12214 results for "cancer rna-seq"

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• RNA-seq dataset of CD34+ HSPCs from LRMDS patients

  To profile transcriptional alterations of HSPCs in LR-MDS patients, 7AAD−CD45+Lin-CD235a−CD34+ cells were isolated from healthy donors and LR-MDS patients for RNA sequencing.

  Dataset EGAD00001015771

• National Cancer Institute Cancer Genome Characterization Initiative (CGCI)

  The Office of Cancer Genomics at the National Cancer Institute sponsored a series of studies as part of the Cancer Genome Characterization Initiative (CGCI) to assess novel emerging sequencing technologies in cancer. The CGCI program included comprehensive characterization of the genetic aberrations found in different pediatric and/or adult tumors. CGCI characterized a number of B-cell non-Hodgkin lymphomas (including diffuse large B-cell lymphoma (DLBCL) from patients with and without HIV+ infection, follicular lymphoma (FL), as well as adult and pediatric Burkitt lymphomas), and additional HIV-associated tumors (including DLBCL, lung, and cervical cancers). All data from these projects is available at the NCI Genomic Data Commons. Individual project descriptions are available by disease on the substudy pages (links are included at the top of this page). Brief summaries are as follows: Non-Hodgkin Lymphoma (NHL) - CGCI investigators probed genomic alterations more deeply than had previously been possible by using state-of-the-art RNA sequencing (mRNA-seq) and whole genome shotgun sequencing (WGS) coupled with leading edge bioinformatics, data management and analysis approaches. The project sequenced tumor DNA and/or RNA from 117 NHL tumor samples and 10 cell lines. This included the genomes or exomes of 1 Follicular Lymphoma (FL) and 13 diffuse large B-cell lymphoma (DLBCL) cases, all with matched constitutional DNA sequenced to comparable depths, RNA-sequencing (mRNA-seq) of 92 DLBCL, 12 FL and 8 B-cell NHL cases with other histologies and 10 DLBCL-derived cell lines. The DLBCL cases and cell-lines are from the two major subtypes of DLBCL: germinal center B-cell (GCB) and activated B-cell (ABC). HIV+ Tumor Molecular Characterization Project (HTMCP) - This project was a joint effort of the Office of Cancer Genomics (OCG) and the Office of HIV and AIDS Malignancy (OHAM). Its goals were to characterize HIV-associated cancers (obtained from HIV-infected patients) and compare them to the same types of cancers from patients without HIV infection. Investigators performed 30X genome sequencing of 100 cases of paired tumor and germline DNA, along with transcriptome sequencing in each of 3 types of HIV+ tumors (DLBCL, lung and cervical cancers). These platforms allow discovery of mutations both in coding and non-coding genomic regions, gene expression and genomic alterations (including translocations, insertions and deletions). Comparing tumors of cancer patients both with and without HIV-infection provides insight into the potential function of this virus in certain cancers. Burkitt Lymphoma Genome Sequencing Project (BLGSP) - This project was a collaborative effort between the National Cancer Institute and the Foundation for Burkitt Lymphoma Research to develop a databank of the many alterations found in Burkitt lymphoma (BL), an uncommon type of Non-Hodgkin lymphoma that occurs most often in children and young adults. The goal of the BLGSP was to explore potential genetic changes in patients with BL that could lead to better prevention, detection and treatment of the cancer. The project characterized the alterations of the tumors' genomes (with matched normal as control) and transcriptomes by sequencing the DNA and RNA of each case. Using the data generated, the ultimate goals of the project was to discover the molecular changes that are present in BL patients and then determine how those changes correlate with treatment regimen and outcome. CGCI data is accessible at the NCI's Genomic Data Commons (GDC) via the GDC's Data Portal and from each of the CGCI Publication Pages at the GDC (Please see the "Supplemental Links" section of any CGCI publication's "Publication Information and Associated Data Files page" at the GDC.). Available datasets include raw sequencing data, datasets generated by the original CGCI research teams (fully annotated clinical information and higher-level/analyzed molecular characterization data), as well as higher level data generated by the GDC. Please see the CGCI Use and Publication Guidelines for updated details on the sharing of any CGCI substudy data, including how to cite CGCI.To learn more about the CGCI studies, please visit the CGCI Program website.

  Study phs000235

• RNA Sequencing datasets - Project "Multi-omics analysis of Parkinson’s disease midbrains"

  The dataset contains FASTQ files referring to the study "Multi-omics analysis of Parkinson’s disease midbrains". For this project, RNA was isolated from human postmortem midbrain tissue (PD and Control samples). Libraries were prepared with the TruSeq Small RNA library prep (Small RNA Seq) and the TruSeq Stranded Total RNA Kit (for transcriptomics), both from Illumina. Sequencing for both experimental setups was conducted in the Illumina HiSeq4000.

