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• scRNA dataset for 15 samples

  This dataset includes single cell (sc)RNA-seq of N=3 patient-derived xenograft (PDX) samples profiled at baseline (no drug treatment) and N=12 samples from one PDX profiled during the course of treatment (N=1 sample each for 4 treatment arms x 3 timepoints). The dataset includes bam files that have been purged of reads mapping to cells where a majority of the reads from that cell mapped to the mouse genome. All scRNA-seq data were generated using the Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) from 10X Genomics.

  Dataset EGAD50000001424

• Genetic regulation of RNA splicing in human pancreatic islets

  Here we provide access to newly generated RNA-seq data for 101 human islet samples used to map genetic effects on gene expression and alternative splicing (eQTLs and sQTLs) in a total of 399 human islets. We also make publicly available genotyping array data for 128 human islets, including the fraction of 101 human islet samples with existing RNA-seq data.

  Dataset EGAD00001009102

• High-Coverage Whole-Exome Sequencing Identifies Candidate Genes for Suicide in Victims with Major Depressive Disorder

  In this study, we applied an Illumina HighSeq platform-based high-coverage WES technique, which, in addition to the exons, allows the determination of 5′- and 3′-UTRs, promoters to a certain length, along with off-target sequences, such as introns, intergenic regions and infecting viruses. Brains from suicide victims (n = 23; 15 males and eight female) who had suffered from major depressive disorder and from control participants (n = 21; 14 males and seven females) who had died from other causes were used for whole-exome sequencing. Alignment files in bam format were uploaded.

  Dataset EGAD00001004082

• Blueprint: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cell types, (RNA-Seq for CD4-positive, alpha-beta T cell, on genome GRCh37)

  RNA-Seq data for 212 CD4-positive, alpha-beta T cell sample(s). 212 run(s), 212 experiment(s), 212 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_rnaseq_analysis_sanger_20160816

  Dataset EGAD00001002671

• Blueprint: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cell types, (ChIP-Seq for CD14-positive, CD16-negative classical monocyte, on genome GRCh37)

  ChIP-Seq data for 172 CD14-positive, CD16-negative classical monocyte sample(s). 572 run(s), 345 experiment(s), 340 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002672

• Blueprint: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cell types, (ChIP-Seq for CD4-positive, alpha-beta T cell, on genome GRCh37)

  ChIP-Seq data for 154 CD4-positive, alpha-beta T cell sample(s). 355 run(s), 265 experiment(s), 250 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002673

• Blueprint: A human variation panel of genetic influences on epigenomes and transcriptomes in three immune cell types, (RNA-Seq for CD14-positive, CD16-negative classical monocyte, on genome GRCh37)

  RNA-Seq data for 197 CD14-positive, CD16-negative classical monocyte sample(s). 197 run(s), 197 experiment(s), 197 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_rnaseq_analysis_sanger_20160816

  Dataset EGAD00001002674

• Relaxed selection during a recent human expansion

  To better understand and quantify the effect of a recent expansion process on the amount and pattern of mutation load, we screened the ascending genealogies of 3916 individuals from the CARTaGENE cohort (Awadalla et al. 2013) that were linked to the BALSAC genealogical database (http://balsac.uqac.ca/). Using stringent criteria on the quality of genealogical information, we selected (front) individuals whose ancestors were as close as possible to the front of the colonization of Quebec, and (core) individuals whose ancestors were as far as possible from the front. We then sequenced these 102 individuals at very high coverage (mean 89.5X, range 67X-128X) for 106.5 Mb of exomic and UTR regions and contrasted their genomic diversity to detect if sites with various degrees of conservation and deleteriousness had been differentially impacted by selection.

  Study EGAS00001001957

• NeoPAL study - RNAseq and Targeted DNA sequencing data

  This dataset is composed of 159 RNAseq data (fastq, bam and count tables) and 35 targeted DNAseq data (fastq).

  Dataset EGAD50000001490

• RNA-seq cohort of non-tumorous breast tissue from BRCA1/2 carriers

  Non-tumorous breast tissues from BRCA1 or BRCA2 carriers were subject to RNA sequencing. The total number of samples is 130.

  Dataset EGAD00001006746