12312 results for "cancer rna-seq"

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• BLUEPRINT release August 2016, ChIP-Seq for monocyte - RPMI_T=6days_LPS_T=4hrs, on genome GRCh38

  ChIP-Seq data for 3 monocyte - RPMI_T=6days_LPS_T=4hrs sample(s). 8 run(s), 7 experiment(s), 7 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_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002495

• BLUEPRINT release August 2016, ChIP-Seq for CD8-positive, alpha-beta thymocyte, on genome GRCh38

  ChIP-Seq data for 1 CD8-positive, alpha-beta thymocyte sample(s). 2 run(s), 2 experiment(s), 2 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_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002494

• BLUEPRINT release August 2016, ChIP-Seq for Acute Promyelocytic Leukemia - MS-275 (20h), on genome GRCh38

  ChIP-Seq data for 1 Acute Promyelocytic Leukemia - MS-275 (20h) sample(s). 5 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_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002493

• BLUEPRINT release August 2016, ChIP-Seq for CD38-negative naive B cell, on genome GRCh38

  ChIP-Seq data for 9 CD38-negative naive B cell sample(s). 48 run(s), 44 experiment(s), 44 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_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002524

• Comparison of protocols for deriving pancreatic progenitors from hPSCs (ATAC-seq)

  This dataset contains 27 mapped bam files. The samples were generated with 3 different protocols for deriving pancreatic progenitors from hPSC. Three parallel differentiations were performed, all done in a hPSC NKX6.1-GFP reporter line. For each protocol there are three cellular populations: total (presort), GFP+ and GFP- . In summary: 3 differentiations x 3 protocols x 3 cellular populations. We prepared ATAC-seq libraries for the 27 samples, and sequenced them on Illumina HiSeq4000.

  Dataset EGAD00001004824

• DNA-seq BAM files from 16 carriers of the BMPR2 p.Arg491Gln mutation in a family affected by HPAH

  Paired-end DNA-seq BAM files from 16 carriers of the BMPR2 p.Arg491Gln mutation in a family affected by hereditary pulmonary arterial hypertension (HPAH). Whole genome sequencing of these samples was performed in an Illumina HiSeq 4000 instrument. Libraries were prepared using the Fisher PE Kit (Kapa Biosystems). FASTQ files were processed at the CNAG (Barcelona) using the GEM short-read aligner on the human genome version hs37d5, producing a total of 16 BAM files.

  Dataset EGAD00001005757

• DNA-seq FASTQ files from 16 patients affected by acute intermittent porphyria

  Paired-end DNA-seq FASTQ files from 16 patients affected by acute intermittent porphyria. Whole genome sequencing of these samples was performed in an Illumina HiSeq 4000 instrument. Libraries were prepared using the Fisher PE Kit (Kapa Biosystems). Each sample was multiplexed across flowcells and lanes, leading to a total number of 83 pairs of FASTQ files.

  Dataset EGAD00001006950

• Tapestri snDNA-seq data along with matched bulk data for validation

  Files from Tapestri snDNA-seq of archival tissue samples from 16 pancreatic ductal adenocarcinoma (PDAC) patients. Matched bulk sequencing (whole-exome, whole-genome, MSK-IMPACT) data are attached for a subset of the patients.

  Dataset EGAD00001009735

• 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

• Cell-free MeDIP-seq of plasma samples from lymphoma patients and healthy controls

  This dataset contains cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq) data generated from plasma samples of lymphoma patients and healthy controls. The study aims to characterize genome-wide methylation patterns of circulating cell-free DNA and identify hypermethylated regions associated with lymphoma. Sequencing libraries were prepared using cfMeDIP with anti-5-methylcytidine antibody enrichment and sequenced on an Illumina platform. The dataset supports differential methylation analyses and the development of classification models for lymphoma detection.

  Dataset EGAD50000002108

• Combining dasatinib and IFN-α in CML – immunomodulatory effects linked to treatment response and adverse events

  We pooled 100,000 cells from the 12 scRNA+TCRab-seq samples from peripheral blood from three time points (n=4, samples at 0, 3, and 12 months) to understand the landscape of immune subsets in CML during the course of dasatinib+IFN-α treatment

  Study EGAS00001005049

• Human scMultiome data (GEX and ATAC paired) from CD34+ Bone Marrow (BM) and mobilized peripheral blood (mPB), including CITE-Seq data from mPB CD34+ samples

  We analyzed healthy CD34+ samples from Bone Marrow (BM) and mobilized Peripheral Blood (mPB) in gene therapy experiments within the X-PAND project. BM samples underwent scMultiome analysis, providing paired GEX and ATAC data. For the mPB samples, both scMultiome and CITE-Seq were performed on the same donors, offering additional protein marker information. These datasets allow for an in-depth exploration of chromatin accessibility, gene expression, and surface protein profiling in hematopoietic progenitor cells from healthy donors.

  Study EGAS50000000750

• ChIP-seq profiling of H3K4me1 and H3K27ac in iPSCs and iPSC-derived endoderm cells in CPRF patients with LSD1 mutations and healthy controls

  LSD1 patient (children) and control (healthy fathers) derived iPSCs and endoderm differentiated cells were expanded and harvested for ChIP-seq experiment following the procedure described in Trovato et al, PMID: 39214979. Cells were cross-linked in PFA, sonicated and soluble fractions were collected for IP with H3K4me1 or H3K27ac antibodies. Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit (New England Biolabs) and sequenced on Illumina NextSeq 500 (75 bp in single-end mode).

