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• scRNAseq of endothelial cells from human iPSC-derived kidney organoids transplanted in the coelomic cavity of chicken embryos compared to untransplanted controls

  This dataset includes scRNA-seq fastq files and Seurat counts and metadata for 6 samples of endothelial cells enriched from hiPSC-derived kidney organoids cultured in vitro or transplanted in chicken embryos. Samples were obtained at 2 timepoints: d7+13 (1 day after transplantation) and day 7+20 (8 days after transplantation).

  Dataset EGAD50000001555

• Raw data (FASTQ) and processed data (VCF) of 7 patient-derived Sézary Syndrome (SS) cells

  We profile the whole-transcriptome (bulk RNAseq) of 7 patient-derived Sézary Syndrome (SS) cells to identify expression patterns, functional programs and expressed gene mutations that may provide clues on new therapeutic options for SS patients. The libraries were sequenced on NextSeq500 (Illumina) with a paired-end read length of 2x75bp. Raw data (FASTQ) and obtained processed data (VCF) including all called raw variants are available.

  Dataset EGAD50000001646

• B cells (CD19) RNAseq dataset of JIA patients with known uveitis status.

  CLUSTER consortium RNA sequencing dataset from UK JIA patient cohort with documented uveitis status. Peripheral blood mononuclear cells (PBMCs) were isolated from blood samples and cryopreserved. Samples were subsequently thawed and flow-sorted for CD19+ B cells prior to RNA sequencing. Clinical metadata includes patient demographics and uveitis status at time of sampling.

  Dataset EGAD50000001616

• 10X single-cell Multiome (RNA+ATAC) of bone marrow-derived HSPC

  10X genomics chromium single-cell ATAC+RNA (Multiome) was use to prepare single-nucleus RNA- and ATAC-seq libraries, sequenced on an Illumina NovaSeq 6000 platform. BAM files are provided. Samples from 6 donors were sequenced after sorting for primitive HSPCs in 5 libraries; each library comprises a single donor, except one with cells from 1 male and 1 female donor.

  Dataset EGAD50000002326

• Omics data of advanced bladder cancer

  To identify the therapeutic targets in a treatment-refractory cancer patient, we performed single-cell RNA sequencing for 3,115 cells from primary bladder cancer (BC159-T#3) and patient-derived xenografts (BC159-T#3-PDX-vehicle and BC159-T#3-PDX-tipifarnib). Matched time-series bulk tumor tissues were also sequenced using whole exome target probe (WES) and whole transcriptome target probe (WTS).

  Dataset EGAD00001005978

• Tumor/Normal WXS and RNASeq from patients dosed with neoTCR T-cell therapy

  Sixteen patients with refractory solid cancers received up to three distinct neoTCR-transgenic cell products, each expressing a patient-specific neoTCR, in a cell dose-escalation, first-in-human phase 1 clinical trial (NCT03970382). Included are the tumor and normal WXS and tumor RNAseq for dosed patients.

  Dataset EGAD00001009830

• Exome reads

  This dataset contains WES data (.bam files) and associated phenotype information from 10 patients included in our microbiome study who went on to anti PD-1 immunotherapy for the treatment of metastatic melanoma at the University of Texas MD Anderson Cancer Center. Both tumor and matching germ line normal were sequenced on each patient using Illumina HiSeq 2500. The average coverage was 283X in tumors and 135X in germline (tumor+germline overall:209, Range: 0-1552).

  Dataset EGAD00001003797

• Sequencing data for oesophageal and related samples - Linossi et al

  Data supporting: "Utility of ctDNA assessment after six weeks of immunotherapy to predict radiological response in advanced oesophageal cancer" Linossi et al

  Dataset EGAD00001015434

• Dataset of 4 WGS and 35 WES tumor and control runs linked for the ImmuNEO publication out of EGAS00001004813

  Sequencing data of 39 tumor and control runs (different tumors and blood controls), which were uploaded to EGAS00001004813 and reused in this ImmuNEO publication. The sequencing was always paired.

  Dataset EGAD00001009671

• Dataset for leiomyosarcoma-EXON

  Rare cancer sequencing data of 96 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008885