paired-end rna sequencing Search Results


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  • 91
    Illumina Inc paired end rna sequencing analysis
    Paired End Rna Sequencing Analysis, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc paired end rna sequencing
    Expression analysis of endothelial cell, artery, pericyte and neuronal/neurite markers in osteolytic and osteoblastic bone metastasis (A) Fold change of genes, associated to endothelial cells, arteries, pericytes and neurons/neurites, measured by <t>RNA</t> sequencing (for PC-3 and <t>MDA-MB231</t> xenografts versus controls) or microarray data (for VCaP xenografts versus controls). B-J. Relative expression levels of endothelial cell (B) , artery (C-E) , pericyte (F-H) and neuron/neurite (I and J) markers in osteolytic (PC-3 and MDA-MB231 xenografts) and osteoblastic (VCaP xenografts) bone metastasis and corresponding sham-operated animals. Expression levels are shown for PC-3 (blue bar), MDA-MB231 (red bar), VCaP (black bar) xenografts and corresponding sham-operated animals (white bar: sham-operated animals of PC3 and MDA-MB231 xenografts models; grey bar: sham-operated animals of VCaP xenografts). Values for each gene is shown as relative expression to mouse B2M (mean ± SD). * , P
    Paired End Rna Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 96/100, based on 527 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/paired end rna sequencing/product/Illumina Inc
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    Illumina Inc rna sequencing data analysis paired end
    Expression analysis of endothelial cell, artery, pericyte and neuronal/neurite markers in osteolytic and osteoblastic bone metastasis (A) Fold change of genes, associated to endothelial cells, arteries, pericytes and neurons/neurites, measured by <t>RNA</t> sequencing (for PC-3 and <t>MDA-MB231</t> xenografts versus controls) or microarray data (for VCaP xenografts versus controls). B-J. Relative expression levels of endothelial cell (B) , artery (C-E) , pericyte (F-H) and neuron/neurite (I and J) markers in osteolytic (PC-3 and MDA-MB231 xenografts) and osteoblastic (VCaP xenografts) bone metastasis and corresponding sham-operated animals. Expression levels are shown for PC-3 (blue bar), MDA-MB231 (red bar), VCaP (black bar) xenografts and corresponding sham-operated animals (white bar: sham-operated animals of PC3 and MDA-MB231 xenografts models; grey bar: sham-operated animals of VCaP xenografts). Values for each gene is shown as relative expression to mouse B2M (mean ± SD). * , P
    Rna Sequencing Data Analysis Paired End, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc truseq paired end rna sequencing
    Expression analysis of endothelial cell, artery, pericyte and neuronal/neurite markers in osteolytic and osteoblastic bone metastasis (A) Fold change of genes, associated to endothelial cells, arteries, pericytes and neurons/neurites, measured by <t>RNA</t> sequencing (for PC-3 and <t>MDA-MB231</t> xenografts versus controls) or microarray data (for VCaP xenografts versus controls). B-J. Relative expression levels of endothelial cell (B) , artery (C-E) , pericyte (F-H) and neuron/neurite (I and J) markers in osteolytic (PC-3 and MDA-MB231 xenografts) and osteoblastic (VCaP xenografts) bone metastasis and corresponding sham-operated animals. Expression levels are shown for PC-3 (blue bar), MDA-MB231 (red bar), VCaP (black bar) xenografts and corresponding sham-operated animals (white bar: sham-operated animals of PC3 and MDA-MB231 xenografts models; grey bar: sham-operated animals of VCaP xenografts). Values for each gene is shown as relative expression to mouse B2M (mean ± SD). * , P
    Truseq Paired End Rna Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Illumina Inc sequencing rna pair end sequencing
