9338 results for "cancer rna-seq"

in 59.14 milliseconds.

• BLUEPRINT release August 2016, Bisulfite-Seq for germinal center B cell, on genome GRCh38

  Bisulfite-Seq data for 3 germinal center B cell sample(s). 37 run(s), 4 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_bisulphite_analysis_CNAG_20160816

  Dataset EGAD00001002511

• 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

• Chromatin 3D interactions mediate genetic effects on gene expression (ChIP-seq)

  ChIP-seq data for Lymphoblastoid Cell Lines (LCL) and Fibroblasts (FIB) from the Gencord Cohort: - 160 LCLs assayed for H3K27ac, H3K4me1 and H3K4me3, - 78 FIB assayed for H3K4me3 and 79 FIB assayed for H3K27ac and H3K4me1 This dataset was generated as part of the following study: Delaneau et al (2019). Chromatin 3D interactions mediate genetic effects on gene expression.

  Dataset EGAD00001004871

• BLUEPRINT release January 2015, ChIP-Seq for Chronic lymphocytic leukemia

  ChIP-Seq data for 3 Chronic lymphocytic leukemia sample(s). 6 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001001187

• BLUEPRINT release January 2015, ChIP-Seq for mature eosinophil

  ChIP-Seq data for 2 mature eosinophil sample(s). 12 run(s), 12 experiment(s), 12 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001001168

• BLUEPRINT release January 2015, Bisulfite-Seq for central memory CD8-positive, alpha-beta T cell

  Bisulfite-Seq data for 2 central memory CD8-positive, alpha-beta T cell sample(s). 27 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001180

• BLUEPRINT release January 2015, ChIP-Seq for Acute myeloid leukemia

  ChIP-Seq data for 7 Acute myeloid leukemia sample(s). 23 run(s), 23 experiment(s), 23 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001001188

• BLUEPRINT release January 2015, Bisulfite-Seq for CD8-positive, alpha-beta T cell

  Bisulfite-Seq data for 4 CD8-positive, alpha-beta T cell sample(s). 56 run(s), 4 experiment(s), 4 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001189

• BLUEPRINT release January 2015, ChIP-Seq for erythroblast

  ChIP-Seq data for 2 erythroblast sample(s). 14 run(s), 14 experiment(s), 14 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001001194

• BLUEPRINT release January 2015, ChIP-Seq for monocyte

  ChIP-Seq data for 2 monocyte sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001001197

• BLUEPRINT release January 2015, Bisulfite-Seq for effector memory CD8-positive, alpha-beta T cell

  Bisulfite-Seq data for 1 effector memory CD8-positive, alpha-beta T cell sample(s). 11 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001200

• BLUEPRINT release January 2015, ChIP-Seq for inflammatory macrophage

  ChIP-Seq data for 6 inflammatory macrophage sample(s). 35 run(s), 35 experiment(s), 35 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001001204

• BLUEPRINT release January 2015, Bisulfite-Seq for CD14-positive, CD16-negative classical monocyte

  Bisulfite-Seq data for 6 CD14-positive, CD16-negative classical monocyte sample(s). 86 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001206

• BLUEPRINT release August 2015, Bisulfite-Seq for cytotoxic CD56-dim natural killer cell, on genome GRCh38

  Bisulfite-Seq data for 2 cytotoxic CD56-dim natural killer cell sample(s). 24 run(s), 2 experiment(s), 2 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_bisulphite_analysis_CNAG_20150820

  Dataset EGAD00001001473

• BLUEPRINT release August 2015, Bisulfite-Seq for memory B cell, on genome GRCh38

  Bisulfite-Seq data for 1 memory B cell sample(s). 20 run(s), 1 experiment(s), 1 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_bisulphite_analysis_CNAG_20150820

  Dataset EGAD00001001479

• BLUEPRINT release August 2015, Bisulfite-Seq for endothelial cell of umbilical vein (resting), on genome GRCh38

