Genome Atlas and (ii) normal testicular tissue data from GTEx from 157 samples . .. To reduce multiple testing, association tests were only performed between SNP and gene pairs where either: (i) a direct promoter variant was observed (as per column six of ) or (ii) a Hi-C contact to a gene promoter was observed (as per column nine of ), together with functionally active chromatin (as per column seven of ).

Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 90
    Thermo Fisher rnase t1
    Rnase T1, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rnase t1/product/Thermo Fisher
    Average 90 stars, based on 16 article reviews
    Price from $9.99 to $1999.99
    rnase t1 - by Bioz Stars, 2020-01
    90/100 stars
      Buy from Supplier

    90
    Thermo Fisher ribolock rnase inhibitor
    Ribolock Rnase Inhibitor, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 90 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ribolock rnase inhibitor/product/Thermo Fisher
    Average 90 stars, based on 90 article reviews
    Price from $9.99 to $1999.99
    ribolock rnase inhibitor - by Bioz Stars, 2020-01
    90/100 stars
      Buy from Supplier

    N/A
    RNase1 Polyclonal Antibody for Western Blot IP ELISA DB
      Buy from Supplier

    Image Search Results