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  • 94
    Worthington Biochemical rna seq
    Rna Seq, supplied by Worthington Biochemical, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna seq/product/Worthington Biochemical
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    99
    Millipore rna seq
    Reverse transcription quantitative <t>PCR</t> validation of <t>RNA-seq</t> data. Eight target genes and five potential reference genes were selected for reverse transcription quantitative PCR (RT-qPCR) (supplemental data set 13). RNA was extracted from Psa grown in vitro (IV) infected ‘Hort16A’ plantlets at 2, 24 and 72 h post infection (HPI). RT-qPCR values (three biological replicates) were based on normalisation against the geometric average/mean of three reference genes (IYO_010670, IYO_009010 and IYO_002170) selected using Bestkeeper and geNorm analysis [ 69 , 70 ]. For comparison with the RNA-seq data, values were displayed by representing maximum expression of each gene as 100. Pearson correlation coefficients (r) > 0.5 between the RT-qPCR and RNA-seq data are displayed all primers are listed in supplemental data set 13. RT-qPCR data is represented by black bars and RNA-seq (reads per kb per million) by grey bars. a : HrpA1 (IYO_006790); b : GDP-mannose dehydrogenase (GMD, IYO_006070); c : Alginate synthase (IYO_006055); d : HopAU1 (IYO_029795); e : IAAL (IYO_002060); f : AvrRpm1 (IYO_008065); g : Amino acid adenylation protein (AAD, IYO_003790); h : DNAA (IYO_000005)
    Rna Seq, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 101 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rna seq/product/Millipore
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    99
    Millipore rna seq analysis
    Maturation of stable RNAs.A. Annotated view of the rrnE operon of E. coli . The tracks from top to bottom show the genome position, differential <t>RNA-seq</t> reads in the absence of TAP treatment and the location of genes within the operon. The track containing the differential RNA-seq reads has been labelled to show the position of known cleavage sites and Class I TSSs. As Fig. 2 , the labelling of the latter also indicates the stand and nucleotide position. Sites of cleavage by RNase III, E and G are labelled III, E and G respectively. The remainder of the labelling and numbering is as in Fig. 4 . Inset shows positions at the 5′ end of 23S rRNA using a lower read scale.B. Annotated view of the rrnA operon of S. <t>coelicolor</t> . Tracks and numbering are as (A). Sites referred to in the text are labelled. Inset shows positions at the 3′ end of 16S rRNA using a lower read scale The 5′ and 3′ ends of the mature rRNAs are as determined using our global RNA-seq data.C. Processing at 5′ and 3′ end of E. coli aspV tRNA. Labelling as (B).D. Processing within the CCA at 3′ end of S. coelicolor bldA (Leu) tRNA. An arrow indicates the position of cleavage within the CCA motif.
    Rna Seq Analysis, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 76 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa rna seq kit
    Comparison of the prokaryotic <t>metatranscriptomic</t> profiles for luminal fluid (LF) and whole termite guts (WG) <t>RNA</t> preparations. a Prokaryotic gene transcripts annotated to Clusters of Orthologous Group (COG) categories. b Distribution of prokaryotic transcripts to CAZy families (only contigs with e-value
    Rna Seq Kit, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 48 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    87
    Illumina Inc illumina rna seq rnaseq
    Expression correlation for ER, PgR, and HER2 genes. Scatterplots reporting the expression correlation of ER, PgR, and HER2 defined by Affymetrix microarray or <t>Illumina</t> <t>RNA-Seq.</t> Each dot is colored according to the corresponding status determined by IHC: green for positive, blue for negative, red for borderline. Spearman correlation coefficient and p-value are provided below the plots.
    Illumina Rna Seq Rnaseq, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 87/100, based on 35 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Reverse transcription quantitative PCR validation of RNA-seq data. Eight target genes and five potential reference genes were selected for reverse transcription quantitative PCR (RT-qPCR) (supplemental data set 13). RNA was extracted from Psa grown in vitro (IV) infected ‘Hort16A’ plantlets at 2, 24 and 72 h post infection (HPI). RT-qPCR values (three biological replicates) were based on normalisation against the geometric average/mean of three reference genes (IYO_010670, IYO_009010 and IYO_002170) selected using Bestkeeper and geNorm analysis [ 69 , 70 ]. For comparison with the RNA-seq data, values were displayed by representing maximum expression of each gene as 100. Pearson correlation coefficients (r) > 0.5 between the RT-qPCR and RNA-seq data are displayed all primers are listed in supplemental data set 13. RT-qPCR data is represented by black bars and RNA-seq (reads per kb per million) by grey bars. a : HrpA1 (IYO_006790); b : GDP-mannose dehydrogenase (GMD, IYO_006070); c : Alginate synthase (IYO_006055); d : HopAU1 (IYO_029795); e : IAAL (IYO_002060); f : AvrRpm1 (IYO_008065); g : Amino acid adenylation protein (AAD, IYO_003790); h : DNAA (IYO_000005)

    Journal: BMC Genomics

    Article Title: Re-programming of Pseudomonas syringae pv. actinidiae gene expression during early stages of infection of kiwifruit

    doi: 10.1186/s12864-018-5197-5

    Figure Lengend Snippet: Reverse transcription quantitative PCR validation of RNA-seq data. Eight target genes and five potential reference genes were selected for reverse transcription quantitative PCR (RT-qPCR) (supplemental data set 13). RNA was extracted from Psa grown in vitro (IV) infected ‘Hort16A’ plantlets at 2, 24 and 72 h post infection (HPI). RT-qPCR values (three biological replicates) were based on normalisation against the geometric average/mean of three reference genes (IYO_010670, IYO_009010 and IYO_002170) selected using Bestkeeper and geNorm analysis [ 69 , 70 ]. For comparison with the RNA-seq data, values were displayed by representing maximum expression of each gene as 100. Pearson correlation coefficients (r) > 0.5 between the RT-qPCR and RNA-seq data are displayed all primers are listed in supplemental data set 13. RT-qPCR data is represented by black bars and RNA-seq (reads per kb per million) by grey bars. a : HrpA1 (IYO_006790); b : GDP-mannose dehydrogenase (GMD, IYO_006070); c : Alginate synthase (IYO_006055); d : HopAU1 (IYO_029795); e : IAAL (IYO_002060); f : AvrRpm1 (IYO_008065); g : Amino acid adenylation protein (AAD, IYO_003790); h : DNAA (IYO_000005)

    Article Snippet: RT-q-PCR validation of RNA-seq data To validate the RNA-seq dataset, total RNA was isolated from an independent infection experiment with three biological replicates using the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich).

