9172 results for "cancer rna-seq"

in 22.50 milliseconds.

• BLUEPRINT release January 2015, RNA-Seq for Leukemia

  RNA-Seq data for 1 Leukemia sample(s). 1 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_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001178

• BLUEPRINT release January 2015, RNA-Seq for macrophage

  RNA-Seq data for 18 macrophage sample(s). 19 run(s), 18 experiment(s), 18 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_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001199

• BLUEPRINT release August 2015, RNA-Seq for granulocyte monocyte progenitor cell, on genome GRCh38

  RNA-Seq data for 3 granulocyte monocyte progenitor cell sample(s). 3 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_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001501

• BLUEPRINT release August 2015, RNA-Seq for hematopoietic stem cell, on genome GRCh38

  RNA-Seq data for 6 hematopoietic stem cell sample(s). 13 run(s), 6 experiment(s), 6 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_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001515

• RNA-Seq of novel miR (nmiR-1 and nmiR-2) overexpression and knockdown in BL

  After overexpression and knockdown of both described novel miRs nmiR-1 and nmiR-2 in BL cell lines (SU-DHL4 for nmiR-1 and Raji for nmiR-2), we performed regular RNA-Seq (including Mock controls for all cell lines) to identify their direct and indirect downstream mRNA targets.

  Dataset EGAD00001001612

• BLUEPRINT release August 2015, RNA-Seq for common lymphoid progenitor, on genome GRCh38

  RNA-Seq data for 5 common lymphoid progenitor sample(s). 20 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_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001558

• BLUEPRINT release August 2015, RNA-Seq for common myeloid progenitor, on genome GRCh38

  RNA-Seq data for 3 common myeloid progenitor sample(s). 3 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_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001538

• BLUEPRINT release August 2016, RNA-Seq for hematopoietic stem cell, on genome GRCh38

  RNA-Seq data for 6 hematopoietic stem cell sample(s). 13 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_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002316

• BLUEPRINT release August 2016, RNA-Seq for granulocyte monocyte progenitor cell, on genome GRCh38

  RNA-Seq data for 3 granulocyte monocyte progenitor cell sample(s). 3 run(s), 3 experiment(s), 3 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_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002306

• BLUEPRINT release August 2016, RNA-Seq for common myeloid progenitor, on genome GRCh38

  RNA-Seq data for 3 common myeloid progenitor sample(s). 3 run(s), 3 experiment(s), 3 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_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002478

• BLUEPRINT release August 2016, RNA-Seq for common lymphoid progenitor, on genome GRCh38

  RNA-Seq data for 5 common lymphoid progenitor sample(s). 20 run(s), 5 experiment(s), 5 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_rnaseq_analysis_crg_20160816

  Dataset EGAD00001002489

• The effect of anti-HER2/CD3 TDB on transcription in human PBMCs (single-cell RNA-seq)

  Single-cell RNA-seq libraries were generated from human PBMCs that were incubated with anti-HER2/CD3 TDB in the presence of KPL-4 cells. This dataset is linked with the following ArrayExpress Experiment: E-MTAB-8212 - The effect of anti-HER2/CD3 TDB on transcription in human PBMCs (single-cell)

  Dataset EGAD00001005188

• Acute myeloid leukemia bulk RNA-seq (Diagnosis and Relapse)

  To gain insight into the clonal heterogeneity of diagnosis (Dx) and relapse (Re) pairs, we employed RNA-seq to longitudinally profile two t(8;21) (AML1-ETO = RUNX1-RUNX1T1), and four FLT3-ITD AML cases. All the samples are bone marrow aspirates.

  Dataset EGAD00001008374

• single-cell RNA-Seq samples of CRC patients

  The dataset contains samples of 11 CRC patients (2 samples for each patient, tumor and normal adjacent tissue site, 22 samples in total). Dataset is composed by fastq file (paired end) type from 10x single-cell RNA-Seq.

  Dataset EGAD00001009634

• RNA-Seq data for Academic and For-Profit researchers.

  RNA-Seq data for both Academic and For-profit use

  Dataset EGAD00001009676

• Deciphering RBP - alternative splicing networks in ALS iPSC-MN: patient and control datasets

  We produce RNA-seq datasets of iPSC-derived motor neurons (iPSC-MN) from healthy controls and sporadic ALS patients and controls and familial ALS patients with pathogenic variants in TARDBP.

  Study EGAS00001005879

• Nascent transcriptome in T-ALL bone marrow

  Nascent RNA expression profiles were generated with Global Run-On sequencing (GRO-seq) from T-ALL patient samples to measure primary transcription genome-wide and to summarize the transcriptional activity at gene loci and enhancers.