    Expression analysis of endothelial cell, artery, pericyte and neuronal/neurite markers in osteolytic and osteoblastic bone metastasis (A) Fold change of genes, associated to endothelial cells, arteries, pericytes and neurons/neurites, measured by <t>RNA</t> sequencing (for PC-3 and <t>MDA-MB231</t> xenografts versus controls) or microarray data (for VCaP xenografts versus controls). B-J. Relative expression levels of endothelial cell (B) , artery (C-E) , pericyte (F-H) and neuron/neurite (I and J) markers in osteolytic (PC-3 and MDA-MB231 xenografts) and osteoblastic (VCaP xenografts) bone metastasis and corresponding sham-operated animals. Expression levels are shown for PC-3 (blue bar), MDA-MB231 (red bar), VCaP (black bar) xenografts and corresponding sham-operated animals (white bar: sham-operated animals of PC3 and MDA-MB231 xenografts models; grey bar: sham-operated animals of VCaP xenografts). Values for each gene is shown as relative expression to mouse B2M (mean ± SD). * , P
    Sequencing Rna Pair End Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Novogene paired end rna sequencing
    Expression analysis of endothelial cell, artery, pericyte and neuronal/neurite markers in osteolytic and osteoblastic bone metastasis (A) Fold change of genes, associated to endothelial cells, arteries, pericytes and neurons/neurites, measured by <t>RNA</t> sequencing (for PC-3 and <t>MDA-MB231</t> xenografts versus controls) or microarray data (for VCaP xenografts versus controls). B-J. Relative expression levels of endothelial cell (B) , artery (C-E) , pericyte (F-H) and neuron/neurite (I and J) markers in osteolytic (PC-3 and MDA-MB231 xenografts) and osteoblastic (VCaP xenografts) bone metastasis and corresponding sham-operated animals. Expression levels are shown for PC-3 (blue bar), MDA-MB231 (red bar), VCaP (black bar) xenografts and corresponding sham-operated animals (white bar: sham-operated animals of PC3 and MDA-MB231 xenografts models; grey bar: sham-operated animals of VCaP xenografts). Values for each gene is shown as relative expression to mouse B2M (mean ± SD). * , P
    Paired End Rna Sequencing, supplied by Novogene, used in various techniques. Bioz Stars score: 93/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Fasteris Life paired end rna sequencing
    Expression analysis of endothelial cell, artery, pericyte and neuronal/neurite markers in osteolytic and osteoblastic bone metastasis (A) Fold change of genes, associated to endothelial cells, arteries, pericytes and neurons/neurites, measured by <t>RNA</t> sequencing (for PC-3 and <t>MDA-MB231</t> xenografts versus controls) or microarray data (for VCaP xenografts versus controls). B-J. Relative expression levels of endothelial cell (B) , artery (C-E) , pericyte (F-H) and neuron/neurite (I and J) markers in osteolytic (PC-3 and MDA-MB231 xenografts) and osteoblastic (VCaP xenografts) bone metastasis and corresponding sham-operated animals. Expression levels are shown for PC-3 (blue bar), MDA-MB231 (red bar), VCaP (black bar) xenografts and corresponding sham-operated animals (white bar: sham-operated animals of PC3 and MDA-MB231 xenografts models; grey bar: sham-operated animals of VCaP xenografts). Values for each gene is shown as relative expression to mouse B2M (mean ± SD). * , P
    Paired End Rna Sequencing, supplied by Fasteris Life, used in various techniques. Bioz Stars score: 90/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Aros Applied Biotechnology paired end rna sequencing
    Expression analysis of endothelial cell, artery, pericyte and neuronal/neurite markers in osteolytic and osteoblastic bone metastasis (A) Fold change of genes, associated to endothelial cells, arteries, pericytes and neurons/neurites, measured by <t>RNA</t> sequencing (for PC-3 and <t>MDA-MB231</t> xenografts versus controls) or microarray data (for VCaP xenografts versus controls). B-J. Relative expression levels of endothelial cell (B) , artery (C-E) , pericyte (F-H) and neuron/neurite (I and J) markers in osteolytic (PC-3 and MDA-MB231 xenografts) and osteoblastic (VCaP xenografts) bone metastasis and corresponding sham-operated animals. Expression levels are shown for PC-3 (blue bar), MDA-MB231 (red bar), VCaP (black bar) xenografts and corresponding sham-operated animals (white bar: sham-operated animals of PC3 and MDA-MB231 xenografts models; grey bar: sham-operated animals of VCaP xenografts). Values for each gene is shown as relative expression to mouse B2M (mean ± SD). * , P