    Techniques: Real-time Polymerase Chain Reaction, RNA Sequencing Assay, Quantitative RT-PCR, In Vitro, Infection, Expressing

    Validation by RIP-qPCR of a set of ARA-lincRNAs, which were detected in the RIP-seq assay as associated to AR. LNCaP cells treated with 0.1 nM androgen (red lines) or with vehicle control (blue lines) were assayed as indicated on the x -axis. The amount of the indicated lincRNA that was co-immunoprecipitated with antiAR antibody or with IgG from non-immunized rabbit (negative control) was measured by RT-qPCR in three different biological replicates (each represented with a different symbol), and the corresponding points for antiAR and IgG for each replicate are connected with a straight line. The results are shown as % input RNA (mean ± SEM) of three technical replicates for each individual biological replicate. For the four lincRNA genes in the experiment with androgen whose experimental points are connected with red dotted lines, the amount of RIP material was only enough for two technical replicates each, and the enrichment t -test was not applied. Red and blue solid lines = significant difference between antiAR and IgG ( p

    Journal: Frontiers in Genetics

    Article Title: Chromatin Landscape Distinguishes the Genomic Loci of Hundreds of Androgen-Receptor-Associated LincRNAs From the Loci of Non-associated LincRNAs

    doi: 10.3389/fgene.2018.00132

    Figure Lengend Snippet: Validation by RIP-qPCR of a set of ARA-lincRNAs, which were detected in the RIP-seq assay as associated to AR. LNCaP cells treated with 0.1 nM androgen (red lines) or with vehicle control (blue lines) were assayed as indicated on the x -axis. The amount of the indicated lincRNA that was co-immunoprecipitated with antiAR antibody or with IgG from non-immunized rabbit (negative control) was measured by RT-qPCR in three different biological replicates (each represented with a different symbol), and the corresponding points for antiAR and IgG for each replicate are connected with a straight line. The results are shown as % input RNA (mean ± SEM) of three technical replicates for each individual biological replicate. For the four lincRNA genes in the experiment with androgen whose experimental points are connected with red dotted lines, the amount of RIP material was only enough for two technical replicates each, and the enrichment t -test was not applied. Red and blue solid lines = significant difference between antiAR and IgG ( p

    Article Snippet: RNA Extraction Preparation for Next-Generation Sequencing For RNA-seq experiments poly(A)+ RNA was extracted from LNCaP cells treated for 24 h with 1 nM of the synthetic androgen R1881 (Sigma) (n = 2) or with an equivalent volume of vehicle (ethanol) (n = 2) using FastTrack MAG Maxi mRNA Isolation Kit (Invitrogen) as described in , which essentially included a modification of the kit protocol to have a larger amount of DNase I and a longer DNase treatment time ( ) in order to ensure the elimination of contaminant genomic DNA from the polyA+ RNA fraction.

    Techniques: Real-time Polymerase Chain Reaction, Acetylene Reduction Assay, Immunoprecipitation, Negative Control, Quantitative RT-PCR

    The androgen-responsive Long Intergenic Non-coding RNAs transcriptome in LNCaP cells. (A) A schematic illustration of the procedure used to discover and define the complement of lincRNAs expressed in LNCaP cells. (B) Pizza plot depicting the LNCaP-expressed transcripts already listed as lincRNAs in the comprehensive reference transcriptome from the literature (purple) as well as the novel lincRNAs (brown) identified here. (C) Violin plot representing the distribution of log2 (FPKM) values of protein-coding genes (blue) and lincRNAs (red) expressed in LNCaP cells (FPKM > 1) in the presence of 1 nM androgen. (D) Mean number of exons per transcript among the protein-coding genes (blue) and the lincRNAs (red) expressed in LNCaP cells. (E,F) Volcano plots displaying the differentially expressed genes when comparing androgen-treated and control LNCaP cells ( n = 2). Significance cutoff at adjusted p -value ≤ 0.05 and fold-change ≥ 2 (red) or ≤–2 (green). (E) Androgen-responsive lincRNAs. (F) Androgen-responsive protein-coding genes. (G,H) GSEA analyses depicting the enrichment of hallmark androgen-responsive genes (G) and of prostate cancer genes (H) among the protein-coding genes with androgen-induced changes in expression in LNCaP cells. The gene sets are ordered by normalized enrichment score (NES). The q -value is the false discovery rate, that is, the estimated probability that the normalized enrichment score represents a false positive finding. (I) Volcano plot representation of the differentially expressed lincRNAs in prostate cancer patient tissue samples compared with adjacent non-tumor tissue [re-analysis of raw RNA-seq data from Ren et al. (2012) to include all lincRNAs described here]; significance cutoff at adjusted p -value ≤ 0.05 and fold-change ≥ 2 (red) or ≤–2 (green).

    Journal: Frontiers in Genetics

    Article Title: Chromatin Landscape Distinguishes the Genomic Loci of Hundreds of Androgen-Receptor-Associated LincRNAs From the Loci of Non-associated LincRNAs

    doi: 10.3389/fgene.2018.00132

    Figure Lengend Snippet: The androgen-responsive Long Intergenic Non-coding RNAs transcriptome in LNCaP cells. (A) A schematic illustration of the procedure used to discover and define the complement of lincRNAs expressed in LNCaP cells. (B) Pizza plot depicting the LNCaP-expressed transcripts already listed as lincRNAs in the comprehensive reference transcriptome from the literature (purple) as well as the novel lincRNAs (brown) identified here. (C) Violin plot representing the distribution of log2 (FPKM) values of protein-coding genes (blue) and lincRNAs (red) expressed in LNCaP cells (FPKM > 1) in the presence of 1 nM androgen. (D) Mean number of exons per transcript among the protein-coding genes (blue) and the lincRNAs (red) expressed in LNCaP cells. (E,F) Volcano plots displaying the differentially expressed genes when comparing androgen-treated and control LNCaP cells ( n = 2). Significance cutoff at adjusted p -value ≤ 0.05 and fold-change ≥ 2 (red) or ≤–2 (green). (E) Androgen-responsive lincRNAs. (F) Androgen-responsive protein-coding genes. (G,H) GSEA analyses depicting the enrichment of hallmark androgen-responsive genes (G) and of prostate cancer genes (H) among the protein-coding genes with androgen-induced changes in expression in LNCaP cells. The gene sets are ordered by normalized enrichment score (NES). The q -value is the false discovery rate, that is, the estimated probability that the normalized enrichment score represents a false positive finding. (I) Volcano plot representation of the differentially expressed lincRNAs in prostate cancer patient tissue samples compared with adjacent non-tumor tissue [re-analysis of raw RNA-seq data from Ren et al. (2012) to include all lincRNAs described here]; significance cutoff at adjusted p -value ≤ 0.05 and fold-change ≥ 2 (red) or ≤–2 (green).