  Bisulfite-Seq data for 2 endothelial cell of umbilical vein (resting) sample(s). 2 run(s), 2 experiment(s), 2 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_bisulphite_analysis_CNAG_20150820

  Dataset EGAD00001001486

• BLUEPRINT release August 2015, Bisulfite-Seq for hematopoietic multipotent progenitor cell, on genome GRCh38

  Bisulfite-Seq data for 1 hematopoietic multipotent progenitor cell sample(s). 5 run(s), 1 experiment(s), 1 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_bisulphite_analysis_CNAG_20150820

  Dataset EGAD00001001493

• BLUEPRINT release August 2015, Bisulfite-Seq for conventional dendritic cell, on genome GRCh38

  Bisulfite-Seq data for 2 conventional dendritic cell sample(s). 30 run(s), 2 experiment(s), 2 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_bisulphite_analysis_CNAG_20150820

  Dataset EGAD00001001497

• BLUEPRINT release August 2015, Bisulfite-Seq for alternatively activated macrophage, on genome GRCh38

  Bisulfite-Seq data for 5 alternatively activated macrophage sample(s). 79 run(s), 5 experiment(s), 5 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_bisulphite_analysis_CNAG_20150820

  Dataset EGAD00001001498

• BLUEPRINT release August 2015, Bisulfite-Seq for CD4-positive, alpha-beta T cell, on genome GRCh38

  Bisulfite-Seq data for 3 CD4-positive, alpha-beta T cell sample(s). 61 run(s), 3 experiment(s), 3 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_bisulphite_analysis_CNAG_20150820

  Dataset EGAD00001001516

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

  ChIP-Seq data for 1 Leukemia sample(s). 2 run(s), 2 experiment(s), 2 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 EGAD00001001528

• BLUEPRINT release August 2015, Bisulfite-Seq for endothelial cell of umbilical vein (proliferating), on genome GRCh38

  Bisulfite-Seq data for 2 endothelial cell of umbilical vein (proliferating) sample(s). 36 run(s), 2 experiment(s), 2 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_bisulphite_analysis_CNAG_20150820

  Dataset EGAD00001001510

• BLUEPRINT release August 2015, Bisulfite-Seq for class switched memory B cell, on genome GRCh38

  Bisulfite-Seq data for 2 class switched memory B cell sample(s). 21 run(s), 2 experiment(s), 2 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_bisulphite_analysis_CNAG_20150820

  Dataset EGAD00001001548

• BLUEPRINT release August 2015, Bisulfite-Seq for regulatory T cell, on genome GRCh38

  Bisulfite-Seq data for 1 regulatory T cell sample(s). 15 run(s), 1 experiment(s), 1 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_bisulphite_analysis_CNAG_20150820

  Dataset EGAD00001001564

• BLUEPRINT release August 2015, Bisulfite-Seq for CD8-positive, alpha-beta T cell, on genome GRCh38

  Bisulfite-Seq data for 4 CD8-positive, alpha-beta T cell sample(s). 56 run(s), 4 experiment(s), 4 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_bisulphite_analysis_CNAG_20150820

  Dataset EGAD00001001571

• BLUEPRINT release August 2015, Bisulfite-Seq for germinal center B cell, on genome GRCh38

  Bisulfite-Seq data for 1 germinal center B cell sample(s). 6 run(s), 1 experiment(s), 1 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_bisulphite_analysis_CNAG_20150820

  Dataset EGAD00001001587

• BLUEPRINT release August 2015, Bisulfite-Seq for CD38-negative naive B cell, on genome GRCh38

  Bisulfite-Seq data for 4 CD38-negative naive B cell sample(s). 44 run(s), 4 experiment(s), 4 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_bisulphite_analysis_CNAG_20150820

  Dataset EGAD00001001590

• BLUEPRINT September 2016, Bisulfite-Seq Acute Lymphocytic Leukemia for precursor B cell from bone marrow, on Genome GRCh38

  Bisulfite-Seq data for 1 sample(s) Acute Lymphocytic Leukemia for precursor B cell from bone marrow, on Genome GRCh38. 3 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001002969

• ATAC-Seq/Hi-C/4C-Seq dataset for Malignant rhabdoid study

  Study describing the dynamics of chromatin organization within malignant rhabdoid tumors. This study describes how this chromatin organization changes upon SMARCB1 rescue within patient-derived organoid models from malignant rhabdoid tumors. Identification of a novel super-enhancer of MYC and identification of patient-specific enhancer utilization to activate MYC expression in these tumors.