    Paired End Rna Sequencing, supplied by Aros Applied Biotechnology, used in various techniques. Bioz Stars score: 90/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/paired end rna sequencing/product/Aros Applied Biotechnology
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    Solexa solexa paired end rna sequencing
    Expression analysis of endothelial cell, artery, pericyte and neuronal/neurite markers in osteolytic and osteoblastic bone metastasis (A) Fold change of genes, associated to endothelial cells, arteries, pericytes and neurons/neurites, measured by <t>RNA</t> sequencing (for PC-3 and <t>MDA-MB231</t> xenografts versus controls) or microarray data (for VCaP xenografts versus controls). B-J. Relative expression levels of endothelial cell (B) , artery (C-E) , pericyte (F-H) and neuron/neurite (I and J) markers in osteolytic (PC-3 and MDA-MB231 xenografts) and osteoblastic (VCaP xenografts) bone metastasis and corresponding sham-operated animals. Expression levels are shown for PC-3 (blue bar), MDA-MB231 (red bar), VCaP (black bar) xenografts and corresponding sham-operated animals (white bar: sham-operated animals of PC3 and MDA-MB231 xenografts models; grey bar: sham-operated animals of VCaP xenografts). Values for each gene is shown as relative expression to mouse B2M (mean ± SD). * , P
    Solexa Paired End Rna Sequencing, supplied by Solexa, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc paired end rna sequencing sample prep kit
    Expression analysis of endothelial cell, artery, pericyte and neuronal/neurite markers in osteolytic and osteoblastic bone metastasis (A) Fold change of genes, associated to endothelial cells, arteries, pericytes and neurons/neurites, measured by <t>RNA</t> sequencing (for PC-3 and <t>MDA-MB231</t> xenografts versus controls) or microarray data (for VCaP xenografts versus controls). B-J. Relative expression levels of endothelial cell (B) , artery (C-E) , pericyte (F-H) and neuron/neurite (I and J) markers in osteolytic (PC-3 and MDA-MB231 xenografts) and osteoblastic (VCaP xenografts) bone metastasis and corresponding sham-operated animals. Expression levels are shown for PC-3 (blue bar), MDA-MB231 (red bar), VCaP (black bar) xenografts and corresponding sham-operated animals (white bar: sham-operated animals of PC3 and MDA-MB231 xenografts models; grey bar: sham-operated animals of VCaP xenografts). Values for each gene is shown as relative expression to mouse B2M (mean ± SD). * , P
    Paired End Rna Sequencing Sample Prep Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/paired end rna sequencing sample prep kit/product/Illumina Inc
    Average 90 stars, based on 4 article reviews
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    Illumina Inc base pair bp single end rna sequencing
    Expression analysis of endothelial cell, artery, pericyte and neuronal/neurite markers in osteolytic and osteoblastic bone metastasis (A) Fold change of genes, associated to endothelial cells, arteries, pericytes and neurons/neurites, measured by <t>RNA</t> sequencing (for PC-3 and <t>MDA-MB231</t> xenografts versus controls) or microarray data (for VCaP xenografts versus controls). B-J. Relative expression levels of endothelial cell (B) , artery (C-E) , pericyte (F-H) and neuron/neurite (I and J) markers in osteolytic (PC-3 and MDA-MB231 xenografts) and osteoblastic (VCaP xenografts) bone metastasis and corresponding sham-operated animals. Expression levels are shown for PC-3 (blue bar), MDA-MB231 (red bar), VCaP (black bar) xenografts and corresponding sham-operated animals (white bar: sham-operated animals of PC3 and MDA-MB231 xenografts models; grey bar: sham-operated animals of VCaP xenografts). Values for each gene is shown as relative expression to mouse B2M (mean ± SD). * , P
    Base Pair Bp Single End Rna Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/base pair bp single end rna sequencing/product/Illumina Inc
    Average 91 stars, based on 4 article reviews
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    Image Search Results