  Study EGAS00001005864

• RNAseq on 20 samples of multiple myeloma patients and 3 normal plasma cells.

  RNAseq was performed using 200 ng of total RNA by GATC Biotech. Directional libraries were performed after mRNA selection by polyA selection using UTP method. RNA-seq libraries were sequenced on HiSeq2500 Illumina machine using 100bp paired-end reads. Reads alignment was performed using the STAR aligner (version 2.4.0f1) and human genome hg19 as reference.

  Study EGAS00001004347

• Genomic and transcriptomic analysis of baseline PDAC patients' tumors from the OXIRI phase 1b clinical trial

  This study was aimed at investigating the genomic and transcriptomic features associated with response to the OXIRI regimen (oxaliplatin, irinotecan, capecitabine) in pancreatic ductal adenocarcinoma (PDAC) tumors. We performed whole-exome sequencing (WES) and RNA sequencing (RNA-seq) on baseline tumor samples obtained from 8 patients recruited in the OXIRI phase 1b clinical trial (NCT02368860).

  Study EGAS00001006073

• Comprehensive Transcriptional Analysis of Early Stage Urothelial Carcinoma using whole transcriptome sequencing

  The expression profile and sequence variants of 476 early stage urothelial carcinoma were studied using whole transcriptome sequencing. RNA-Seq libraries were prepared by Ribo-Zero treatment of total-RNA followed by library preparation using ScriptSeq (both Epicentre/Illumina). RNA-Seq libraries were paired-end sequenced (2x 101 bp) on Illumina HiSeq 2000 and the resulting fastq files were processed using tools from the Genome Analysis Toolkit (GATK and from the Tuxedo suite. Access to the sequence data (mapped and un-mapped bam and vcf files), containing person identifying information, needs signature on a controlled access form, and can be accessed at The European Genome-phenome Archive (EGA) following request. An expression matrice of FPKM values are available without restriction at ArrayExpress (E-MTAB-4321).

  Study EGAS00001001236

• Single Cell Analysis of Pulmonary Fibrosis

  Pulmonary fibrosis is a heterogenous syndrome in which fibrotic scar replaces normal lung tissue. We performed massively parallel single-cell RNA-Seq on lung tissue from eight lung transplant donors and eight patients with pulmonary fibrosis. Combined with in situ RNA hybridization, with amplification, these data provide a molecular atlas of disease pathobiology. We identified a distinct, novel population of profibrotic alveolar macrophages exclusively in patients with fibrosis. Within epithelial cells, the expression of genes involved in Wnt secretion and response was restricted to non-overlapping cells. We identified rare cell populations including airway stem cells and senescent cells emerging during pulmonary fibrosis. Analysis of a cryobiopsy specimen from a patient with early disease supports the clinical application of single-cell RNA-Seq to develop personalized approaches to therapy.

  Study phs001750

• Uncovering RNA Signatures of C9orf72-Linked ALS and Related Disorders

  Substantial clinical and pathological variability has been reported in patients carrying an expanded repeat in C9orf72, who are generally diagnosed with amyotrophic lateral sclerosis (ALS) and/or frontotemporal dementia (FTD). Emerging evidence suggests that C9orf72 expression, RNA foci, and dipeptide-repeat proteins contribute to C9orf72-related diseases; however, the majority of the clinicopathological variability remains unexplained. We hypothesize that RNA sequencing (RNA-Seq) might reveal individual genes or groups of highly correlated genes (modules) that could account for this variability, which may help to identify much-needed druggable targets and/or biomarkers. Our preliminary studies performed in the frontal cortex, where we compared C9orf72 expansion carriers to (disease) controls, demonstrated that the top differentially expressed gene was C9orf72 itself. We also noticed that differentially expressed genes were enriched for the endocytosis pathway, which is consistent with the reported function of the C9orf72 protein in vesicle trafficking. Furthermore, we detected a module enriched for vesicular pathways, and additionally, we discovered an association with survival after onset for several promising candidates involved in vesicular transport. To find new therapeutic targets and biomarkers, here we have completed RNA-Seq on an increased number of samples to examine another relevant region: the cerebellum. As such, we performed RNA-Seq on a well-characterized cohort of C9orf72 expansion carriers, patients without this expansion, and control subjects without neurological diseases. We used multivariable linear regression models for gene-level analysis, weighted correlation network analysis for module-level analysis, and leafcutter for splicing analysis. Using the cerebellar RNA-Seq data, we found a large number (>6,000) of differentially expressed genes, with a notable increase in expression of homeobox genes in C9orf72 expansion carriers, as well as many gene modules that were associated with C9orf72 expansion status. Additionally, using leafcutter, we detected over 1,000 differential splicing events and an increase in the number of cryptic splicing events in C9orf72 expansion carriers.

