9182 results for "cancer rna-seq"

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• TCR sequencing of TIL in breast cancer data access committee

  Dac EGAC00001003173

• DAC - The Netherlands Cancer Institute - Antoni van Leeuwenhoek

  Dac EGAC00001003316

• Common and rare germline variants in Japanese prostate cancer patients

  Study JGAS000487

• Single Cell RNAseq of PBMC from renal cancer patients

  Dac EGAC00001001605

• Human primary and metastatic colorectal cancer (CRC) samples

  Study EGAS00001006746

• Targeted sequence of MDS cases treated with azacitidine

  Study EGAS00001007030

• BRCA-deficiency/HRD in individuals with HBOC

  Study EGAS00001007258

• Berlin Neuroblastoma Dataset Update 2021

  Study EGAS00001005604

• Expression quantitative trait locus mapping in human pancreatic islets of Langerhans

  The intersection of genome-wide association analyses with physiological and functional data indicates that variants regulating islet gene transcription influence type 2 diabetes (T2D) predisposition and glucose homeostasis. However, the specific genes through which these regulatory variants act remain poorly characterized. To identify such effector transcripts for T2D and glycemic traits, we generated expression quantitative trait locus (eQTL) data in 118 human islet samples using RNA-sequencing and high-density genotyping.

  Dataset EGAD00001001601

• DCM-cases

  DCM-cases (149 human DCM samples) human heart biopsies from 149 patients with dilated cardiomyopathy (DCM) were subjected to RNA sequencing in order to assess transcriptome variation. We used Illumina HiSeq2000 technology. Each sample-dataset contains the output from tophat-1.4.1 (one *.bam file with the aligned reads and two *.fq files one with the not aligned forward read and one with the revers unaligned reads). We reveal extensive differences of gene expression and splicing between dilated cardiomyopathy patients and controls.

  Dataset EGAD00001003390

• ETMR_Nanostring

  Total RNA (100ng) from 21 ETMRs with C19MC structural alterations and 28 other PBTs was prepared with nCounter miRNA Sample Prep Kit according to standard protocol. miRNA expression profiling was conducted with human v1, v2, or v3 miRNA panel on nCounter miRNA expression platform (NanoString Technologies, Seattle, WA) according to manufacturer’s protocol. Signal normalization was done using nSolver Analysis and batch corrected using ComBat (Johnson et al. Biostatistics. 2007). 565 miRNAs overlapped between all three versions and was used for further analyses. Fold change and supervised t-test with FDR correction was calculated between the ETMRs and other PBTs.

  Dataset EGAD00010001701

• PIVUS study - Longitudinal transcriptomics - Advanced aging

  We performed RNA sequencing in whole-blood from the same 65 individuals from the PIVUS study at ages 70 and 80 (130 samples) to quantify how gene expression, alternative splicing, and their genetic regulation are altered during this 10-year period of advanced aging. Each individual has four fastq files, two for each age. Consecutive sample IDs refer to the sample individual, e.g. PIVUS003 and PIVUS004 are the age 70 and age 80 samples of the first individual.

  Dataset EGAD00001004965

• Targeted gene panel sequencing of matched diagnosis-remission-relapse B cell precursor acute lymphoblastic leukemia samples

  Bone marrow mononuclear cells from patients diagnosed with B cell precursor acute lymphoblastic leukemia were obtained at three sequential time points: first diagnosis, remission after chemotherapy and relapse. Genomic DNA was isolated and targeted gene panel sequencing was performed using a customized biotinylated RNA oligo pool (SureSelect, Agilent, Santa Clara, California) to hybridize the target regions comprising 362 kbp on a HiSeq2000. Target regions were selected to validate mutations previously identified in these samples using whole exome sequencing.

  Dataset EGAD00001004977

• Mapping genetic variants underlying gene regulation in healthy intestinal cell types to identify novel IBD drug targets (2020-05-12)

  Biopsies from the terminal ileum and rectum of healthy individuals are digested on ice to single cells and processed for single-cell RNA-sequencing (10X Genomics and Illumina) This data is 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/ . This dataset contains all the data available for this study on 2020-05-12.

  Dataset EGAD00001006139

• Processed microarray gene expression data from NPC samples_Cohort 2

  We retrospectively collected 150 non-metastatic, pretreatment, formalin-fixed, paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) samples as validation cohort 1. Also, we prospectively collected 32 FFPE samples from NPC patients enrolled in a trial evaluating anti-PD-1 antibody as validation cohort 2. Total RNA was extracted and hybridised to an Affymetrix HTA 2.0 microarray. In this study, we investigated the immune status of the tumour microenvironment (TME) based on gene expression profiles to classify NPC into biologically distinct immune subtypes, and clarify their associations with prognosis and immunotherapy response.