    Expression analysis of endothelial cell, artery, pericyte and neuronal/neurite markers in osteolytic and osteoblastic bone metastasis (A) Fold change of genes, associated to endothelial cells, arteries, pericytes and neurons/neurites, measured by RNA sequencing (for PC-3 and MDA-MB231 xenografts versus controls) or microarray data (for VCaP xenografts versus controls). B-J. Relative expression levels of endothelial cell (B) , artery (C-E) , pericyte (F-H) and neuron/neurite (I and J) markers in osteolytic (PC-3 and MDA-MB231 xenografts) and osteoblastic (VCaP xenografts) bone metastasis and corresponding sham-operated animals. Expression levels are shown for PC-3 (blue bar), MDA-MB231 (red bar), VCaP (black bar) xenografts and corresponding sham-operated animals (white bar: sham-operated animals of PC3 and MDA-MB231 xenografts models; grey bar: sham-operated animals of VCaP xenografts). Values for each gene is shown as relative expression to mouse B2M (mean ± SD). * , P

    Journal: Oncotarget

    Article Title: Osteolytic cancer cells induce vascular/axon guidance processes in the bone/bone marrow stroma

    doi: 10.18632/oncotarget.25608

    Figure Lengend Snippet: Expression analysis of endothelial cell, artery, pericyte and neuronal/neurite markers in osteolytic and osteoblastic bone metastasis (A) Fold change of genes, associated to endothelial cells, arteries, pericytes and neurons/neurites, measured by RNA sequencing (for PC-3 and MDA-MB231 xenografts versus controls) or microarray data (for VCaP xenografts versus controls). B-J. Relative expression levels of endothelial cell (B) , artery (C-E) , pericyte (F-H) and neuron/neurite (I and J) markers in osteolytic (PC-3 and MDA-MB231 xenografts) and osteoblastic (VCaP xenografts) bone metastasis and corresponding sham-operated animals. Expression levels are shown for PC-3 (blue bar), MDA-MB231 (red bar), VCaP (black bar) xenografts and corresponding sham-operated animals (white bar: sham-operated animals of PC3 and MDA-MB231 xenografts models; grey bar: sham-operated animals of VCaP xenografts). Values for each gene is shown as relative expression to mouse B2M (mean ± SD). * , P

    Article Snippet: MDA-MB231 xenografts The paired-end RNA sequencing was performed using an Illumina HiSeq 2000 sequencer.

    Techniques: Expressing, RNA Sequencing Assay, Multiple Displacement Amplification, Microarray

    A unique set of EMT genes are altered at the splicing level but not at the gene level Donut charts for RNA‐Seq analysis showing the differentially regulated alternative splicing events (ASEs) and their corresponding genes in ESRP1 knockdown cells compared to control cells; SE: skipped exon, RI: retained intron, MXE: mutually exclusive exons, A5SS: alternative 5′ splice site, and A3SS: alternative 3′ splice site. The “percent spliced in” (PSI or ψ) value was estimated. Differences in inclusion levels (∆ψ) between samples and their significance were calculated ( P

    Journal: EMBO Reports

    Article Title: Splicing factor ESRP1 controls ER‐positive breast cancer by altering metabolic pathways

    doi: 10.15252/embr.201846078

    Figure Lengend Snippet: A unique set of EMT genes are altered at the splicing level but not at the gene level Donut charts for RNA‐Seq analysis showing the differentially regulated alternative splicing events (ASEs) and their corresponding genes in ESRP1 knockdown cells compared to control cells; SE: skipped exon, RI: retained intron, MXE: mutually exclusive exons, A5SS: alternative 5′ splice site, and A3SS: alternative 3′ splice site. The “percent spliced in” (PSI or ψ) value was estimated. Differences in inclusion levels (∆ψ) between samples and their significance were calculated ( P

    Article Snippet: We next performed an Illumina paired‐end RNA sequencing (RNA‐Seq) of the 2C3 and 9C2‐ ESRP1 shRNA knockdown cells and their control counterparts (2‐control and 9‐control).

    Techniques: RNA Sequencing Assay

    High ESRP2 expression is not associated with prognosis in both ER+ and ER− breast tumors BreastMark microarray platform; Kaplan–Meier curves of overall survival (OS) in ER‐positive (ER+) breast cancer. A log rank test was used to calculate the P = 0.47 ( n = 708, number of events = 171) and P = 0.13 ( n = 253, number of events = 96)]. BreastMark microarray platform; Kaplan–Meier curves of overall survival (OS) in ER‐negative (ER−) breast cancer. A log rank test was used to calculate the P = 0.13 ( n = 253, number of events = 96). TCGA Breast Invasive Carcinoma (BRCA) RNA‐Seq dataset; Kaplan–Meier curves of overall survival (OS) in ER+ breast cancer. A log rank test was used to calculate the P = 0.45 ( n = 210, number of events = 49). TCGA Breast Invasive Carcinoma (BRCA) RNA‐Seq dataset; Kaplan–Meier curves of overall survival (OS) in ER− breast cancer. Red, high ESRP1 expression; black, low ESRP1 expression. A log rank test was used to calculate the P = 0.24 ( n = 129, number of events = 21). ESRP1 expression in breast cancer with poor prognosis. RT–qPCR assay showing that expression of ESRP1 is higher in patients with high recurrence scores in a Onco type DX cohort n = 59 (19 LS, 20 IS, and 20 HS); LS, low score; IS, intermediate score; and HS, high score, * represents P