  Dataset EGAD00001006883

• Whole transcriptome profiling of liquid biopsies from tumour xenografted mouse models enables specific monitoring of tumour-derived extracellular RNA

  Total RNA sequencing (SMARTer Stranded Total RNA-Seq Kit v2) data of extracellular RNA (exRNA) from liquid biopsies of a BRC0004PR PDX and SK-N-BE(2C) CDX mouse model, and total RNA sequencing profiles of the matching PDX tumors.

  Dataset EGAD00001008318

• The Epigenomic Atlas of Early Human Craniofacial Development

  Parallel profiling of six distinct histone modifications via ChIP-Seq in craniofacial tissue samples from individual human embryos was performed. Epigenomic marks imputed with ChromImpute and a 25-state chromatin state model of uniformly processed epigenomic data was produced through ChromHMM. Samples were obtained from the MRC-Wellcome Trust Human Developmental Biology Resource (HDBR) tissue bank. HDBR provided karyotypically and developmentally normal pharyngeal arch or craniofacial tissue from embryos between 4.5 and 10 post-conception weeks. This repository contains raw data (fastq) files from ChIP-seq and RNA-seq experiments associated with this project. Processed ChIP-seq data and imputed data for additional histone marks are available at GEO (Series GSE97752).

  Study phs002008

• ERa ChIP-seq in breast healthy, primary cancer and metastatic tissues

  ChIP-seq has been perfomed on fresh-frozen tissue derived from healthy breast (HB), primary breast cancer (PB), BCa-derived liver metastasis (LM). Immunoprecipitation has been performed for ERa (sc-542, SantaCruz). Raw paired-end fastq.gz files are provided for both immunoprecipitated DNA and input samples.

  Dataset EGAD50000000642

• ChIP-seq ERa in primary breast cancer tissues

  ChIP-seq has been perfomed on 5 tumor fresh-frozen primary breast cancer tissues from female patients. Immunoprecipitation has been performed for ERa (SC-543, Santa Cruz). Raw single-end fastq data have been aligned using bwa-mem using Hg19 genome assebly as reference. Unfiltered aligment bam files are provided.

  Dataset EGAD50000000014

• CITE-seq for peripheral blood samples of 5 breast cancer patients

  We have 5 breast cancer patients who received VEN therapy. We collected their peripheral blood samples before and after long-term Venetoclax treatment. We apply CITE-seq protocol to these samples. This collection contains the all CITE-seq data for patients.

  Dataset EGAD00001008751

• Multidimensional and Longitudinal Immune Profiling of Sepsis in Uganda

  We conducted a prospective, observational cohort study of adults (RESERVE-U-2-TOR) admitted to Tororo General Hospital in eastern Uganda with severe, undifferentiated infection (i.e., suspected sepsis). Briefly, whole-blood samples were collected in PAXgene blood RNA tubes (PreAnalytiX, Qiagen, Germantown, MD, USA), from which RNA was extracted using PAXgene Blood RNA Kits (cat. no. 762164) (Qiagen). Sequencing libraries were constructed with the NEBNext Ultra II RNA Library Preparation Kit for Illumina, after which libraries were multiplexed and sequenced on the Illumina NovaSeq X Plus platform (Illumina, Inc, San Diego, CA). Data from this study available through dbGaP include raw RNA-Seq data generated from whole-blood samples collected upon RESERVE-U-2-TOR study enrollment (N=274).

  Study phs003914

• mUM patient biopsies pre and post treatment with tebentafusp

  The dataset includes 141 RNA-seq samples form mUM patietns. Tumour biopsies were obtained from uveal melanoma patients pre and post treatment with tebentafusp. Biopsies, which were either snap frozen or put in RNA later, were analysed by bulk RNA sequencing (50 million reads per sample) using the Illumina NovaSeq system.

  Dataset EGAD50000001258

• RNA-seq of CML074 Tumor tissue; Timpepoint 1

  Dataset EGAD00001001259

• RNA-seq of CML074 Tumor tissue; Timpepoint 2

  Dataset EGAD00001001260

• The paired FF/FFPE colon set, RNA-Seq

  Dataset EGAD00001000831

• Single-Cell Sequencing of Genomic DNA, RNA, and ADT in CRISPR-Edited Cells

  CRAFTseq data containing multi-modal single-cell genomic DNA amplicon, cDNA and surface-protein from various primary cell types and cell lines, including human CD4 T cells, Jurkat cells, HH cells, Daudi cells and HEK293T cells. Cells were edited with CRISPR HDR or base editing. Also contains bulk RNA-seq data for edited human primary CD4 T cells and Daudi cells.

  Study phs004042

• Genetic and Epigenetic Screens in Primary Human T Cells Link Candidate Causal Autoimmune Variants to T Cell Networks

  We aimed to define the target genes and pathways in which autoimmune disease-associated genetic variants operate. We performed single cell-CRISPR-interference screens in primary human T cells and bulk RNA-seq on T cells containing CRISPRi and single gRNAs to assess how T cell regulatory regions containing autoimmune-associated genetic variants affect nearby gene expression and cellular programs.