  Study EGAS00001008242

• scRNA-seq of human follicular lymphoma and lymph node

  Cryopreserved cells from human nodal follicular lymphoma and lymph node samples were thawed and processed for scRNA-seq analysis. CD3+ CD19− 7-AAD− live T cells (six FL samples from the Original cohort) or 7-AAD− whole live hematopoietic cells (five lymph node and nine FL samples from Validation cohort 1) were sorted using a FACS Aria II or III instrument (BD Biosciences). To generate single-cell emulsions, 6,000–10,000 live cells were loaded into the 10X Genomics Chromium Controller for single-cell partitioning, along with the reverse transcriptase reagent mixture and 3' or 5' gel beads. Sorted T or whole hematopoietic cells were converted to barcoded scRNA-seq libraries using 10X Genomics Chromium single cell 3' reagent kits (v3) for the Validation cohort 1, 5' reagent kits (v1) for the Original cohort, according to the manufacturer’s instructions. The libraries were sequenced on an Illumina HiSeq X Ten or NovaSeq X Plus system, mapped to the human genome (build GRCh38), and demultiplexed using CellRanger pipelines (v3.1.0, 10x Genomics).

  Dataset EGAD50000001143

• Genome-wide identification of distinct miRNA-mRNA target regulation pairs in Non-Hodgkin lymphomas: a report from the ICGC MMML-Seq consortium

  We obtained miRNA profiles by miRnome sequencing from ICGC MMML-Seq patients diagnosed with Burkitt lymphoma, diffuse large B-cell lymphoma and follicular lymphoma and provide evidence of subtype-specific miRNA expression differences. We describe differentially expressed, mutated, edited and not previously annotated miRNAs. Addditionally, by performing argonaute-2 photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP) experiments, we obtained a set of biochemically-validated miRNA binding sites and identified miRNA-mRNA interaction pairs with a negative correlation in patient RNASeq data.

  Study EGAS00001001394

• A single-cell multi-omic atlas of nodal B-cell non-Hodgkin lymphomas

  Nodal B-cell non-Hodgkin lymphomas (B-NHL) are a clinically diverse set of cancers thought to originate from distinct stages of B-cell maturation. To characterize intratumor heterogeneity across B-NHL entities, we performed CITE-Seq (cellular indexing of transcriptomes and epitopes) on 51 lymph node samples including mantle cell lymphoma (MCL, n = 8), follicular lymphoma (FL, n = 12), germinal center (GCB, n = 5) or activated B-cell (non-GCB/ABC, n = 7) diffuse large B-cell lymphoma (DLBCL) and marginal zone lymphoma (MZL, n = 11) tumors, in addition to non-malignant reactive lymph nodes (rLN, n = 8). We also performed 5 prime scRNA-seq with immune receptor profiling for 11 of these samples (2 rLN, 2 MCL, 3 FL, 2 DLBCL, and 2 MZL).

  Study EGAS50000000342

• Transcriptional and epigenetic profiling of bone marrow blood progenitors across age

  Bone marrow from donors without known malignancy was isolated and CD34-enriched, FACS-purified to further enrich for CD34+CD38- primitive cells, and then profiled by single-cell 10X genomics chromium Multiome (RNA+ATAC).

  Study EGAS50000001623

• Morphological and gene expression changes in SCA1 cerebral organoids suggest neurodevelopmental disease characteristics

  Cerebral organoids were generated from controls, individuals with SCA1 and gene-edited SCA1 hiPS cells. At day 31 and day 60, RNA sequencing was performed showing differential of several genes involved in neural development.

  Study EGAS50000001720

• miRNASeq profiles from Indian HFrEF Cohort

  The dataset contains miRNA profiling from a cohort of 49 HFrEF patients. The myocardium samples were collected from these patients during heart transplant of LVAD implantation procedure. The RNA samples were collected in RNAlater. Small RNA libraries were prepared using QIAseq miRNA Library Kit, Qiagen and sequenced on Illumina HiSeq4000.

  Dataset EGAD50000001194

• Dataset for WGS and RNA samples of acute myeloid leukemia with MNX1 expression

  This dataset contains 10 samples of WGS, ATAC, 4C and RNAseq samples of patients with acute myeloid leukemia. The sequencing was performed on Illumina HiSeq 4000, 2000 and HiSeq X using Illumina TruSeq Nano DNA and Agilent Strand Specific RNA Kits. The sequencing was always paired.

  Dataset EGAD50000001098

• Dataset of CageKid Tumor RNA samples

  Dataset of CageKid Tumor RNA samples

  Dataset EGAD00001000718

• RNA sequencing data of pediatric hyperdiploid acute lymphoblastic leukemia (set 5)

  The dataset includes RNA sequencing FASTQ files from diagnostic tumor samples of five hyperdiploid ALL patients (ALLT-502, ALLK-130, ALLK-134, ALLK-137, ALLK-139). Novogene's internal method was used in directional library preparation including rRNA removal. The diagnostic tumor samples were sequenced using Illumina Novaseq X Plus, and the target sequencing depth was 21 Gb per sample.

  Dataset EGAD50000002592

• RNA sequencing of paediatric glioblastoma in the ICGC PedBrain project

  RNA sequencing of paediatric glioblastoma in the ICGC PedBrain project

  Dataset EGAD00001001944

• Poikiloderma syndrome RNAseq

  We will sequence the RNA of lymphoblast samples, transformed with EBV, which have poikiloderma syndrome with mutations in c16orf57. The aim of the experiment is to characterise RNA structural effects in this disease.

  Dataset EGAD00001000324

• RNA expression profiling of melanoma patient-derived xenograft

  Patient-derived xenografts (n=96) were derived from metastatic melanoma patients. RNA expression profiling will be preformed to study 1. HLA-typing and 2. the effect of the tumour microenvironment on tumour growth 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/

  Dataset EGAD00001002230