  Dataset EGAD00001006274

• Processed microarray gene expression data from NPC samples_Cohort 1

  We retrospectively collected 150 non-metastatic, pretreatment, formalin-fixed, paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) samples as validation cohort 1. Also, we prospectively collected 32 FFPE samples from NPC patients enrolled in a trial evaluating anti-PD-1 antibody as validation cohort 2. Total RNA was extracted and hybridised to an Affymetrix HTA 2.0 microarray. In this study, we investigated the immune status of the tumour microenvironment (TME) based on gene expression profiles to classify NPC into biologically distinct immune subtypes, and clarify their associations with prognosis and immunotherapy response.

  Dataset EGAD00001006275

• Detection of Gene Fusions using Targeted Next-Generation Sequencing

  Five commercially available parallel sequencing assays were evaluated for their ability to detect gene fusions in eight cell lines and 18 FFPE tissue samples carrying a variety of known gene fusions. Four RNA-based assays and one DNA-based assay were compared; two were hybrid capture-based, TruSight Tumor 170 Assay (Illumina) and SureSelect XT HS Custom Panel (Agilent), and three were amplicon-based, Archer FusionPlex Lung Panel (ArcherDX), QIAseq RNAscan Custom Panel (Qiagen) and Oncomine Focus Assay (Thermo Fisher Scientific).

  Dataset EGAD00001006913

• single cell RNA sequencing of resting and IAV-stimulated mononuclear phagocytes of Africans and Europeans

  CD14+ monocytes from 4 African and 4 Europeans individuals with varying degree of ex-vivo susceptibility to Influenza, were either stimulated with Influenza A virus, or left resting. Cells from all 16 samples were collected at 4 time points (0, 2, 4, 6h post infection), and pooled across 13 libraries. Samples were processed on the 10x chromium with 3' reagents kits, V3 chemistry and sequenced with Hiseq X ten.

  Dataset EGAD00001006938

• Patient-derived gene and protein expression signatures of NGLY1 deficiency

  Single-end bulk RNA sequencing results of cell lines derived from patients described with NGLY1 deficiency as well as parent and CRISPR edited controls. The cell lines represent 4 different cell types: fibroblasts, lymphoblastoid cells, induced pluripotent stem cells (iPSCs) and neural progenitor cells (NPCs.).

  Dataset EGAD00001008094

• Single-cell GoT sequencing from CH, MDS and AML patients with CH mutations

  Single-cell targeted amplicon RNA sequencing from CH (n = 3), MDS (n = 6, MDS02 in 2 replicates) and AML (n =1, in 2 replicates) samples with mutations in splicing factors (SF3B1 - n = 8 [2 -CH, 6 MDS], U2AF1 n = 1) or transcription regulators (DNMT3A - CH04). The transcripts are targeted to detect a particular CH mutation in the listed genes. U2AF1 GoT are full-length cDNA, while the rest follow the 10x 3' V3 protocol.

  Dataset EGAD00001011284

• Next Generation Sequencing Characterization of Hematopoietic Stem and Progenitors Cells in Human Systemic Lupus Eryhtematosus (2)

  This dataset contains RNA-sequencing of Bone marrow-derived CD34+ cells from Healthy Controls (n=2) and SLE patients (n=10). SLE patients are divided into two categories based on severity: patients with moderate/mild disease (n=4) and patients with severe disease (n=6). Libraries were generated using the Illumina TruSeq Sample Preparation kit v2. Single-end 75-bp mRNA sequencing was performed on Illumina NextSeq 500. The raw fastq files are uploaded.

  Dataset EGAD00001009744

• EGAD00010000554

  SNP 6.0 arrays of small cell lung cancer

  Dataset EGAD00010000554

• EGAD00010000556

  SNP 6.0 arrays of small cell lung cancer

  Dataset EGAD00010000556

• OvCan2

  Digital images of ovarian cancer metastases

  Dataset EGAD00010001099

• Genomic Analysis of a Metastatic Fusion-negative Embryonal Rhabdomyosarcoma

  Study EGAS00001006946

• Data Access Commitee of Nanjing Medical University Affiliated Jiangsu Cancer Hospital

  Dac EGAC00001003206

• Treated and control Patient Derived Xenografts of colorectal cancer (CRC) samples

  Dac EGAC00001003073

• GBM stem cell lines and PRMT5 inhibitor

  Study EGAS00001004397

• Resident memory CD8 T cell in human lung cancer

  Study EGAS00001004707

• Cancer Genomics Project RCC Data Access Committee

  Dac EGAC00001000109

• Single cell RNAseq of PBMC from bladder cancer patients

  Study EGAS00001004458

• Fasting-mimicking diet reshapes antitumor immunity in cancer patients

  Study EGAS00001004944

• Data Access Committee for German Consortium for Translational Cancer Research (DKTK)

  Dac EGAC00001000217

• Ludwig Data Access Committee for the Study of Oesophageal Cancer

  Dac EGAC00001000978

• Latency and interval therapy affect the evolution in metastatic colorectal cancer.

