15020 results for "cancer studies using rna-seq"

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• BLUEPRINT release August 2015, ChIP-Seq for Multiple myeloma, on genome GRCh38

  ChIP-Seq data for 2 Multiple myeloma sample(s). 16 run(s), 14 experiment(s), 14 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001592

• BLUEPRINT release August 2016, ChIP-Seq for Acute Promyelocytic Leukemia - MC2884 (4h), on genome GRCh38

  ChIP-Seq data for 1 Acute Promyelocytic Leukemia - MC2884 (4h) sample(s). 6 run(s), 6 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002372

• BLUEPRINT release August 2016, ChIP-Seq for Chronic Lymphocytic Leukemia, on genome GRCh38

  ChIP-Seq data for 106 Chronic Lymphocytic Leukemia sample(s). 174 run(s), 163 experiment(s), 162 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002384

• BLUEPRINT release August 2016, ChIP-Seq for Mantle Cell Lymphoma, on genome GRCh38

  ChIP-Seq data for 5 Mantle Cell Lymphoma sample(s). 35 run(s), 35 experiment(s), 35 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002397

• BLUEPRINT release August 2016, ChIP-Seq for monocyte - RPMI_BG_T=24hrs, on genome GRCh38

  ChIP-Seq data for 3 monocyte - RPMI_BG_T=24hrs sample(s). 8 run(s), 8 experiment(s), 8 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002408

• BLUEPRINT release August 2016, ChIP-Seq for Acute Promyelocytic Leukemia - MC3324, on genome GRCh38

  ChIP-Seq data for 1 Acute Promyelocytic Leukemia - MC3324 sample(s). 2 run(s), 1 experiment(s), 1 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002431

• BLUEPRINT release August 2016, ChIP-Seq for neutrophilic metamyelocyte, on genome GRCh38

  ChIP-Seq data for 4 neutrophilic metamyelocyte sample(s). 32 run(s), 23 experiment(s), 23 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002435

• BLUEPRINT release August 2016, ChIP-Seq for mature eosinophil, on genome GRCh38

  ChIP-Seq data for 2 mature eosinophil sample(s). 14 run(s), 14 experiment(s), 14 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002477

• BLUEPRINT release August 2016, Bisulfite-Seq for CD38-negative naive B cell, on genome GRCh38

  Bisulfite-Seq data for 4 CD38-negative naive B cell sample(s). 51 run(s), 5 experiment(s), 8 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816

  Dataset EGAD00001002520

• mRNA-seq of in vitro differentiation from induced pluripotent stem cells to hepatocyte-like cells

  Fastq files of mRNA-seq data of induced pluripotent stem cells (iPSC), definitive endoderm (DE) and hepatocyte-like cells (HLC). The dataset comprises data from the in vitro differentiation protocol Cellartis (Takara Bio, "CEL", n = 4) and several interventions (11x3 replicates).

  Dataset EGAD00001005935

• Whole genome sequencing

  Whole genome sequencing of high-grade serous ovarian cancer (HGSC) tumours and matched normals from 15 patients with homologous recombination deficiencies. The dataset includes fastq files from 56 HGSC tumours (1 primary, 1 relapse, 54 end-stage) and 15 matched normals. Sequence libraries were generated from tumour and matched normal genomic DNA using the KAPA HyperPrep PCR-free library preparation kit (Roche), or the Illumina TruSeq DNA Nano kit according to manufacturer’s instructions. Sequencing was carried out by the Kinghorn Centre for Clinical Genomics Sequencing Laboratory (Sydney, Australia) on the HiSeq X Ten System (Illumina) or by the Australian Genome Research Facility (Melbourne, Australia) on an Illumina NovaSeq to a minimum base coverage of 30-fold for normal DNA and 60-fold for tumour DNA samples.

  Dataset EGAD00001009746

• POETIC clinical Trial Ki67 Bookend Breast Cancer Targeted Exome and RNAseq Project

  Using RNAseq, we compare the 15% of poorest responders (PRs, n=177) as measured by proportional Ki67 changes after 2 weeks of neoadjuvant aromatase inhibitors to good responders (GRs, n=190) selected from the top 50% responders in the POETIC trial and matched for baseline Ki67 categories. In the POETIC trial, 4,480 postmenopausal women with primary ER+ BC were randomised 2:1 to receive either treatment with a non-steroidal AI (letrozole or anastrozole) for 2 weeks before and 2 weeks after surgery or to no perisurgical treatment. Only AI-treated patients with HER2- tumors, paired baseline and surgery Ki67 available, and baseline Ki67 immunohistochemistry (IHC) >10% (to minimise imprecision in proportional Ki67 falls) were included for selection. Data is baseline RNAseq and targeted exome DNA sequencing analysis of POETIC Good/Poor Responders to aromatase inhibitors based on change in Ki67.

  Dataset EGAD00001010919

• Single-cell gene expression data from CD8+ T cells from two Austrian COVID19 patients stimulated with wildtype and mutant SARS-Cov-2 peptides

  The data contains single-cell gene sequencing data (10x Genomics) from FACS-purified CD8 T lymphocytes from two Austrian patients. The cells were stimulated with one MHC class I peptides obtained from a common (wild type) variant and an emerging mutant variant of the SARS-Cov-2 virus. Then the samples were multiplexed using hashtag oligos. We provide the raw and aligned sequence data for: i. The single-cell experiments ii. The PCR-amplified samples for enrichment of the hashtag oligo multiplexing barcodes iii. The PCR-amplified samples for enrichment of the T Cell Receptor (TCR) VDJ region for immuno-profiling. The samples and libraries were processed and obtained in collaboration between St. Anna Children's Cancer Research Institute (CCRI), CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, and the Medical University of Vienna. The cell barcodes and processed data has been submitted to the GEO database with GEO accession GSE166651.

  Dataset EGAD00001006995

• Integrated Genomic Analyses of Cutaneous T Cell Lymphomas Reveal the Molecular Bases for Disease Heterogeneity

  Cutaneous T cell lymphomas (CTCLs) are a clinically diverse collection of lymphomas of the skin-homing T cell. In the present study, we performed DNA and RNA sequencing on a cohort of CTCLs with representative samples from varying disease subtypes and stages. We characterized the landscape of putative driver genes, identified genetic relationships between CTCLs across disease stages, and inferred molecular subtypes in patients with stage-matched leukemic disease. Collectively, our findings clarify CTCL genetics and provide novel insights into pathways that drive diverse disease phenotypes. DNA and RNA sequencing was performed on 114 and 96 samples respectively. Tumor samples were obtained from University of Chicago (Chicago, IL), Northwestern University (Chicago, IL) and Yale University (New Haven, CT). 

  Study phs002456