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• Single-cell GoT sequencing from CH, MDS and AML patients with CH mutations

  Single-cell targeted amplicon RNA sequencing from CH (n = 3), MDS (n = 6, MDS02 in 2 replicates) and AML (n =1, in 2 replicates) samples with mutations in splicing factors (SF3B1 - n = 8 [2 -CH, 6 MDS], U2AF1 n = 1) or transcription regulators (DNMT3A - CH04). The transcripts are targeted to detect a particular CH mutation in the listed genes. U2AF1 GoT are full-length cDNA, while the rest follow the 10x 3' V3 protocol.

  Dataset EGAD00001011284

• V(D)J and 5' Gene Expression data of bone marrow cells from patients with aplastic anemia

  Viably frozen blood MNCs from 9 cGVHD patients were sorted with BD Influx Cell sorter, to enrich for CD45+ cells. Gene and V(D)J transcript profiles were studied with 10x Genomics Chromium Single Cell Immune Profiling platform. The Chromium Single Cell 5’RNAseq run and library preparation were done using the Chromium Next GEM Single Cell Immune Profiling version 1.1 chemistry. The raw data was processed using Cell Ranger v3.1 pipelines.

  Dataset EGAD00001012117

• RNA sequencing of in vitro generated suppressive myeloid cells using parental and Sialidase expressing A549 cancer cell lines

  Fresh peripheral blood mononuclear cells of four human donors were cultured together with either lung adenocarcinoma A549 cancer cells or A549-expressing H1N1 Sialidase cancer cells. These treatments induced the differentiation of donor cells into immunosuppressive MDSC-like cells, which were further subjected to bulk RNA sequencing. RNA-seq TruSeq libraries were generated from polyA-enriched mRNA isolated from the samples, and sequenced in paired-end mode on 4 lanes of an Illumina NextSeq 500 flow-cell

  Dataset EGAD00001012437

• RNA-seq dataset of A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories

  Study describing the differentiation trajectory of atypical teratoid rhabdoid tumors (ATRTs) at single-cell level. This study describes how the differentiation trajectory differs per subtype of ATRTs, and how those findings could contribute to develop so-called "maturation therapy" tailored towards ATRTs.

  Dataset EGAD00001015544

• ATAC-Seq/Hi-C/4C-Seq dataset for Malignant rhabdoid study

  Study describing the dynamics of chromatin organization within malignant rhabdoid tumors. This study describes how this chromatin organization changes upon SMARCB1 rescue within patient-derived organoid models from malignant rhabdoid tumors. Identification of a novel super-enhancer of MYC and identification of patient-specific enhancer utilization to activate MYC expression in these tumors.

  Dataset EGAD00001011820

• RNAseq of human breast cancer tumors from the PEARL study

  Formalin fixed, paraffin-embedded human breast cancer tumor samples had RNA extracted using the Thermo Scientific KingFisher Flex instrument and the Applied Biosystems MagMAX FFPE DNA/RNA Ultra Kit; Total RNA libraries were created using the Bravo Automated Liquid-Handling Platform and the TruSeq Stranded Total RNA Library Prep Gold Kit; libraries were sequenced on the Illumina NovaSeq 6000 machine using a 2x50 bp paired-end configuration to target a read depth of 120 million clusters per library.

  Dataset EGAD00001015613

• Mapping genetic variants underlying gene regulation in intestinal cell types to identify novel IBD drug targets

  Biopsies from the terminal ileum and rectum of healthy individuals and terminal ileum and blood from Crohns disease patients are collected and processed single cells and processed for single-cell RNA-sequencing using 10X Genomics 3 v3 and v3.1 and Illumina sequencing. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001016069

• DNA methylation (RRBS) data for the validation the glioblastoma progression study (GBMatch).

  Genome-wide profiling of DNA methylation levels by RRBS in 150 glioblastoma tumor samples. Patients were selected to represent the general population of glioblastoma patients based on Austrian Brain Tumor Registry. These DNA methylation profiles were created for the validation of the glioblastoma progression study (GBMatch) and consist of 106 profiles from FFPE samples and 44 profiles from fresh-frozen samples. For the 44 fresh-frozen samples also WGS data (43 genomes) and RNA-seq data (37 transcriptomes) have been produced for validation purposes.

  Dataset EGAD00001004074

• Deep WGS of matched tumor-normal pairs for HGSOC copy-number signatures study

  This dataset includes 111 bam files from WGS sequence data aligned to human genome assembly GRCh37 (hg19) from 56 tumour and matched normal samples. Libraries were constructed with ~350-bp insert length using the TruSeq Nano DNA Library prep kit (Illumina) and sequenced on an Illumina HiSeq X Ten System in paired-end 150-bp reads mode. The average depth was 60× (range 40-101×) in tumours and 40× (range 24-73×) in matched blood samples.

  Dataset EGAD00001004189

• RNAseq of human fetal pancreas development

  The dataset comprises RNA-seq information of 4 subpopulations sorted from human fetal pancreas of 3 different donors. Low input libraries were generated using the Smart-seq2 protocol after Ampure XP cleanup of the total RNA extracted from the sorted cells. Libraries were multiplexed and sequenced paired-end over 2 lanes of HiSeq4000 each. Raw data was aligned to the human genome refernence GRCh37 using STAR v2.5.1b with GENCODE v19 as transcriptome reference, and unaligned reads were folded into the final uploaded bams.

  Dataset EGAD00001004210