  Dac EGAC00001001198

• High-grade serous ovarian cancer (MDACC) data access committee

  Dac EGAC00001001288

• Single Cell RNAseq of blood and tumor from renal cancer patients

  Dac EGAC00001001494

• Data Access Commitee of Nanjing Medical University Affiliated Jiangsu Cancer Hospital

  Dac EGAC00001001774

• Long-read isoform in breast cancer - Data Access Commitee

  Dac EGAC00001001821

• Data Access Commitee of Nanjing Medical University Affiliated Jiangsu Cancer Hospital

  Dac EGAC00001002086

• Garvan/St Vincent’s Prostate Cancer Tissue and Data Access Committee

  Dac EGAC00001002769

• Peter MacCallum Cancer Centre Research Data Access Committee

  Dac EGAC00001002975

• Human Throid Cancer and CDK4/6 inhibition Data Access Commitee

  Dac EGAC00001003446

• Mechanisms of duodenal adenoma development in familial polyposis syndromes

  Study EGAS00001006561

• Unraveling the genetics of transformed splenic marginal zone lymphoma

  Study EGAS00001006389

• Integrated genetic analysis of primary CNS lymphoma

  Study EGAS00001007222

• Targeted sequencing of 72 prostate cancer driver in 712 plasma cell free DNA samples

  Dataset contains targeted sequencing data of 712 plasma cell free DNA samples and 428 white blood cell samples collected from 428 men with metastatic prostate cancer. Target capture was performed using a hydridization-based custom Roche SeqCap EZ Choice kit, designed to capture all exons of 72 prostate cancer driver genes. Cell free DNA was extracted from 10 mL blood samples. Libraries were sequenced using Illumina HiSeq 2500 or Illumina MiSeq instruments to a median coverage of 750x. 62% of samples had ctDNA fraction above 2% of total cfDNA. Note that "Dataset type" is erroneously listed as "Amplicon sequencing", because "Captured-based targeted sequencing" or "Hybridization-based targeted sequencing" were not available options in EGA at the time of submission.

  Dataset EGAD00001004208

• Genomic Evolution of Breast Cancer Metastasis and Relapse

  Recurrent breast cancer is almost universally fatal. We characterize 170 patients locally relapsed or distant metastatic cancers using massively parallel sequencing. We identify that the relapse-seeding clone disseminates late from the primary tumor. TP53 and AKT1 appear to be enriched in ER-positive cancers predisposed to relapse. Mutation acquisition continues at relapse as the same mutation signatures continue to operate and new signatures, such as that caused by radiotherapy appear de novo. In 49% of cases we identify drivers mutations private to the relapse and these are sampled from a wider range of cancer genes, including SWI-SNF complex and JAK-STAT signaling.

  Dataset EGAD00001002696

• Cholangiocarcinoma

  Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here we are submitting two datasets that contain NGS files from gastrointestinal rare cancers (n=119): - Dataset 2 (87 patients): Intra-hepatic cholangiocarcinoma (n=47), Extra-hepatic, cholangiocarcinoma (n=16), Not specified Cholangiocarcinoma (n=9), Small bowel adenocarcinoma (n=6) and other rare GI cancer (n=9)

  Dataset EGAD00001008968

• The Natural History of Human Prostate Cancer

  Whole genome DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of 3 men. For each of three different prostates, multiple tumour samples (4, 5, and 3 depending on the case) and one normal tissue sample were whole genome sequenced with a matched blood sample using the Illumiuna HiSeq platform. Tumour samples were sequenced to a target depth of 50X and normals and blood to a target depth of 30X. As of September 2020, some of the studies using these data include: Cooper et al, Nature Genetics 2015 (PMID: 25730763) Wedge et al, Nature Genetics 2018 (PMID: 29662167) Pan-Cancer Analysis of Whole Genomes, Nature 2020 (PMID: 32025007)

  Dataset EGAD00001000689