  Dataset EGAD00001011820

• Single-cell RNA-sequencing reveals that glioblastoma recapitulates a normal neurodevetlopmental hierarchy

  Dac EGAC00001001625

• RNA sequencing of control OM cells exposed to traffic-related air pollutants

  Study EGAS00001007528

• RNA Sequencing of paediatric patients with B lymphoblastic leukemia

  Study EGAS00001003726

• Tumor-derived cell lines as pharmacogenomic models to predict therapeutic vulnerabilities in hepatocellular carcinoma

  Hepatocellular carcinoma (HCC) is a heterogeneous aggressive malignancy with low efficacy of current therapies at advanced stages. We integrated molecular and pharmacological profiling of a large panel of liver cancer cell lines (LCCL) to assess their clinical relevance as HCC preclinical models and identify new effective therapies and biomarkers of response. We performed multi-omic analysis including whole-exome, RNA and miRNA sequencing and quantification of 126 proteins in a series 34 LCCL coupled with a screening of 29 anti-cancer agents. Molecular profiles of LCCL and primary HCC were compared and we searched for molecular features associated with drug response. Our panel of LCCL faithfully recapitulated the most aggressive molecular "proliferation class" of HCC. Genomic alterations of the RAS-MAPK pathway correlated with trametinib sensitivity that was more potent than FGFR4 inhibitors in tumor cells depending on the FGF19/FGFR4 pathway. Moreover, we showed that FGF19 amplification was only functional in tumor cells that retained a hepatocyte differentiation program with expression of FGFR4, KLB and NR1H4 highlighting the complex interplay between the genomic and transcriptomic context in drug response. We also identified drugs/combination that could target efficiently the transcriptomic "progenitor subclass of HCC", as well as specific genetic contexts such as inactivating mutations in TSC1/TSC2 and TP53 associated with higher sensitivity to the mTOR inhibitor rapamycin and the AURKA inhibitor alisertib, respectively. LCCL represent relevant preclinical models for drug-biomarker discovery in HCC and enabled to identify molecular contexts linked with particular therapeutic vulnerabilities that may be useful to stratify patients in future clinical trials

  Study EGAS00001003536

• Rapid Idiosyncratic Mechanisms of Clinical Resistance to KRAS G12C Inhibition

  Using deep RNA and whole exome sequencing of pre- and post-treatment autopsy samples, we reveal diverse clonal populations that occurred through altered cell intrinsic, tumor microenvironment and immunologic remodeling mechanisms of resistance.

  Study phs002734

• The study on genomic profiling using clinical specimens (tissue, blood, etc.) form patients with lung and thymic tumors

  The objective is to generate a comprehensive immunogenomic profiling in thymoma using RNA sequencing and TCR repertoire analysis and to evaluate the potential of immunotherapy in thymoma from multiple perspectives.

  Study JGAS000552

• Single-cell RNA sequencing on 5063 single T cells from six hepatocellular carcinoma patients

  T cells isolated from peripheral blood, tumors and adjacent normal tissues from six hepatocellular carcinoma patients. SmartSeq2 and Tang2009 protocol were used to amplify RNA from single T cells. High depth enables simultaneously expression profiling and TCR assembling.

  Dataset EGAD00001003337

• Single Cell RNA sequencing of Organoids from TSC2+/- patient IPSCs in H- and L-medium

  This dataset contains single cell RNA sequencing data from Organoids grown in high nutrient (H) and low nutrient (L) medium. Organoids were grown for 110 days. Organoids were grown from a patient IPS cell line with a heterozygous mutation in TSC2 (Patient 1 TSC2+/- iPSCs) and an isogenic control cell line (TSC2+/+).

