10121 results for "cancer rna-seq"

in 35.73 milliseconds.

• 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

• BLUEPRINT release August 2014, RNA-Seq for common myeloid progenitor

  RNA-Seq data for 3 common myeloid progenitor 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 EGAD00001000907

• BLUEPRINT release August 2014, RNA-Seq for common lymphoid progenitor

  RNA-Seq data for 3 common lymphoid progenitor sample(s). 15 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 EGAD00001000918

• BLUEPRINT release August 2014, RNA-Seq for hematopoietic stem cell

  RNA-Seq data for 3 hematopoietic stem cell sample(s). 8 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 EGAD00001000939

• BLUEPRINT release August 2014, RNA-Seq for granulocyte monocyte progenitor cell

  RNA-Seq data for 3 granulocyte monocyte progenitor cell 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 EGAD00001000922

• BLUEPRINT release January 2015, RNA-Seq for granulocyte monocyte progenitor cell

  RNA-Seq data for 3 granulocyte monocyte progenitor cell 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 EGAD00001001146

• BLUEPRINT release January 2015, RNA-Seq for hematopoietic stem cell

  RNA-Seq data for 6 hematopoietic stem cell sample(s). 13 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_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001156

• BLUEPRINT release January 2015, RNA-Seq for common myeloid progenitor

  RNA-Seq data for 3 common myeloid progenitor 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 EGAD00001001169

• 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 common lymphoid progenitor

  RNA-Seq data for 5 common lymphoid progenitor sample(s). 20 run(s), 5 experiment(s), 5 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 EGAD00001001184

• 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

• Illumina RNA-Seq paired of 10 different tumor samples from the Master program (H021)

  Fastq files of paired RNA-Seq of 10 different tumor samples, for which Nanopore and Illumina sequencing was compared. Illumina sequencing was carried out with HiSeq4000 or HiSeq X-Ten using the Illumina TruSeq stranded mRNA Kit.

  Dataset EGAD00001008971

• 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

• ABCB1 expression in HCC biopsies

  We analyzed the ABCB1 expression in RNA-seq data of 134 HCCs (120 of these were previously published), including the biopsies from which the 3 doxorubicin-sensitive and 3 doxorubicin-resistant HCCOs were derived.

  Study EGAS50000000041

• 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 Pair End

  RNA analysis of two patients 11 and 15 with WGS done on Illumina HiSeq2000. For research purpose and authorised user only.

  Dataset EGAD00001003429

• RNA-seq data of HGG PDOX study

  Study EGAS00001004633

• Data Access Commitee Hidradenitis suppurativa RNA-Seq

  Dac EGAC00001002270

• Pheochromocytoma and paraganglioma single nuclei RNA-seq

  Dac EGAC00001002657

• COVID-19 RNA-seq Data Access Commitee

  Dac EGAC00001002979

• Breast Cancer Single-Cell RNA-Seq Dataset

  Single-cell RNA-Sequencing of 26 primary breast cancers from Wu et al. (2021) study. Data was generated using the Chromium controller (10X Genomics) and sequenced on the NextSeq 500 platform.

  Dataset EGAD00001007495

• 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

• Cancer and germline exomes, and cancer RNA-seq consisiting of FASTQ paired-end reads from melanoma, lung and colon cancer samples

  Discovery of patient-specific tumor antigens usually requires in vitro-expanded autologous tumor infiltrating lymphocytes (TILs), among which tumor antigen-specific T cells are however often rare, thus limiting sensitivity. We designed in vitro culture conditions to improve the identification of rare tumor antigen-specific CD8 TILs. This innovative yet accessible pipeline allows highly-sensitive identification of tumor antigens and cognate T cell receptors (TCRs), greatly improving the selection of candidates for personalized cancer vaccines and TCR-based cellular immunotherapies.

  Study EGAS00001005513

• H005 RNA-seq CLL

  Paired-end RNA sequencing using total RNA from 136 primary lymphoma samples. Sequencing was performed on the Illumina HiSeq2000 with 300bp insert size. The dataset contains FASTQ files.