  Study phs003065

• RNA seq data (56 cases) for study EGAS00001001394

  Part of RNA sequencing data of Malignant Lymphoma Study (ICGC)

  Dataset EGAD00001001672

• RNA-Seq Single End

  RNA analysis of six patients 34, 35, 36, 37, 38 and 39 with WGS done on Illumina HiSeq2500. For research purpose and authorised user only.

  Dataset EGAD00001003430

• RNA sequencing of human lung fibroblasts

  Bulk RNA seq data from human lung fibroblasts isolated from fresh and cryopreserved lung tissue (18 samples, 3 donors)

  Dataset EGAD00001010252

• RNA Seq fastq files generated for the "Proteogenomic landscape of medulloblastoma subgroups"

  Dac EGAC00001000792

• RNA-sequencing of Non-muscle Invasive Bladder cancer (NMIBC)

  This RNA-sequencing cohort includes 78 Non-muscle Invasive Bladder cancer (NMIBC) samples and 7 Muscle Invasive Bladder cancer (MIBC) samples.

  Study EGAS00001004358

• RNA-seq analysis of megakaryocytes and granulocytes in Quebec platelet disorder

  Quebec Platelet disorder (QPD) is a unique bleeding disorder that markedly increases urokinase plasminogen activator (uPA) in megakaryocytes and platelets but not in plasma or urine. The cause is tandem duplication of a 77 kb region of chromosome 10 containing PLAU and C10orf55. Blood cells and cultured megakaryocytes from donors (7 QPD, 10 control subjects) were prepared for total and allele-specific, quantitative reverse transcription polymerase chain reaction, immunoassays, Western blots and RNA-seq. Transcriptomes for cultured megakaryocytes and peripheral blood granulocytes from 4 control and 3 QPD individuals were analyzed using mRNA-seq.

  Study EGAS00001001840

• Epigenomes and Transcriptomes of Brain Samples of Schizophrenics and Controls

  We examined the effects of antipsychotic medications on the cell-specific epigenomics and transcriptomics in the frontal cortex of schizophrenic subjects. We performed ChIP-seq (H3K4me3 and H3K27ac) and RNA-seq on neuronal and non-neuronal nuclei of postmortem frontal cortex samples from two cohorts of schizophrenics, either previously treated or not with antipsychotic medications, and control subjects individually matched by sex and age. In total, we tested 29 schizophrenics (15 untreated and 14 treated patients) and their matched control samples. Two replicates were produced on each brain sample for each assay. ChIP-seq data were generated using MOWChIP-seq (Zhu et al., PMID: 31666743) and RNA-seq data were produced using the combination of SMART-seq2 (Picelli et al., PMID: 24385147) and a Nextera XT DNA library preparation kit. The filename contains the information on the experimental group, the number of the sample within the group, the type of the brain nuclei, the epigenomic/transcriptomic data set (either H3K27ac or mRNA), and the number of replicate. For example, “SCZ-1-untreated-neuron-H3K4me3-R1” refers untreated schizophrenic sample #1, replicate 1 ChIP-seq data on H3K4me3.

  Study phs002487

• Discovery of immunotherapy targets for pediatric solid and brain tumors by exon-level expression

  Immunotherapy with chimeric antigen receptor T cells for pediatric solid and brain tumors is constrained by available targetable antigens. Cancer-specific exons present a promising reservoir of targets; however, these have not been explored and validated systematically in a pan-cancer fashion. To identify cancer specific exon targets, we analyze 1,532 RNA-seq datasets from 16 types of pediatric solid and brain tumors for comparison with normal tissues using a newly developed workflow. We find 2,933 exons in 157 genes encoding proteins of the surfaceome or matrisome with high cancer specificity either at the gene (n=148) or the alternatively spliced isoform (n=9) level. Expression of selected alternatively spliced targets, including the EDB domain of fibronectin 1, and gene targets, such as COL11A1, are validated in pediatric patient derived xenograft tumors. We generate T cells expressing chimeric antigen receptors specific for the EDB domain or COL11A1 and demonstrate that these have antitumor activity. The full target list, explorable via an interactive web portal (https://cseminer.stjude.org/), provides a rich resource for developing immunotherapy of pediatric solid and brain tumors using gene or AS targets with high expression specificity in cancer.