    Journal: EMBO Reports

    Article Title: Splicing factor ESRP1 controls ER‐positive breast cancer by altering metabolic pathways

    doi: 10.15252/embr.201846078

    Figure Lengend Snippet: High ESRP2 expression is not associated with prognosis in both ER+ and ER− breast tumors BreastMark microarray platform; Kaplan–Meier curves of overall survival (OS) in ER‐positive (ER+) breast cancer. A log rank test was used to calculate the P = 0.47 ( n = 708, number of events = 171) and P = 0.13 ( n = 253, number of events = 96)]. BreastMark microarray platform; Kaplan–Meier curves of overall survival (OS) in ER‐negative (ER−) breast cancer. A log rank test was used to calculate the P = 0.13 ( n = 253, number of events = 96). TCGA Breast Invasive Carcinoma (BRCA) RNA‐Seq dataset; Kaplan–Meier curves of overall survival (OS) in ER+ breast cancer. A log rank test was used to calculate the P = 0.45 ( n = 210, number of events = 49). TCGA Breast Invasive Carcinoma (BRCA) RNA‐Seq dataset; Kaplan–Meier curves of overall survival (OS) in ER− breast cancer. Red, high ESRP1 expression; black, low ESRP1 expression. A log rank test was used to calculate the P = 0.24 ( n = 129, number of events = 21). ESRP1 expression in breast cancer with poor prognosis. RT–qPCR assay showing that expression of ESRP1 is higher in patients with high recurrence scores in a Onco type DX cohort n = 59 (19 LS, 20 IS, and 20 HS); LS, low score; IS, intermediate score; and HS, high score, * represents P

    Article Snippet: We next performed an Illumina paired‐end RNA sequencing (RNA‐Seq) of the 2C3 and 9C2‐ ESRP1 shRNA knockdown cells and their control counterparts (2‐control and 9‐control).

    Techniques: Expressing, Microarray, RNA Sequencing Assay, Quantitative RT-PCR

    High ESRP1 expression correlates with poor prognosis in estrogen receptor positive (ER+) but not in estrogen receptor negative (ER−) breast cancer BreastMark microarray platform; Kaplan–Meier curves of overall survival (OS), demonstrating that high expression of ESRP1 (red line ) is associated with poor prognosis in ER+ breast cancer. A log rank test was used to calculate P = 2.8 e‐07 ( n = 934, number of events = 216). BreastMark microarray platform; Kaplan–Meier curves of overall survival (OS) of ER− breast cancer. A log rank test was used to calculate P = 0.4481 ( n = 322, number of events = 130). BreastMark microarray platform; correlation of ESRP1 expression with overall survival in tamoxifen‐treated patients. A log rank test was used to calculate P = 1.218, e‐06 ( n = 210, number of events = 49). BreastMark microarray platform; correlation of ESRP1 expression with overall survival in chemotherapy‐treated patients. A log rank test was used to calculate the P = 0.28 ( n = 129, number of events = 21) The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA‐BRCA) RNA‐Seq dataset; Kaplan–Meier curves of overall survival (OS) in ER+ breast cancer, demonstrating that high expression of ESRP1 (red line ) is associated with poor prognosis in ER+ breast cancer. A log rank test was used to calculate P = 0.00011 ( n = 656, number of events = 62). The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA‐BRCA) RNA‐Seq dataset; Kaplan–Meier curves of overall survival (OS) in ER− breast cancer. Red‐high ESRP1 expression; Black‐low ESRP1 expression. A log rank test was used to calculate P = 0.19 ( n = 100, number of events = 17).