  Dataset EGAD00001002056

• Whole transcriptome profiling of liquid biopsies from tumour xenografted mouse models: validation cohort

  Total RNA sequencing (SMARTer Stranded Total RNA-Seq Kit v2) data of extracellular RNA (exRNA) from liquid biopsies of the validation PDX/CDX cohort

  Dataset EGAD00001009413

• GEP-NEN Bulk-RNA-seq dataset

  This dataset entails 40 Bulk-RNA sequenced patient-derived gastro-intestinal neuroendocrine (GEP-NEN) neoplasms.

  Dataset EGAD00001006657

• RNA-seq data from the EUROBATS Project in four tissues: Fat, LCL, Skin and whole Blood.

  EUROBATS consists of RNA-seq data for female twins in lisphoblastoide cell lines (LCL), abdominal adipose tissue (Fat), abdominal skin tissue (Skin) and whole blood (Blood). The samples are a combination of MZ twins, DZ twins and singletons. The goal of the project is to find biomarkers related with the ageing process and cellular senescence.

  Study EGAS00001000805

• Sequencing Lymphoma

  This repository contains sequencing data to describe the genomic profiles of several B-cell lymphomas including follicular lymphoma and Hodgkin lymphoma. We have used several different high throughput sequencing technologies to interrogate genomic DNA and RNA from tumor cells obtained from lymph node biopsies and normal cells obtained from skin biopsies and peripheral blood mononuclear cells. A number of sequencing platforms for DNA, RNA, and protein were used to generate the data. These platforms include exome sequencing and a custom capture panel (NimbleGen) that targets 7.05 MB corresponding to the exons and splice sites of 1716 genes related to lymphoma biology (WUSM-LP). Other platforms include single-cell RNA-seq and Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), which was used to describe transcriptional and proteomic changes in immune cell subsets within lymphoma patients pre- and post-therapy.

  Study phs001229

• RNA-seq data from 27 glioblastoma samples

  Study EGAS00001005807

• Leiden University Medical Center Adipose tissue RNA-seq

  Dac EGAC00001000503

• Board considering access to BELOB RNA-seq data

  Dac EGAC00001001686

• fibroblast RNAseq from a GINS3 patient and two parents

  RNA-seq was performed from 3 separate GINS3 patient fibroblast cultures and 1 replicate of fibroblasts derived from each of the two parents. RNA-seq libraries were generated with NEBNext Ultra II Directional RNA library prep for Illumina with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and sequenced on Illumina NextSeq500 with paired-end 150 bp read length. SIRV Set 3 (Lexogen) spike-ins were added. Two fastq files are provided for each RNAseq sample.

  Dataset EGAD00001008571

• Single-cell RNA and DNA sequencing data obtained after genome-and-transcriptome separation.

  This dataset contains single-cell RNA and DNA sequencing data (fastq, n=928) obtained after genome-and-transcriptome separation. The RNA-seq data was obtained by Smart-seq2 amplification and Nextera XT library preparation. The DNA-seq data was obtained either by Gtag library preparation and amplification or by PicoPlex whole-genome amplification followed by Nextera XT library preparation. The single cells originate from a human PDX melanoma model and from HCC38 and HCC38 BL cell lines. The sequencing libraries were sequenced with Illumina instruments.

  Dataset EGAD00001010096

• Exploration of coding and non-coding variants in cancer using GenomePaint.