  Study phs004072

• RNA-seq and Hi-C data of a chromothripsis patient's iPS cells

  This dataset contains RNA-seq and Hi-C data files of induced pluripotent stem (iPS) cells and iPS cell-derived neural progenitors (NPCs) derived from a germline chromothripsis patient and both parents. iPS cells of the patient (cell lines 14 and 15), the father (lines 23 (with two replicates) and 32) and mother (line 30) were differentiated to NPCs and RNA was collected on day 0, day 7 and day 10 of differentiation. In addition, Hi-C data for two iPS cell-derived NPC lines from the patient (14 and 15) and two lines from the father (23 and 32) was generated.

  Dataset EGAD00001002242

• RNA-seq analysis refines molecular subtypes of hepatocellular carcinoma

  This work aims to identify homogeneous and robust molecular subtypes in HCC based on a large, homogenous and well-annotated cohort. We performed RNA sequencing (RNA-seq) on 529 HCC from 461 patients collected mainly in France. Based on the consistency between genomic and transcriptomic data, we identified 9 robust HCC subtypes mainly based on driver mutations. We further characterized HCC subtypes using transcriptomic and clinicopathological features. Our study provided a robust molecular classification based on a large HCC dataset from a Western country, improving our understanding of the mechanisms of carcinogenesis and facilitating the development of genome-based precision medicine in HCC.

  Dataset EGAD00001015427

• RNA-Seq

  RNA Sequencing

  Dataset EGAD00001001121

• RNA sequencing of osteoarthritis patients in subchondral bone

  This dataset contains RNA-seq (Illumina Hiseq 4000) from macroscopically preserved and lesioned OA subchondral bone of patients that underwent joint replacement surgery due to OA (N=48).

  Dataset EGAD00001006197

• RNA sequencing of PTCL-NOS

  This dataset contains raw .fastq files of a paired-end RNA-seq experiment on 15 PTCL-NOS samples. Samples were prepared with Truseq stranded mRNA library kit.

  Dataset EGAD00001006925

• Intratumoral plasma cells predict outcomes to PD-L1 blockade in non-small cell lung cancer

  Inhibitors of the programmed cell death-1 (PD-1/PD-L1) signaling axis are approved to treat non-small cell lung cancer (NSCLC) patients, based on their significant overall survival (OS) benefit. Using transcriptomic analysis of 891 NSCLC tumors from patients treated with either the PD-L1 inhibitor atezolizumab or chemotherapy from two large randomized clinical trials, we found a significant B cell association with extended OS with PD-L1 blockade, independent of CD8+ T cell signals. We then derived gene signatures corresponding to the dominant B cell subsets present in NSCLC from single-cell RNA-seq data. Importantly, we found increased plasma cell signatures to be predictive of OS in patients treated with atezolizumab, but not chemotherapy. B cells were also associated with the presence of tertiary lymphoid structures and organized lymphoid aggregates. Our results suggest an important contribution of B and plasma cells to PD-L1 blockade efficacy in NSCLC.

  Study EGAS00001005013

• Molecular_risk_stratification_in_patients_with_T1_colorectal_cancer_WES

  The introduction of bowel cancer screening has led to a significant increase in the proportion of patients being diagnosed with asymptomatic, early-stage colorectal cancer (CRC). Although the majority of these patients are successfully treated with surgery alone, a small proportion of patients have ‘born-to-be-bad’ aggressive lesions with early dissemination leading to distant metastases. Current standard of care histological assessment is unable to distinguish between these aggressive versus non-aggressive early lesions which is essential to provide appropriate clinical management decisions. This study aims to carry out molecular and histological profiling of approximately 300 T1 CRCs in order to develop a molecular stratifier based on the risk of relapse in early-invasive CRC. This novel T1 cohort will represent the world’s largest molecularly characterised T1 cohort of samples, with digital pathology assessment alongside whole exome sequencing, copy number variation analysis and 3’ RNA-seq. This data will be used to generate a robust panel of molecular and/or histological markers applicable to formalin-fixed paraffin embedded (FFPE) archival tissue which discriminates between T1 lesions based on risk of relapse, which will ultimately be used to inform clinical management of CRC at the earliest stages of the disease.

  Study EGAS00001005734

• CMV infection during pregnancy

  This study aims to characterize the transcriptional diversity, clonal composition, and viral target antigens of CMV-specific CD8 T cells among pregnant women with different anti-CMV serological patterns. Single-cell RNA sequencing (scRNA-seq) combined with MHC-peptide dextramers were performed using CD8 T cells from pregnant donors.

  Study JGAS000728

• The role of MALT1 in driving IBN resistance in MCL

  The bulk RNA-seq dataset was generated for the cell lines below and used for two major purposes: 1. DEG analysis and GSEA analysis comparing IBN-R and IBN-S cells 2. DEG analysis and GSEA analysis comparing MCL cells with/without MI-2 treatment.

  Study EGAS00001006832

• Microinjection_of_hIPSC_derived_intestinal_organoids_with_Salmonella_Typhimurium

  To generate an RNA-Seq dataset for organoids apically stimulated with Salmonella Typhimurium.These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001253