    Article Snippet: RNA Extraction Preparation for Next-Generation Sequencing For RNA-seq experiments poly(A)+ RNA was extracted from LNCaP cells treated for 24 h with 1 nM of the synthetic androgen R1881 (Sigma) (n = 2) or with an equivalent volume of vehicle (ethanol) (n = 2) using FastTrack MAG Maxi mRNA Isolation Kit (Invitrogen) as described in , which essentially included a modification of the kit protocol to have a larger amount of DNase I and a longer DNase treatment time ( ) in order to ensure the elimination of contaminant genomic DNA from the polyA+ RNA fraction.

    Techniques: Expressing, RNA Sequencing Assay

    AggR‐regulated genes in EAEC strain 042. The figure shows the differential gene expression observed between wild‐type EAEC 042 and its aggR mutant on A. the chromosome and B. plasmid pAA2, as determined by RNA‐seq. A. The data are displayed in rings from the outside inwards. The outermost red lines identify some of the differentially expressed genes (which are labelled with their gene name or number), followed by the base coordinates of the chromosome (labelled in Mb). The annotated genes of EAEC 042 are indicated in the forward and reverse orientation (light blue and dark blue respectively). The EAEC 042 chromosomal regions of difference (RODs) as identified by Chaudhuri et al. ( 2010 ) are presented in orange. The inner most circle shows the log 2 fold difference for each gene compared between wild‐type EAEC 042 and the aggR mutant. Positively differential expressed genes are presented in green and negatively differentially expressed genes are in red. B. The rings depicting the data for plasmid pAA2 are the same as for the EAEC 042 chromosome in A. Note that base numbering for pAA2 is in Kb.

    Journal: Molecular Microbiology

    Article Title: Organization and architecture of AggR‐dependent promoters from enteroaggregative Escherichia coli

    doi: 10.1111/mmi.14172

    Figure Lengend Snippet: AggR‐regulated genes in EAEC strain 042. The figure shows the differential gene expression observed between wild‐type EAEC 042 and its aggR mutant on A. the chromosome and B. plasmid pAA2, as determined by RNA‐seq. A. The data are displayed in rings from the outside inwards. The outermost red lines identify some of the differentially expressed genes (which are labelled with their gene name or number), followed by the base coordinates of the chromosome (labelled in Mb). The annotated genes of EAEC 042 are indicated in the forward and reverse orientation (light blue and dark blue respectively). The EAEC 042 chromosomal regions of difference (RODs) as identified by Chaudhuri et al. ( 2010 ) are presented in orange. The inner most circle shows the log 2 fold difference for each gene compared between wild‐type EAEC 042 and the aggR mutant. Positively differential expressed genes are presented in green and negatively differentially expressed genes are in red. B. The rings depicting the data for plasmid pAA2 are the same as for the EAEC 042 chromosome in A. Note that base numbering for pAA2 is in Kb.

    Article Snippet: RNA isolation, rRNA depletion and cDNA synthesis for RNA‐seq Triplicate overnight cultures of EAEC 042 and EAEC 042 ΔaggR were used to inoculate 50 ml of Dulbecco’s modified Eagle’s medium with 0.45% glucose (DMEM high glucose) (Sigma) to an OD600 of 0.05.

    Techniques: Expressing, Mutagenesis, Plasmid Preparation, RNA Sequencing Assay

    Analysis of the aafD 100 promoter fragment from EAEC strain 042. A. The panel shows the base sequence of the EAEC 042 aafD 100 regulatory region fragment, which includes the start of the aafD coding sequence. The sequence is flanked by upstream EcoRI and downstream HindIII sites and is numbered from the base immediately upstream of the HindIII site. The limits of the aafD 99, aafD 98, aafD 97, aafD 96, aafD 95 and aafD 94 nested deletions are indicated by flags. The proposed promoter −10 hexamer element is underlined, the experimentally determined transcript start sites are indicated by bent horizontal arrows and the initiating ATG codon is in bold. Potential AggR‐binding sites are indicated by horizontal arrows, with functional and non‐functional sites denoted by dark and light shading respectively. Each site is aligned with the AggR‐binding consensus (Morin et al. , 2010 ). The locations of the 65 C and 92 C /90 C substitutions, which disrupt the −10 element and the functional AggR‐binding site, respectively, are shown. B. The panel illustrates measured β‐galactosidase activities in E. coli K‐12 BW25113 ∆ lac cells, containing pRW50 carrying the aafD 100 fragment, shortened derivatives or no insert. Cells also carried either pBAD/ aggR (grey bars) or pBAD24 (black bars). C. The panel shows an autoradiogram of a denaturing polyacrylamide gel run to determine the primer extension products from RNA synthesis initiating at the aafD promoter in BW25113 cells carrying pRW50/ aafD 96. AggR (+) and AggR (‐) indicates cells carried pBAD/ aggR or pBAD24. Reactions are calibrated with the M13mp18 phage reference sequence (A, C, G and T), which serves as sequence ladder. Primer extension products, produced in the presence of AggR, are indicated by arrows. D. The panel shows the β‐galactosidase activities of BW25113 cells, containing pRW50 carrying either the aafD 96 fragment or mutant derivatives. Cells also carried either pBAD/ aggR (grey bars) or pBAD24 (black bars). In panels B. and D. cells were grown in LB medium in presence (+) or absence (−) of 0.2% arabinose. β‐galactosidase activities are expressed as nmol of ONPG hydrolysed min –1 mg –1 dry cell mass. Each activity is the average of three independent determinations and standard deviations are shown for all data points.

