Search Results - EGA European Genome-Phenome Archive

Organoid Derivation Project TGS: Release 2

Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients.

Dataset EGAD00001004999

Organoid Derivation Project WGS: Release 1

Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients.

Dataset EGAD00001005000

Dataset for the study of ulcerative colitis

Whole exome sequencing and RNAseq data.

Dataset EGAD00001005237

Gene expression of transduced human primary germinal centre B-cells

RNA-seq sequencing data of human germinal centre B-cells (42 samples)

Dataset EGAD00001005281

Berlin Neuroblastoma Dataset

Paired tumor/normal WGS and RNA-seq of primary neuroblastoma.

Dataset EGAD00001005488

WGS files for Mullighan_GL_reALL

WGS files for Mullighan_GL_reALL paper titled "Mutational landscape and patterns of clonal evolution in relapsed pediatric acute lymphoblastic leukemia"

Dataset EGAD00001005506

WXS files for Mullighan_GL_reALL

WXS files for Mullighan_GL_reALL paper titled "Mutational landscape and patterns of clonal evolution in relapsed pediatric acute lymphoblastic leukemia"

Dataset EGAD00001005509

Single-cell characterization of human GBM reveals regional differences in tumor-infiltrating leukocyte activation

Background: Glioblastoma (GBM) harbors a highly immunosuppressive tumor microenvironment (TME) which influences glioma growth. Major efforts have been undertaken to describe the TME on a single-cell level. However, human data on regional differences within the TME remain scarce. Goals: we performed single-cell RNA sequencing (scRNAseq) on paired biopsies from the tumor center, peripheral infiltration zone and blood of five patients with primary GBM Details: This EGA study includes raw data sequencing files for the scRNA-seq samples. The processed data (output from Alevin, UMI count matrix and cell metadata) are available from GEO https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197543

Study EGAS50000000302

Multi-omics analysis of cocaine use disorder in postmortem brain tissue of the ventral striatum [Proteomics data to study EGAS50000000623]

We performed a multi-omics analysis of cocaine use disorder in postmortem human brain tissue of the ventral striatum in N=41 individuals (N=20 CUD cases, N=21 non-affected individuals). From the postmortem brain tissue samples, we generated miRNA-seq, RNA-seq, proteomics, and snRNA-seq data. The miRNA-seq, RNA-seq and snRNA-seq datasets can be found in the EGA under study ID EGAS50000000623. Proteomics data is deposited under study ID EGAS00001007945 (this study). The proteomic dataset was obtained using TMT-labeling. Measurement was performed on an Orbitrap Fusion Lumos device.

Study EGAS00001007945

Link to the Finnish FEGA Node's service provider

We would like to direct you to the service provider for the Finnish FEGA Node, which is CSC – IT Center for Science (https://research.csc.fi/-/fega). It's important to note that this is not a genuine DAC and does not serve as the data controller. To obtain access to data stored in FI-FEGA, it is essential to utilize the local access management system SD Apply. Please be aware that applications submitted through the EGA DAC portal will not be processed. For a seamless experience, we kindly request you to refer to the policy of your selected dataset and submit your access application through SD Apply (https://sd-apply.csc.fi/). Your cooperation is highly appreciated.

Dac EGAC50000000022

singel cell RNAseq dataset for the study "Composition and functional status of T and NK cells in Extramedullary myeloma tumor microenvironment""

Dataset contains all newly generated single cell RNAseq data generated for the study. It includes 5 EMM soft tissue samples, 5 EMM bone marrow samples (EMM_BM) and 6 RRMM BM samples without EMM (RRMM_BM). Samples that are sequenced twice are marked by _1 or _2 in the sample name. The sample name mentioned corresponds to the sample name used in the publication. The rest of the EMM single cell RNAseq samples mentioned int the publication, EMM_03_1, EMM_11, EMM_14_1, EMM_14_2, EMM_16, and EMM_15_1 are already uploaded in EGA archive – dataset id EGAD50000000053.

Dataset EGAD50000001511

The study provides comprehensive access to the set of EGA studies which may be useful as controls.

The subjects studies in these datasets were selected due to being healthy control individuals or otherwise provide well characterised phenotype or exclude certain disease phenotype categories such that they may be useful as control population, such as to derive allele frequencies from a known reference population.

Study EGAS00001000646

Single cell sequencing of human normal luminal cells

The dataset includes 12 paired FASTQ files (6 samples) with single cell transcriptome sequencing data of normal breast luminal cells from ducts and TDLUs derived from reduction mammoplasties from three patients. Chromium Single Cell 3’ Reagent Kit v2 or v3 (10x Genomics) were used for processing of cells, whereafter sequencing was performed using the Illumina® NextSeq500/550 High Output Kit v2. Cell Ranger was used for generating FASTQ files and files from different lanes were concatenated prior to uploading the data to EGA. "R1" files include the feature barcodes and UMIs, while "R2" files include the reads.

Dataset EGAD00001008499