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• Dataset-linking-WGS-via-README-for-EGAS00001004884

  This dataset contains 139 Tumor and Control WGS files for samples for Gerhauser et al.,Cancer Cell, 2018, 34:996-1011. WGS and sequencing protocol was earlier described in Weischenfeldt et al, Cancer Cell, 2013.

  Dataset EGAD00001007669

• Single-cell transcriptome of human fetal pancreas and in vitro pancreatic spheroids

  This dataset combines single cell transcriptome data from fetal pancreas at 7-10 wpc, embryonic stem cell-derived pancreas progenitors and spheroids generated from both fetal pancreas and human pluripotent stem cell-derived pancreas progenitors.

  Dataset EGAD00001007506

• PhIP-Seq Serum 1000IBD

  PhIP-Seq experiment conducted in Eran Sigal's group at WIS.

  Dataset EGAD00001010118

• 300BCG trained immunity scRNAseq

  We have paired 39 individuals in 4 conditions: T0_RPMI (baseline, before BCG and without LPS); T0_LPS (before BCG and with LPS); T3m_RPMI (3 months after BCG, without LPS); T3m_LPS (3 months after BCG, with LPS).

  Dataset EGAD00001010055

• ChIP-seq ERa and H3K27ac in endometrial healthy and tumor tissues

  ChIP-seq has been perfomed on 4 healthy and 5 tumor fresh-frozen endometrial tissues from post-menopausal patients. Immunoprecipitation has been performed for H3K27ac and ERa. Raw single-end fastq data have been aligned using bwa-mem using Hg19 genome assebly as reference. Aligment bam files are provided.

  Dataset EGAD00001010896

• DNA methylation changes upon growth hormone treatment in children with idiopathic short stature

  This dataset includes DNA methylation profiles before and after GH treatment (with a duration of ~18 months in average) on 47 healthy children using customized methylC-seq capture sequencing. It includes 360 fastq files (i.e. 180 paired-end fastq files) where 40 fastq files were generated with HiSeq and 320 fastq files were generated with NovaSeq.

  Dataset EGAD00001008641

• WGS data for manuscript titled: Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy

  WGS data for manuscript titled: Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy

  Dataset EGAD00001008646

• DAC Johns Hopkins University - AML scRNAseq study

  This is the Data Access Committee (DAC) from Johns Hopkins University for the study scRNAseq of acute myeloid leukemia

  Dac EGAC50000000242

• sc-DECISION

  Data derived from PBMC and blood samples for the single cell and bulk RNAseq analysis for the sc-DECISION paper. https://doi.org/10.1101/2025.02.04.25321370

  Dac EGAC50000000642

• Mater Research Translational Bioinformatics DAC

  Data Access Committee for controlled-access sequence data published by the Translational Bioinformatics Group at the Mater Research Institute (Brisbane, Australia).

  Dac EGAC50000000755

• Reactive Lymph Node Gene Expression Profiling

  Reactive lymph nodes were processed as controls for the study.

  Study EGAS50000001010

• Methylome profiling of epithelioid sarcoma

  Explore the methylome landscape of epithelioid sarcoma using array data.

  Study EGAS00001007257

• MPNST exome and genome

  This is the complete dataset (exome and genome) for the EGAS00001000974 study.

  Dataset EGAD00001001040

• WGS of cell-free DNA derived from plasma of patients with pediatric sarcoma and healthy controls, and lcWGS/RRBS of matched tumor tissue