    Journal: Molecular Microbiology

    Article Title: Organization and architecture of AggR‐dependent promoters from enteroaggregative Escherichia coli

    doi: 10.1111/mmi.14172

    Figure Lengend Snippet: Analysis of the aafD 100 promoter fragment from EAEC strain 042. A. The panel shows the base sequence of the EAEC 042 aafD 100 regulatory region fragment, which includes the start of the aafD coding sequence. The sequence is flanked by upstream EcoRI and downstream HindIII sites and is numbered from the base immediately upstream of the HindIII site. The limits of the aafD 99, aafD 98, aafD 97, aafD 96, aafD 95 and aafD 94 nested deletions are indicated by flags. The proposed promoter −10 hexamer element is underlined, the experimentally determined transcript start sites are indicated by bent horizontal arrows and the initiating ATG codon is in bold. Potential AggR‐binding sites are indicated by horizontal arrows, with functional and non‐functional sites denoted by dark and light shading respectively. Each site is aligned with the AggR‐binding consensus (Morin et al. , 2010 ). The locations of the 65 C and 92 C /90 C substitutions, which disrupt the −10 element and the functional AggR‐binding site, respectively, are shown. B. The panel illustrates measured β‐galactosidase activities in E. coli K‐12 BW25113 ∆ lac cells, containing pRW50 carrying the aafD 100 fragment, shortened derivatives or no insert. Cells also carried either pBAD/ aggR (grey bars) or pBAD24 (black bars). C. The panel shows an autoradiogram of a denaturing polyacrylamide gel run to determine the primer extension products from RNA synthesis initiating at the aafD promoter in BW25113 cells carrying pRW50/ aafD 96. AggR (+) and AggR (‐) indicates cells carried pBAD/ aggR or pBAD24. Reactions are calibrated with the M13mp18 phage reference sequence (A, C, G and T), which serves as sequence ladder. Primer extension products, produced in the presence of AggR, are indicated by arrows. D. The panel shows the β‐galactosidase activities of BW25113 cells, containing pRW50 carrying either the aafD 96 fragment or mutant derivatives. Cells also carried either pBAD/ aggR (grey bars) or pBAD24 (black bars). In panels B. and D. cells were grown in LB medium in presence (+) or absence (−) of 0.2% arabinose. β‐galactosidase activities are expressed as nmol of ONPG hydrolysed min –1 mg –1 dry cell mass. Each activity is the average of three independent determinations and standard deviations are shown for all data points.

    Article Snippet: RNA isolation, rRNA depletion and cDNA synthesis for RNA‐seq Triplicate overnight cultures of EAEC 042 and EAEC 042 ΔaggR were used to inoculate 50 ml of Dulbecco’s modified Eagle’s medium with 0.45% glucose (DMEM high glucose) (Sigma) to an OD600 of 0.05.

    Techniques: Sequencing, Binding Assay, Functional Assay, Produced, Mutagenesis, Activity Assay

    Analysis of afaB 100 promoter fragment from EAEC strain 042. A. The panel shows the base sequence of the EAEC 042 afaB 100 regulatory region fragment flanked by upstream EcoRI and downstream HindIII sites. The sequence is numbered from the base immediately upstream of the HindIII site. The limits of the afaB 99, afaB 98 and afaB 97 nested deletions are indicated by flags. The proposed −10 hexamer element is underlined and the experimentally determined transcript start sites are indicated by bent horizontal arrows. Potential AggR‐binding sites are indicated by horizontal arrows, with functional and non‐functional sites denoted by dark and light shading respectively. Each site is aligned with the AggR‐binding consensus (Morin et al. , 2010 ). The location of the 293 C and 320 C /318 C substitutions, which disrupt the −10 element and the functional AggR‐binding site, respectively, is shown. B. The panel illustrates measured β‐galactosidase activities in E. coli K‐12 BW25113 cells containing pRW50, carrying the afaB 100 fragment, shortened derivatives, or no insert. Cells also carried either pBAD/ aggR (grey bars) or pBAD24 (black bars). C. The panel shows an autoradiogram of a denaturing polyacrylamide gel run to determine the primer extension products from RNA initiating from the afaB promoter in BW25113 cells, carrying pRW50/ afaB 100. AggR (+) and AggR (–) indicates cells carried pBAD/ aggR or pBAD24. Reactions are calibrated with the M13mp18 phage reference sequence (A, C, G and T), which serves as sequence ladder. Primer extension products, produced in the presence of AggR, are indicated by arrows. D. The panel shows the β‐galactosidase activities in BW25113 cells containing pRW50 carrying either the afaB 100 fragment or mutant derivatives. Cells also carried either pBAD/ aggR (grey bars) or pBAD24 (black bars). In panels B. and D. cells were grown in LB medium in presence (+) or absence (−) of 0.2% arabinose. β‐galactosidase activities are expressed as nmol of ONPG hydrolysed min –1 mg –1 dry cell mass. Each activity is the average of three independent determinations and standard deviations are shown for all data points.

    Journal: Molecular Microbiology

    Article Title: Organization and architecture of AggR‐dependent promoters from enteroaggregative Escherichia coli

    doi: 10.1111/mmi.14172

    Figure Lengend Snippet: Analysis of afaB 100 promoter fragment from EAEC strain 042. A. The panel shows the base sequence of the EAEC 042 afaB 100 regulatory region fragment flanked by upstream EcoRI and downstream HindIII sites. The sequence is numbered from the base immediately upstream of the HindIII site. The limits of the afaB 99, afaB 98 and afaB 97 nested deletions are indicated by flags. The proposed −10 hexamer element is underlined and the experimentally determined transcript start sites are indicated by bent horizontal arrows. Potential AggR‐binding sites are indicated by horizontal arrows, with functional and non‐functional sites denoted by dark and light shading respectively. Each site is aligned with the AggR‐binding consensus (Morin et al. , 2010 ). The location of the 293 C and 320 C /318 C substitutions, which disrupt the −10 element and the functional AggR‐binding site, respectively, is shown. B. The panel illustrates measured β‐galactosidase activities in E. coli K‐12 BW25113 cells containing pRW50, carrying the afaB 100 fragment, shortened derivatives, or no insert. Cells also carried either pBAD/ aggR (grey bars) or pBAD24 (black bars). C. The panel shows an autoradiogram of a denaturing polyacrylamide gel run to determine the primer extension products from RNA initiating from the afaB promoter in BW25113 cells, carrying pRW50/ afaB 100. AggR (+) and AggR (–) indicates cells carried pBAD/ aggR or pBAD24. Reactions are calibrated with the M13mp18 phage reference sequence (A, C, G and T), which serves as sequence ladder. Primer extension products, produced in the presence of AggR, are indicated by arrows. D. The panel shows the β‐galactosidase activities in BW25113 cells containing pRW50 carrying either the afaB 100 fragment or mutant derivatives. Cells also carried either pBAD/ aggR (grey bars) or pBAD24 (black bars). In panels B. and D. cells were grown in LB medium in presence (+) or absence (−) of 0.2% arabinose. β‐galactosidase activities are expressed as nmol of ONPG hydrolysed min –1 mg –1 dry cell mass. Each activity is the average of three independent determinations and standard deviations are shown for all data points.