    Journal: EMBO Reports

    Article Title: Splicing factor ESRP1 controls ER‐positive breast cancer by altering metabolic pathways

    doi: 10.15252/embr.201846078

    Figure Lengend Snippet: High ESRP1 expression correlates with poor prognosis in estrogen receptor positive (ER+) but not in estrogen receptor negative (ER−) breast cancer BreastMark microarray platform; Kaplan–Meier curves of overall survival (OS), demonstrating that high expression of ESRP1 (red line ) is associated with poor prognosis in ER+ breast cancer. A log rank test was used to calculate P = 2.8 e‐07 ( n = 934, number of events = 216). BreastMark microarray platform; Kaplan–Meier curves of overall survival (OS) of ER− breast cancer. A log rank test was used to calculate P = 0.4481 ( n = 322, number of events = 130). BreastMark microarray platform; correlation of ESRP1 expression with overall survival in tamoxifen‐treated patients. A log rank test was used to calculate P = 1.218, e‐06 ( n = 210, number of events = 49). BreastMark microarray platform; correlation of ESRP1 expression with overall survival in chemotherapy‐treated patients. A log rank test was used to calculate the P = 0.28 ( n = 129, number of events = 21) The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA‐BRCA) RNA‐Seq dataset; Kaplan–Meier curves of overall survival (OS) in ER+ breast cancer, demonstrating that high expression of ESRP1 (red line ) is associated with poor prognosis in ER+ breast cancer. A log rank test was used to calculate P = 0.00011 ( n = 656, number of events = 62). The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA‐BRCA) RNA‐Seq dataset; Kaplan–Meier curves of overall survival (OS) in ER− breast cancer. Red‐high ESRP1 expression; Black‐low ESRP1 expression. A log rank test was used to calculate P = 0.19 ( n = 100, number of events = 17).

    Article Snippet: We next performed an Illumina paired‐end RNA sequencing (RNA‐Seq) of the 2C3 and 9C2‐ ESRP1 shRNA knockdown cells and their control counterparts (2‐control and 9‐control).

    Techniques: Expressing, Microarray, RNA Sequencing Assay

    Pipeline to identify and characterize novel RNA variants in CRC Analysis of genome-scale exon level microarray data revealed 25 candidate genes with overexpression of their 3′ parts, here exemplified with the BPIFA2 gene. The candidate genes were characterized with RACE-seq, a combination of 5′ RACE and deep sequencing. For the 25 candidate genes and also 3 positive control genes, nested RACE-primers were designed downstream of the suspected breakpoints (orange arrows). The resulting pools of RACE fragments (28 assays per sample) were prepared for sequencing with the Nextera XT protocol (Illumina), using tagmentation to simultaneously fragment and tag RACE-amplicons with adapters for sequencing. The fusion transcripts VWA2-TCF7L2, DHX35-BPIFA2 and CASZ1-MASP2 , and also 55 transcript junctions were identified by two separate computational approaches from the RACE-seq data. These were probed for in external datasets from TCGA, CCLE and the Illumina body map.

    Journal: Oncotarget

    Article Title: Novel RNA variants in colorectal cancers

    doi:

    Figure Lengend Snippet: Pipeline to identify and characterize novel RNA variants in CRC Analysis of genome-scale exon level microarray data revealed 25 candidate genes with overexpression of their 3′ parts, here exemplified with the BPIFA2 gene. The candidate genes were characterized with RACE-seq, a combination of 5′ RACE and deep sequencing. For the 25 candidate genes and also 3 positive control genes, nested RACE-primers were designed downstream of the suspected breakpoints (orange arrows). The resulting pools of RACE fragments (28 assays per sample) were prepared for sequencing with the Nextera XT protocol (Illumina), using tagmentation to simultaneously fragment and tag RACE-amplicons with adapters for sequencing. The fusion transcripts VWA2-TCF7L2, DHX35-BPIFA2 and CASZ1-MASP2 , and also 55 transcript junctions were identified by two separate computational approaches from the RACE-seq data. These were probed for in external datasets from TCGA, CCLE and the Illumina body map.

    Article Snippet: As additional normal control samples, paired-end RNA sequencing data from the Illumina Human Body Map v2 dataset consisting of 16 non-malignant miscellaneous tissue types was downloaded (ArrayExpress accession ID E-MTAB-513 and European Nucleotide Archive study accession ID ERP000546; paired-end fastq files; 50 nucleotides read-length).

    Techniques: Microarray, Over Expression, Sequencing, Positive Control