  Study EGAS00001007766

• The application of RNA sequencing for the diagnosis and genomic classification of pediatric acute lymphoblastic leukemia

  RNA-seq data for ALL patients as described in "The application of RNA sequencing for the diagnosis and genomic classification of pediatric acute lymphoblastic leukemia"

  Dataset EGAD00001006335

• Paired-end RNA-seq analysis of Juvenile Myelomonocytic Leukemia samples

  Dataset EGAD00001003794

• Human MPN RNA-seq and DNA methylation data requests committee

  Dac EGAC00001001688

• RNA-seq data of BRCA1/2 carriers from non-tumorous breast tissue

  Dac EGAC00001001859

• RNA-seq from FFPE - Englander Institute for Precision Medicine - Weill Cornell Medicine DAC

  Dac EGAC00001002098

• Epigenetic profiling of colorectal cancer initiating cells (CC-ICs) to identify bivalently marked genes (H3K4me3 and H3K27me3 ChIP-seq), and investigation of changes in transcriptome following EZH2 inhibition using RNA-seq.

  Epigenetic regulation of transcription plays a crucial role in lineage commitment of embryonic stem cells. Promoters of key lineage-specific differentiation genes are found in a repressed bivalent state, having both activating H3K4me3 and repressive H3K27me3 histone marks, making them poised for transcription upon loss of H3K27me3 in response to environmental cues. Whether the tumour-initiating, self-renewing, cancer-initiating cells (C-ICs) have similar epigenetic regulatory mechanism that prevent lineage commitment is unknown. In order to investigate bivalently marked and repressed promoters, we used a patient-derived CC-IC enriched model to identify the changes in transcriptome following inhibition of EZH2, the H3K27 methyltransferase. We also performed ChIP-seq for H3K27me3 and H3K4me3 at baseline in order to identify repressed and bivalently marked promoters.

  Study EGAS00001003003

• Genomic, transcriptomic and epigenomic profiling of GCTB

  Giant cell tumor of bone is a rare bone neoplasm driven by oncogenic hotspot G34W/L/V mutations in the non-canonical histone variant H3.3. This study provides primary data of genomic (WGS), transcriptomic (RNA-seq) and epigenomic (histone mark ChIP-seq, WGBS, ATAC-seq) profiling of primary GCTB samples from several cohorts in Germany and Korea. We confirm the H3.3-G34 mutations as sole genetic drivers of GCTB, and describe the epigenetic alterations in mutant GCTB stromal cells.

  Study EGAS00001003730

• HCC.GNE RNA-Seq

  RNA-Sequencing data (raw read sequences) for 23 samples, from 12 patients, for the study "Diverse modes of genomic alterations in Hepatocellular Carcinoma"

  Dataset EGAD00001000886

• RNA-seq of pcAECyTCL

  RNA sequencing of frozen tumor biopsies from patients with primary cutaneous CD8+ aggressive epidermotropic cytotoxic T-cell lymphoma. 6 samples. Illumina HiSeq 4000.

  Dataset EGAD00001006085

• RNA-Seq of paediatric patients with B lymphoblastic leukemia

  Whole transcriptome RNA-Sequencing was performed on 148 bone marrow or peripheral blood samples of B-ALL patients.

  Dataset EGAD00001006257

• BLUEPRINT release August 2014, RNA-Seq for inflammatory macrophage

  RNA-Seq data for 3 inflammatory macrophage sample(s). 3 run(s), 3 experiment(s), 3 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001000908

• BLUEPRINT release August 2014, RNA-Seq for mature neutrophil

  RNA-Seq data for 7 mature neutrophil sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001000904

• BLUEPRINT release August 2014, RNA-Seq for alternatively activated macrophage

  RNA-Seq data for 1 alternatively activated macrophage sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001000937

• BLUEPRINT release January 2015, RNA-Seq for mature neutrophil

  RNA-Seq data for 10 mature neutrophil sample(s). 10 run(s), 10 experiment(s), 10 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_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001129

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

  RNA-Seq data for 3 inflammatory macrophage sample(s). 3 run(s), 3 experiment(s), 3 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_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001132

• BLUEPRINT release January 2015, RNA-Seq for conventional dendritic cell

  RNA-Seq data for 1 conventional dendritic cell sample(s). 1 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_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001170

• BLUEPRINT release January 2015, RNA-Seq for memory B cell

  RNA-Seq data for 1 memory B cell sample(s). 1 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_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001171

• BLUEPRINT release January 2015, RNA-Seq for regulatory T cell

  RNA-Seq data for 1 regulatory T cell sample(s). 1 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_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001174

• BLUEPRINT release January 2015, RNA-Seq for Acute promyelocytic leukemia

  RNA-Seq data for 7 Acute promyelocytic leukemia 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_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001181

• BLUEPRINT release January 2015, RNA-Seq for alternatively activated macrophage

  RNA-Seq data for 4 alternatively activated macrophage sample(s). 6 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_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001202