    Article Snippet: RNA isolation, rRNA depletion and cDNA synthesis for RNA‐seq Triplicate overnight cultures of EAEC 042 and EAEC 042 ΔaggR were used to inoculate 50 ml of Dulbecco’s modified Eagle’s medium with 0.45% glucose (DMEM high glucose) (Sigma) to an OD600 of 0.05.

    Techniques: Sequencing, Binding Assay, Functional Assay, Produced, Mutagenesis, Activity Assay

    Maturation of stable RNAs.A. Annotated view of the rrnE operon of E. coli . The tracks from top to bottom show the genome position, differential RNA-seq reads in the absence of TAP treatment and the location of genes within the operon. The track containing the differential RNA-seq reads has been labelled to show the position of known cleavage sites and Class I TSSs. As Fig. 2 , the labelling of the latter also indicates the stand and nucleotide position. Sites of cleavage by RNase III, E and G are labelled III, E and G respectively. The remainder of the labelling and numbering is as in Fig. 4 . Inset shows positions at the 5′ end of 23S rRNA using a lower read scale.B. Annotated view of the rrnA operon of S. coelicolor . Tracks and numbering are as (A). Sites referred to in the text are labelled. Inset shows positions at the 3′ end of 16S rRNA using a lower read scale The 5′ and 3′ ends of the mature rRNAs are as determined using our global RNA-seq data.C. Processing at 5′ and 3′ end of E. coli aspV tRNA. Labelling as (B).D. Processing within the CCA at 3′ end of S. coelicolor bldA (Leu) tRNA. An arrow indicates the position of cleavage within the CCA motif.

    Journal: Molecular Microbiology

    Article Title: A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing

    doi: 10.1111/mmi.12810

    Figure Lengend Snippet: Maturation of stable RNAs.A. Annotated view of the rrnE operon of E. coli . The tracks from top to bottom show the genome position, differential RNA-seq reads in the absence of TAP treatment and the location of genes within the operon. The track containing the differential RNA-seq reads has been labelled to show the position of known cleavage sites and Class I TSSs. As Fig. 2 , the labelling of the latter also indicates the stand and nucleotide position. Sites of cleavage by RNase III, E and G are labelled III, E and G respectively. The remainder of the labelling and numbering is as in Fig. 4 . Inset shows positions at the 5′ end of 23S rRNA using a lower read scale.B. Annotated view of the rrnA operon of S. coelicolor . Tracks and numbering are as (A). Sites referred to in the text are labelled. Inset shows positions at the 3′ end of 16S rRNA using a lower read scale The 5′ and 3′ ends of the mature rRNAs are as determined using our global RNA-seq data.C. Processing at 5′ and 3′ end of E. coli aspV tRNA. Labelling as (B).D. Processing within the CCA at 3′ end of S. coelicolor bldA (Leu) tRNA. An arrow indicates the position of cleavage within the CCA motif.

    Article Snippet: Isolation of bacterial RNA and transcriptome analysis RNA for RNA-seq analysis was isolated from S. coelicolor grown in YEME broth (Kieser et al ., ), as described previously for P. acnes (Lin et al ., ), and from E. coli BW25113 grown in Luria–Bertani broth (Sigma), as described previously for this organism (Kime et al ., ).

    Techniques: RNA Sequencing Assay

    Northern blot analysis of S. coelicolor sRNAs. Labelling of sRNAs in parentheses indicates whether the sRNA is upstream (u) or downstream (d) of the nearest protein-coding gene and whether on the same (+) or opposite (−) strand.A. Annotated views of sRNAs downstream of SCO2100 on the opposite strand, downstream of SCO2822 on the opposite strand and upstream of SCO3871 on the opposite strand. The tracks from top to bottom show the genome positions, gene locations, TSSs and gRNA-seq reads.B. Northern blot analysis of sRNAs depicted in (A). The tmRNA and RNA component of the signal recognition particle were probed to provide controls. The expected sizes of the most abundant species of these controls as judged from gRNA-seq data were ∼ 400 and 80 nt respectively.C. Examples of active ribo-switching (attenuation) and a possible cis -encoded antisense RNA. The yybP element is reported to be pH responsive (Nechooshtan et al ., 2009 ) and is found in a large number of bacteria (Barrick et al ., 2004 ) including E. coli (Argaman et al ., 2001 ), SCO2347 encodes an integral membrane protein. The gcvT element binds the amino acid glycine (Mandal et al ., 2004 ), SCO1378 encodes glycine dehydrogenase. The RFN element (or FMN riboswitch) binds flavin mononucleotide (Serganov et al ., 2009 ), SCO1443 encodes riboflavin synthase. SCO0627, the target of the putative cis- encoded asRNA, encodes a putative ATP-utilizing protein.

    Journal: Molecular Microbiology

    Article Title: A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing

    doi: 10.1111/mmi.12810

    Figure Lengend Snippet: Northern blot analysis of S. coelicolor sRNAs. Labelling of sRNAs in parentheses indicates whether the sRNA is upstream (u) or downstream (d) of the nearest protein-coding gene and whether on the same (+) or opposite (−) strand.A. Annotated views of sRNAs downstream of SCO2100 on the opposite strand, downstream of SCO2822 on the opposite strand and upstream of SCO3871 on the opposite strand. The tracks from top to bottom show the genome positions, gene locations, TSSs and gRNA-seq reads.B. Northern blot analysis of sRNAs depicted in (A). The tmRNA and RNA component of the signal recognition particle were probed to provide controls. The expected sizes of the most abundant species of these controls as judged from gRNA-seq data were ∼ 400 and 80 nt respectively.C. Examples of active ribo-switching (attenuation) and a possible cis -encoded antisense RNA. The yybP element is reported to be pH responsive (Nechooshtan et al ., 2009 ) and is found in a large number of bacteria (Barrick et al ., 2004 ) including E. coli (Argaman et al ., 2001 ), SCO2347 encodes an integral membrane protein. The gcvT element binds the amino acid glycine (Mandal et al ., 2004 ), SCO1378 encodes glycine dehydrogenase. The RFN element (or FMN riboswitch) binds flavin mononucleotide (Serganov et al ., 2009 ), SCO1443 encodes riboflavin synthase. SCO0627, the target of the putative cis- encoded asRNA, encodes a putative ATP-utilizing protein.