  Dataset EGAD00001006332

• 5' single cell RNA sequencing

  Pared-end fastq files of 22 AML and 2 normal bone marrow samples were generated using 10x Genomics 5' single cell RNA sequencing following manufacturer's protocol (CG000086 User Guide RevG) for chemistry version 1.0 and targeting 10000 cells per sample. Libraries were sequenced using Illumina HiSeq 4000 using recommended cycling parameters.

  Dataset EGAD00001007672

• Dataset on keratinocytic gene expression pattern in Hidradenitis suppurativa

  Human skin samples were obtained from HS patients after informed consent (Ethical vote, University of Würzburg; No. 306/12). Lesional and perilesional were taken and epidermis and dermis separated. Isolated epidermal keratinocytes were further processed for RNA isolation. mRNA was extracted from five pairwise-matched lesional and perilesional epidermal HS pellets and RNA sequencing was performed.

  Dataset EGAD00001008005

• RNA-sequencing data of post-mortem brain tissue taken from individuals with SCA3 and controls

  Spinocerebellar ataxia type 3 (SCA3) is the most common autosomal dominant inherited ataxia worldwide, caused by a CAG repeat expansion in the Ataxin-3 gene resulting in a polyglutamine (polyQ)-expansion in the corresponding protein. Here we have RNA-sequencing data from the cerebellum of individuals with SCA3 and matched controls.

  Dataset EGAD00001009317

• AML scRNA-seq

  Dataset EGAD00001006537

• ChIP_2PEAKS

  Second batch of ChIP-seq narrowPeaks. Software: MACS2 v2.1.2

  Dataset EGAD00010002051

• DNA and RNA sequencing data from Ovarian Carcinosarcoma patients from the Glasgow Cohort.

  In this study, we analysed DNA and RNA sequencing data from Ovarian Carcinosarcoma patients, from isolated carcinoma and sarcoma components and investigated DNA variants as well as gene expression. Genomic analyses from this data and further investigation from preclinical models of ovarian carcinosarcoma support the conversion theory for disease development and indicate that microtubule inhibitors could be used to suppress EMT and stimulate anti-tumour immunity.

  Study EGAS00001006605

• RNAseq data of polyA+ RNA from Leukocytes from 624 individuals of the ProgeNIA cohort.

  We sequenced the polyA+ fraction of the RNA of the leukocytes from 624 sardinian individuals with RNAseq. Prior to library preparation we added either ERCC ExFold RNA Spike-In. An average of 60M reads per samples with 51 bp paired-end reads were generated on a HiSeq 2000 (Illumina). Sequencing reads were then aligned using STAR-2.2.0c2 to the h37d5 reference genome supplemented with the ERCC spike-ins sequences. We further provided an exon-exon junction database that we generated from the GENCODE v14 annotation. In order to remove a contamination from a parallel experiment, we discarded any reads that mapped to the genomic regions of CBLB (chr3:105370773-105592330) and BCL11A (chr2:60672555-60784156). Filtered aligned reads (bam format) are shared.

  Dataset EGAD00001003102

• DAC: Whole transcriptome RNA sequencing as comprehensive diagnostic tool for acute myeloid leukemia.

  Dac EGAC00001000956

• RNA sequencing of chondrosarcoma

  To profile chondrosarcoma patients.

  Study EGAS00001004585

• Performance assessment of Total RNA sequencing of human biofluids and extracellular vesicles

  Study EGAS00001004428

• RNA Editing Genotype

  Genotyping using Affymetrix SNP6.0

  Dataset EGAD00010000847

• Dataset that contains analyses of submission 27

  Description of analyses dataset of submission 27

  Dataset EGAD50000000113

• Single cell RNA-sequencing of tissues from NSCLC patients treated with chemoimmunotherapy

  Study EGAS00001006728