  This dataset contains: i) 241 deep (median 12x) whole-genome sequencing profiles of 95 patients with Ewing sarcoma, 31 patients with other pediatric sarcomas, and 22 additional profiles from healthy controls. Sequencing was performed on a NovaSeq 6000 instrument using the NovaSeq S4 2x100 bp configuration. In addition, pilot experiments for 18 cfDNA samples were performed using Illumina HiSeq 2000/2500 machines (2x75 bp configuration). Data is provided as .fastq.gz files (2 files, .R1 and .R2, per sample). i) Low coverage whole-genome-sequencing on 43 tumor biopsy samples from patients with Ewing sarcoma with matched cfDNA samples. The samples were sequenced using a NovaSeq 6000 instrument with the NovaSeq S4 1x100 bp configuration. Data are provided as unmapped (raw) .bam files. iii) Reduced-representation bisulfite sequencing data for 38 tumor biopsy samples from patients with Ewing sarcoma with matched cfDNA samples, and 2 control samples. RRBS libraries were sequenced on Illumina HiSeq 2000/2500 machines. Data are provided as unmapped (raw) .bam files.

  Dataset EGAD00001007080

• Sutherland Nine Ancient DNA DAC

  This Data Access Committee controls access for the genetic data from the Sutherland Nine. It consists of involved Scientists and Family respresentatives.

  Dac EGAC50000000529

• The genetic structure of Norway

  The genetic structure of Norway

  Dataset EGAD00010002032

• Osteosarcoma_X10

  This is a continuation of the osteosarcoma work we have undertaken.

  Study EGAS00001002167

• Brain_Disease_Wellcome_Leap_Delta_Tissue_DNA

  Investigating how the tumour microenvironment regulates glioblastoma cell states using genomic analysis.

  Study EGAS00001005799

• Genomic characterization of metastatic breast cancers

  This dataset contains all the .bam files used for the study.

  Dataset EGAD00001004772

• Extended longitudinal single-cell RNA-seq data from ovarian cancer across multiple treatment phases

  The dataset contains single-cell RNA-seq data of 73 tumor samples high-grade serous carcinoma (HGSC) patients sequenced with Novaseq. The samples were collected at primary, interval, and relapse treatment phases from multiple tissue sites. The files provided are fastq files.

  Dataset EGAD50000001855

• Spatial Dynamics of the Developing Human Heart

  68 paired-end raw FASTQ files obtained from 38 tissue sections across 16 hearts, spanning embryonic human heart development between 5.5 and 14 postconceptional weeks. Some libraries were re-sequenced for better coverage. The tissue sections were processed using the 10x Genomics Visium Gene Expression kit, and libraries were paired-end sequenced using Nextseq2000 (Illumina).

  Dataset EGAD50000001615

• ResolveCRPS study - Transcriptomics

  Transcriptome profiling of CRPS-affected skin using low-input total RNA-seq (paired-end mode with 54 and 68 nt read length for R1 and R2 respectively, Illumination NextSeq2000). 42 snap-frozen skin biopsies were analyzed together with longitudinal clinical data. The dataset contains FASTQ files, the processed read count matrix, and the corresponding clinical metadata.

  Dataset EGAD50000001545

• Shallow whole genome sequencing data from circulating tumour DNA (ctDNA) data of High Grade Serous Ovarian Cancer Patients (batch 1)

  The dataset contains shallow whole genome sequencing data of 128 high-grade serous carcinoma (HGSC) patients sequenced with Novoseq 6000. The 128 samples are plasma samples that have been collected before treatment. The files provided are paired fastq files.

  Dataset EGAD50000000949

• Dataset for Direct Detection of Early-Stage Cancers using Circulating Tumor DNA

  The dataset for Direct Detection of Early-Stage Cancers using Circulating Tumor DNA includes 602 bam files from next-generation sequencing on the Illumina HiSeq2500 or MiSeq. The samples analyzed include cancer cell lines as well as plasma and tissue specimens from healthy individuals and patients with cancer.

  Dataset EGAD00001003601

• ICR1000 UK exome series

  Exome sequencing of 1000 samples from the UK 1958 Birth Cohort. DNA library preps prepared with Illumina TruSeq sample preparation kit. The captured DNA libraries were PCR amplified using the supplied paired-end PCR primers. Sequencing was performed with an Illumina HiSeq2000 (SBS Kit v3, one pool per lane) generating 2x101-bp reads.

  Dataset EGAD00001001021