    Article Snippet: Isolation of bacterial RNA and transcriptome analysis RNA for RNA-seq analysis was isolated from S. coelicolor grown in YEME broth (Kieser et al ., ), as described previously for P. acnes (Lin et al ., ), and from E. coli BW25113 grown in Luria–Bertani broth (Sigma), as described previously for this organism (Kime et al ., ).

    Techniques: Northern Blot

    Comparison of global RNA-seq and microarray data for S. coelicolor . The mean RNA-seq reads for each base within the 60 bp region targeted by a microarray probe is directly compared with the microarray signal for the same probe target. Trendline calculated by the linear model fit within R.

    Journal: Molecular Microbiology

    Article Title: A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing

    doi: 10.1111/mmi.12810

    Figure Lengend Snippet: Comparison of global RNA-seq and microarray data for S. coelicolor . The mean RNA-seq reads for each base within the 60 bp region targeted by a microarray probe is directly compared with the microarray signal for the same probe target. Trendline calculated by the linear model fit within R.

    Article Snippet: Isolation of bacterial RNA and transcriptome analysis RNA for RNA-seq analysis was isolated from S. coelicolor grown in YEME broth (Kieser et al ., ), as described previously for P. acnes (Lin et al ., ), and from E. coli BW25113 grown in Luria–Bertani broth (Sigma), as described previously for this organism (Kime et al ., ).

    Techniques: RNA Sequencing Assay, Microarray

    Cleavage sites within mRNAs. (A), (B), (C), (D) and (E) show annotated views of the E. coli rpsT (b0023), ompA (b0957), eno (b2779), pnp (b3165) and adhE (b1241) respectively. The tracks from top to bottom show the genome positions, gRNA-seq reads, gene locations and differential RNA-seq reads (in the absence of TAP treatment). The labelled RNase E sites in rpsT mRNA produce the previously described downstream products of 147 and 106 nt (Coburn and Mackie, 1998 ). An additional site referred to in the text is labelled with a question mark. The labelled RNase E site in the 5′ UTR of ompA mRNA is located just downstream of the 5′ stem-loop (Rasmussen et al ., 2005 ). The labelled RNase E sites at the 3′ end of rpsO were identified previously as M2 and M (Regnier and Portier, 1986 ; Regnier and Hajnsdorf, 1991 ). (F) shows an annotated view of the S. coelicolor pnp (SCO5737) gene. Tracks, as the other panels, except that the order is reversed. TSSs and cleavage sites referred to specifically in the text are labelled. The RNase III site on the downstream side was detected using a lower range of reads. As Fig. 2 , the gRNA-seq data for the forward strand are colour black and have positive values, while the reverse strand is coloured red and has negative values. TSSs are labelled according to the strand, class and nucleotide position.

    Journal: Molecular Microbiology

    Article Title: A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing

    doi: 10.1111/mmi.12810

    Figure Lengend Snippet: Cleavage sites within mRNAs. (A), (B), (C), (D) and (E) show annotated views of the E. coli rpsT (b0023), ompA (b0957), eno (b2779), pnp (b3165) and adhE (b1241) respectively. The tracks from top to bottom show the genome positions, gRNA-seq reads, gene locations and differential RNA-seq reads (in the absence of TAP treatment). The labelled RNase E sites in rpsT mRNA produce the previously described downstream products of 147 and 106 nt (Coburn and Mackie, 1998 ). An additional site referred to in the text is labelled with a question mark. The labelled RNase E site in the 5′ UTR of ompA mRNA is located just downstream of the 5′ stem-loop (Rasmussen et al ., 2005 ). The labelled RNase E sites at the 3′ end of rpsO were identified previously as M2 and M (Regnier and Portier, 1986 ; Regnier and Hajnsdorf, 1991 ). (F) shows an annotated view of the S. coelicolor pnp (SCO5737) gene. Tracks, as the other panels, except that the order is reversed. TSSs and cleavage sites referred to specifically in the text are labelled. The RNase III site on the downstream side was detected using a lower range of reads. As Fig. 2 , the gRNA-seq data for the forward strand are colour black and have positive values, while the reverse strand is coloured red and has negative values. TSSs are labelled according to the strand, class and nucleotide position.

    Article Snippet: Isolation of bacterial RNA and transcriptome analysis RNA for RNA-seq analysis was isolated from S. coelicolor grown in YEME broth (Kieser et al ., ), as described previously for P. acnes (Lin et al ., ), and from E. coli BW25113 grown in Luria–Bertani broth (Sigma), as described previously for this organism (Kime et al ., ).

    Techniques: RNA Sequencing Assay

    M-A scatterplots of values from the differential RNA-seq analysis. (A) and (B) show data for S. coelicolor M145 and E. coli BW25113 (seq). The M values correspond to Log 2 (plus/minus) and A values to (Log 2 plus + Log 2 minus)/2, where minus and plus refer to the number of reads before and after treatment with TAP. The points correspond to individual genome positions, not genes. For further details, see Experimental procedures . In each panel, the red line represents the upper boundary of the population of values corresponding to sites of processing and degradation (see main text). The upper boundaries were placed manually to enclose the majority of the lower population, while taking into consideration the spread of M values scattered around 0. The boundaries were then described by polynomial equations. These were M = 0.054A 2 − 0.96A + 4.68 and M = −0.003A 3 + 0.13A 2 − 1.57A + 7.08 for S. coelicolor and E. coli respectively.