  GenomePaint (https://proteinpaint.stjude.org/genomepaint) is a dynamic visualization platform for whole-genome, whole-exome, transcriptome, and epigenomic data, featuring a novel design that captures the inter-relatedness between DNA variations and RNA expression. Regulatory non-coding variants can be inspected and discovered along with coding variants, and their functional impact further explored by examining 3D genome and/or ChIP-seq data generated from cancer cell lines. Further, GenomePaint correlates mutation and expression patterns with patient outcomes, and can display external data such as adult cancer datasets and user-provided custom tracks. We used GenomePaint to analyze multi-omics data from 3,652 pediatric cancers representing 16 histotypes, and demonstrate the visualization features through examples, including two that led to new insights into oncogenic mechanisms in pediatric cancer. The first is the discovery of a new class of pathogenic recurrent variants that cause aberrant splicing, disrupting the RING domain of CREBBP, a driver gene frequently mutated in relapsed pediatric leukemia. The second is the cis-activation of the MYC oncogene in a subset of B-lineage acute lymphoblastic leukemia (B-ALL) via duplication of the NOTCH1-MYC enhancer (N-ME), previously discovered only in T-lineage ALL. The regulatory impact of N-ME enhancer amplification was initially confirmed by allelic imbalance in published gene expression and ChIP-seq data and verified by additional Capture-C and fluorescence in situ hybridization data generated by follow-up experiments. These examples demonstrate the power of GenomePaint in enabling not only data visualization but also integrative genomic analysis that can lead to novel biological insight for follow-up experimental validation.

  Study EGAS00001004669

• Pharmacogenomics of T-ALL

  Whole exome seq (N=21) and RNA-seq (N=36) data of additional T-ALL

  Dataset EGAD00001006434

• RNA-seq of pcALCL

  RNA sequencing of frozen tumor biopsies from patients with primary cutaneous anaplastic large cell lymphoma. 12 samples. Illumina HiSeq 4000.

  Dataset EGAD00001006178

• rna-seq data of multiple myeloma patients

  6 samples from individuals with multiple myeloma with selective elimination of immunosuppressive T cells, rna sequencing

  Dataset EGAD00001006866

• Circulating RNAs prior to endometrial cancer diagnosis

  We analyzed circulating RNA levels using small RNA sequencing, targeting RNA in the size range 17 to 47 nucleotides, in samples collected prior to endometrial cancer diagnosis compared to cancer-free controls. The analysis included 316 cases with samples collected 1-11 years prior to diagnosis , and 316 matched controls, both from the Janus Serum Bank Cohort in Norway.

  Study EGAS50000000267

• InsPIRE islets

  We explored the relationship between genetic variants influencing predisposition to type 2 diabetes (T2D) and related glycemic traits, and human pancreatic islet transcription using RNA-Seq and genotyping data from 420 islet donors and 26 FAC sorted beta-cells.

  Study EGAS00001003997

• BLUEPRINT release August 2014, RNA-Seq for megakaryocyte-erythroid progenitor cell

  RNA-Seq data for 4 megakaryocyte-erythroid progenitor cell sample(s). 4 run(s), 4 experiment(s), 4 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 EGAD00001000915

• BLUEPRINT release August 2014, RNA-Seq for hematopoietic multipotent progenitor cell

  RNA-Seq data for 3 hematopoietic multipotent progenitor cell sample(s). 9 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 EGAD00001000919

• BLUEPRINT release January 2015, RNA-Seq for megakaryocyte-erythroid progenitor cell

  RNA-Seq data for 4 megakaryocyte-erythroid progenitor cell sample(s). 4 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 EGAD00001001140

• 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 hematopoietic multipotent progenitor cell

  RNA-Seq data for 3 hematopoietic multipotent progenitor cell sample(s). 9 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 EGAD00001001186

• 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

• 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

• Ewing's Sarcoma RNA-Seq

  28 Pretreated Ewing sarcoma tumor blood samples were collected from the Hospital for Sick Children (SickKids) and Mount Sinai Hospital in Toronto, Canada in accordance with each institution’s Research Ethical Board (REB) guidelines. Detailed clinical information (age at presentation, gender, tumor site, stage, etc.) were obtained from the corresponding institutional tumor banks. Transcriptome (RNA-Seq) sequencing was performed using established protocols on Illumina instruments.

  Dataset EGAD00001004188

• 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