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• Reproducibility of variant calls in replicate next generation sequencing experiments

  In this study, we examined the reproducibility of nucleotide variant calls in replicate sequencing experiments of the same genomic DNA. We performed targeted sequencing of all known human protein kinase genes (kinome) (~3.3 Mb) using the SOLiD v4 platform. Seventeen breast cancer samples were sequenced in duplicate (n=14) or triplicate (n=3) to assess concordance of all calls and single nucleotide variant (SNV) calls.

  Study EGAS00001000826

• Error-corrected targeted sequencing of rectal mucus from patients suspected to have colorectal cancer

  This dataset contains error-corrected next-generation sequencing (ecNGS) data generated from 161 rectal mucus samples. These samples belong to colorectal cancer, adenoma, and control participants. Genomic DNA was extracted and processed using a hybrid-capture panel targeting 50 colorectal cancer–associated genes, incorporating unique molecular identifiers (UMIs) for duplex consensus error correction. Libraries were sequenced on an Illumina NovaSeq 6000 (paired-end 150 bp) producing paired-end FASTQ files. These data support analyses of DNA mutations in CRC detection and progression.

  Dataset EGAD50000002032

• Single-cell RNA sequencing of metastatic colorectal cancer patient-derived xenografts treated with cetuximab

  Tumor implantation and expansion were performed in two 6-week-old NOD/SCID mice. Once tumors reached an average volume of approximately 700 mm³, mice were randomly assigned to one of two treatment arms: vehicle (physiological saline, intraperitoneally, twice weekly) or cetuximab (20 mg/kg, intraperitoneally, twice weekly). After 1 week of treatment, mice were sacrificed, and tumors were harvested and preserved in sCelLiVE® Buffer for downstream single-cell RNA sequencing analysis.

  Dataset EGAD50000002103

• Integrated analysis of whole genome and RNA sequencing in 22 HBV-associated HCCs

  RIKEN collection WGS and RNA-seq reads for 66 HBV-associated HCC and matched blood or liver samples from 22 donors.

  Dataset EGAD00001001035

• Sequencing data for oesophageal and related samples - Scott et al (WGS, RNA)

  Data supporting: "Evidence that polyploidy in esophageal adenocarcinoma originates from mitotic slippage caused by defective chromosome attachments" Scott et al. WGS and RNAseq sequencing data Organoid, tumour and normal samples BAM files

  Dataset EGAD00001006738

• Single cell RNA sequencing of bone marrow mononuclear cells from healthy donors and B-cell lymphoma patients following CD19 CAR T-cell therapy

  Bone marrow aspirates were obtained from patients with relapsed/refractory large B cell lymphoma (rrLBCL), mononuclear cells isolated by ficoll density-gradient centrifugation, and loaded onto a 10X Chromium for single cell RNA-sequencing using 5’ chemistry without prior cryopreservation. Healthy donor bone marrow mononuclear cells were obtained from healthy allogeneic stem cell transplant donors and analyzed following viable cryopreservation.

  Dataset EGAD00001009774

• STAT1 AM RNAseq

  The transcriptome of peripheral blood cells (PBMCs) from control or patients with an activation mutation on the STAT1 gene was analyzed. This analysis aimed to identify the major changes in the circulating immune cells of patients with STAT1 mutation and compare this with the result of the perturbation prediction tool huva (human variation, R).

  Dataset EGAD00001006962

• Siberia.Pakendorf

  The tar archive contains a) the txt file with the genotypes, b) illumina annotation file with info on SNPs, c) sample info file unfiltered illumina data, autosomes only data from Pugach et al MBE 2016 The Complex Admixture History and Recent Southern Origins of Siberian Populations

  Dataset EGAD00010002304

• Deep sequencing of the gut microbiome from donors of the Milieu Intérieur cohort

  This dataset includes 1,359 paired-end shotgun metagenomics samples from 946 healthy donors of the Milieu Intérieur cohort. 413 of the donors provided two samples (V1 and V2).

  Dataset EGAD00001006554

• Shared disease specific B cell clones in Crohn’s disease

  We performed deep sequencing of the B cell receptor (BCR) repertoire in four cohorts of patients with Crohn’s disease (CD) together with healthy and disease controls. Using sequence homology, we identified BCR clones that were shared between patients with CD but not found in healthy individuals nor in patients with ulcerative colitis (UC), indicating CD-associated B cell immune responses. Shared clones were present in inflamed gut mucosa, draining intestinal lymph nodes and blood, suggesting the presence of common CD-associated antigens that drive B cell responses in CD patients.

  Study EGAS50000000912