    Journal: Molecular Microbiology

    Article Title: A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing

    doi: 10.1111/mmi.12810

    Figure Lengend Snippet: M-A scatterplots of values from the differential RNA-seq analysis. (A) and (B) show data for S. coelicolor M145 and E. coli BW25113 (seq). The M values correspond to Log 2 (plus/minus) and A values to (Log 2 plus + Log 2 minus)/2, where minus and plus refer to the number of reads before and after treatment with TAP. The points correspond to individual genome positions, not genes. For further details, see Experimental procedures . In each panel, the red line represents the upper boundary of the population of values corresponding to sites of processing and degradation (see main text). The upper boundaries were placed manually to enclose the majority of the lower population, while taking into consideration the spread of M values scattered around 0. The boundaries were then described by polynomial equations. These were M = 0.054A 2 − 0.96A + 4.68 and M = −0.003A 3 + 0.13A 2 − 1.57A + 7.08 for S. coelicolor and E. coli respectively.

    Article Snippet: Isolation of bacterial RNA and transcriptome analysis RNA for RNA-seq analysis was isolated from S. coelicolor grown in YEME broth (Kieser et al ., ), as described previously for P. acnes (Lin et al ., ), and from E. coli BW25113 grown in Luria–Bertani broth (Sigma), as described previously for this organism (Kime et al ., ).

    Techniques: RNA Sequencing Assay

    Examples of leaderless mRNAs. (A), (B), (C), (D) and (E) correspond to E. coli genes dicA (Qin prophage; b1570), pgpA (b0418), racR (Rac prophage; b1356), rhlB (b3780) and ymfK (e14 prophage; b1145) respectively. (F) corresponds to an unnamed paralogue (SCO1678) of the S. coelicolor gene whiH . The panels are modified screenshots from the UCSC Microbial Genome Browser (Chan et al ., 2012 ). In each panel the tracks depict from top to bottom, the genome position, location of annotated genes, the positions of TSSs identified by the analysis of M-A scatterplots (Fig. 1 ), and the number of times each position on the corresponding strand was sequenced following fragmentation of the transcriptome (gRNA-seq). The numbers at the left of the RNA-seq tracks indicate the scale of the sequencing reads.

    Journal: Molecular Microbiology

    Article Title: A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing

    doi: 10.1111/mmi.12810

    Figure Lengend Snippet: Examples of leaderless mRNAs. (A), (B), (C), (D) and (E) correspond to E. coli genes dicA (Qin prophage; b1570), pgpA (b0418), racR (Rac prophage; b1356), rhlB (b3780) and ymfK (e14 prophage; b1145) respectively. (F) corresponds to an unnamed paralogue (SCO1678) of the S. coelicolor gene whiH . The panels are modified screenshots from the UCSC Microbial Genome Browser (Chan et al ., 2012 ). In each panel the tracks depict from top to bottom, the genome position, location of annotated genes, the positions of TSSs identified by the analysis of M-A scatterplots (Fig. 1 ), and the number of times each position on the corresponding strand was sequenced following fragmentation of the transcriptome (gRNA-seq). The numbers at the left of the RNA-seq tracks indicate the scale of the sequencing reads.

    Article Snippet: Isolation of bacterial RNA and transcriptome analysis RNA for RNA-seq analysis was isolated from S. coelicolor grown in YEME broth (Kieser et al ., ), as described previously for P. acnes (Lin et al ., ), and from E. coli BW25113 grown in Luria–Bertani broth (Sigma), as described previously for this organism (Kime et al ., ).

    Techniques: Modification, RNA Sequencing Assay, Sequencing

    Cohesin binding is remodeled in response to stress and negatively correlates with the transcription induction of p53 target genes. ( A ) Heatmaps of Rad21 signal measured by ChIP-seq in non-treated and daunorubicin treated HCT116 p53 +/+ cells. Rad21 binding sites with a log2 fold change Z-score inferior to -2 and superior to 2 are presented. p53 target genes harboring a Rad21 site within their gene bodies and for which p53 is an activator are shown in green, those for which p53 is a repressor are shown in red ( B ) RNA-seq and Rad21 ChIP-seq tracks obtained in non-treated (NT) and daunorubicin-treated (Dauno) HCT116 p53 +/+ cells. The signal obtained at the CDKN1A locus is presented. ( C ) Correlation of Rad21 binding signal fold change with gene transcription fold change for Rad21 binding sites located within p53 target genes. ( D ) Correlation of Rad21 peak height and gene transcription FPKM for all Rad21 binding sites located within genes. Data obtained in non-treated HCT116 p53 +/+ cells. ( E ) ChIP of Rad21 in HCT116 p53 +/+ and p53 -/- cells at the intragenic CDKN1A cohesin binding site. ( F ) ChIP of Smc1A in HCT116 p53 +/+ and p53 -/- cells at the intragenic CDKN1A cohesin binding site.

    Journal: PLoS ONE

    Article Title: High-Resolution 4C Reveals Rapid p53-Dependent Chromatin Reorganization of the CDKN1A Locus in Response to Stress

    doi: 10.1371/journal.pone.0163885

    Figure Lengend Snippet: Cohesin binding is remodeled in response to stress and negatively correlates with the transcription induction of p53 target genes. ( A ) Heatmaps of Rad21 signal measured by ChIP-seq in non-treated and daunorubicin treated HCT116 p53 +/+ cells. Rad21 binding sites with a log2 fold change Z-score inferior to -2 and superior to 2 are presented. p53 target genes harboring a Rad21 site within their gene bodies and for which p53 is an activator are shown in green, those for which p53 is a repressor are shown in red ( B ) RNA-seq and Rad21 ChIP-seq tracks obtained in non-treated (NT) and daunorubicin-treated (Dauno) HCT116 p53 +/+ cells. The signal obtained at the CDKN1A locus is presented. ( C ) Correlation of Rad21 binding signal fold change with gene transcription fold change for Rad21 binding sites located within p53 target genes. ( D ) Correlation of Rad21 peak height and gene transcription FPKM for all Rad21 binding sites located within genes. Data obtained in non-treated HCT116 p53 +/+ cells. ( E ) ChIP of Rad21 in HCT116 p53 +/+ and p53 -/- cells at the intragenic CDKN1A cohesin binding site. ( F ) ChIP of Smc1A in HCT116 p53 +/+ and p53 -/- cells at the intragenic CDKN1A cohesin binding site.

    Article Snippet: RNA-seq Total RNA was extracted from HCT116 p53+/+ cells using GenElute (Sigma) and treated with DNaseI (Ambion).

    Techniques: Binding Assay, Chromatin Immunoprecipitation, RNA Sequencing Assay

    Comparison of the prokaryotic metatranscriptomic profiles for luminal fluid (LF) and whole termite guts (WG) RNA preparations. a Prokaryotic gene transcripts annotated to Clusters of Orthologous Group (COG) categories. b Distribution of prokaryotic transcripts to CAZy families (only contigs with e-value

    Journal: BMC Genomics

    Article Title: Optimization of a metatranscriptomic approach to study the lignocellulolytic potential of the higher termite gut microbiome

    doi: 10.1186/s12864-017-4076-9

    Figure Lengend Snippet: Comparison of the prokaryotic metatranscriptomic profiles for luminal fluid (LF) and whole termite guts (WG) RNA preparations. a Prokaryotic gene transcripts annotated to Clusters of Orthologous Group (COG) categories. b Distribution of prokaryotic transcripts to CAZy families (only contigs with e-value

    Article Snippet: Metatranscriptomic analysis of termite gut bacteria SMARTer Stranded RNA-Seq Kit (Clontech) was used according to the manufacturer’s instructions to prepare metatranscriptomic libraries.

    Techniques:

    Comparison of the efficacy of the two studied metatranscriptomic pipelines versus the non-depleted control. The performance of two pipelines, RZ and ME, was tested for three termite species: N. ephratae , N. sp. and T. hospes. LF corresponds to luminal fluid and WG to whole termite gut RNA preparations. a Proportion of rRNA reads detected in the different metatranscriptomic libraries for the two studied pipelines and the non-depleted control. WG sampling strategy was only assessed with the pipeline RZ for T. hospes and N. sp. preparations. b Relative abundance of transcripts with no taxonomic assignment and assigned as of prokaryotic (archaea and bacteria), eukaryotic or viral origin

    Journal: BMC Genomics

    Article Title: Optimization of a metatranscriptomic approach to study the lignocellulolytic potential of the higher termite gut microbiome

    doi: 10.1186/s12864-017-4076-9

    Figure Lengend Snippet: Comparison of the efficacy of the two studied metatranscriptomic pipelines versus the non-depleted control. The performance of two pipelines, RZ and ME, was tested for three termite species: N. ephratae , N. sp. and T. hospes. LF corresponds to luminal fluid and WG to whole termite gut RNA preparations. a Proportion of rRNA reads detected in the different metatranscriptomic libraries for the two studied pipelines and the non-depleted control. WG sampling strategy was only assessed with the pipeline RZ for T. hospes and N. sp. preparations. b Relative abundance of transcripts with no taxonomic assignment and assigned as of prokaryotic (archaea and bacteria), eukaryotic or viral origin

    Article Snippet: Metatranscriptomic analysis of termite gut bacteria SMARTer Stranded RNA-Seq Kit (Clontech) was used according to the manufacturer’s instructions to prepare metatranscriptomic libraries.

    Techniques: Sampling

    Expression correlation for ER, PgR, and HER2 genes. Scatterplots reporting the expression correlation of ER, PgR, and HER2 defined by Affymetrix microarray or Illumina RNA-Seq. Each dot is colored according to the corresponding status determined by IHC: green for positive, blue for negative, red for borderline. Spearman correlation coefficient and p-value are provided below the plots.

    Journal: BMC Genomics

    Article Title: Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology

    doi: 10.1186/1471-2164-15-1008

    Figure Lengend Snippet: Expression correlation for ER, PgR, and HER2 genes. Scatterplots reporting the expression correlation of ER, PgR, and HER2 defined by Affymetrix microarray or Illumina RNA-Seq. Each dot is colored according to the corresponding status determined by IHC: green for positive, blue for negative, red for borderline. Spearman correlation coefficient and p-value are provided below the plots.

    Article Snippet: Contingency table for breast cancer subtype classifiers (SCMs and SSPs) using Affymetrix microarray (AFFY) and Illumina RNA-Seq (RNASEQ) platforms.

    Techniques: Expressing, Microarray, RNA Sequencing Assay, Immunohistochemistry

    Correlation values for the evaluated subtype classifiers and gene expression signatures. A: Cohen’s Kappa coefficients for subtype classifiers (orange: SCMs; purple: SSPs). B: Spearman correlation values for prognostic (orange), immune (green), stroma (blue) and pathway (purple) signature scores as computed using Affymetrix microarray and Illumina RNA-Seq platforms.

    Journal: BMC Genomics

    Article Title: Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology

    doi: 10.1186/1471-2164-15-1008

    Figure Lengend Snippet: Correlation values for the evaluated subtype classifiers and gene expression signatures. A: Cohen’s Kappa coefficients for subtype classifiers (orange: SCMs; purple: SSPs). B: Spearman correlation values for prognostic (orange), immune (green), stroma (blue) and pathway (purple) signature scores as computed using Affymetrix microarray and Illumina RNA-Seq platforms.

    Article Snippet: Contingency table for breast cancer subtype classifiers (SCMs and SSPs) using Affymetrix microarray (AFFY) and Illumina RNA-Seq (RNASEQ) platforms.

    Techniques: Expressing, Microarray, RNA Sequencing Assay

    Gene expression correlation between Affymetrix microarray and Illumina RNA-Seq platforms. A: Expression correlation of the 16,097 genes measured both on Affymetrix microarray and Illumina RNA-Seq platforms after selecting the best Affymetrix probeset using jetset. B: and C: Box plots showing median level of gene expression for both Affymetrix and RNA-Seq for the genes with low (

    Journal: BMC Genomics

    Article Title: Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology

    doi: 10.1186/1471-2164-15-1008

    Figure Lengend Snippet: Gene expression correlation between Affymetrix microarray and Illumina RNA-Seq platforms. A: Expression correlation of the 16,097 genes measured both on Affymetrix microarray and Illumina RNA-Seq platforms after selecting the best Affymetrix probeset using jetset. B: and C: Box plots showing median level of gene expression for both Affymetrix and RNA-Seq for the genes with low (

    Article Snippet: Contingency table for breast cancer subtype classifiers (SCMs and SSPs) using Affymetrix microarray (AFFY) and Illumina RNA-Seq (RNASEQ) platforms.

    Techniques: Expressing, Microarray, RNA Sequencing Assay