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• McGill Sperm Methylome Sequencing Data

  The study includes NGS-based WGBS on one sperm DNA sample pooled from 30 participants, and methylC-capture sequencing (MCC-Seq) on the same pooled sperm sample as well as 45 sperm DNA samples derived from both fertile and infertile individuals in two cohorts (Toronto, a fertile cohort; Montreal, an idiopathic infertility cohort). All the data were generated with 100bp paired-end reads using the Illumina HiSeq2000 or 4000 systems.

  Dataset EGAD00001004978

• WES patient 368

  Whole Exome Sequencing of blood and FFPE tumour of patient #368.  150–300 ng of DNA was fragmented to approximately 200 bp using a focal acoustic device. Libraries were prepared with the Kapa Hyper Prep Kit and SureSelectXT adaptors. Hybridisation capture was performed with SureSelect Clinical Research Exome V2 baits following the SureSelectXT recommended protocol (Agilent). Indexed libraries were sequenced on an Illumina NovaSeq 6000 to generate paired-end 150 bp reads with average of 70-fold base coverage for the germline sample and 330-fold coverage for tumour sample.

  Dataset EGAD00001011272

• CCTG IND.231 WGS DNA Sequencing Data

  41 WGS DNA sequences from: Phase I trial of CX-5461, a first-in-class G-quadruplex stabilizer in patients with advanced solid tumors enriched for DNA-repair deficiencies (CCTG IND.231)

  Dataset EGAD00001008756

• scRNA-seq dataset of patient with immune dysregulation

  scRNA-seq dataset on a patient (P_IKZF2-het) presenting with immune dysregulation. This dataset contains raw and processed files from scRNA-seq performed on samples using the 10x Genomics Chromium Controller with the Chromium Single Cell 3′ Reagent Kit (v3 chemistry). There are three paired-end (75 bp) fastq files (I1, R1, R2) and three processed files generated with 10x Genomics Cell Ranger v3.0.2 software against GRCh38 human reference transcriptome (scrnaseq_P_IKZF2-het_barcodes.tsv.gz, scrnaseq_P_IKZF2-het_features.tsv.gz, scrnaseq_P_IKZF2-het_matrix.mtx.gz).

  Dataset EGAD00001008443

• 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

• Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation.

  We profiled CD34+ enriched cells from GCSF mobilized bone marrow samples (n = 4) using single-cell RNA sequencing (10X) with targeted genotyping, and single-cell DNA methylation (RRBS) with single-cell RNA sequencing (Smart-Seq2) and targeted genotyping. A 5th CH bone marrow aspirate sample was obtained to validate observed results.

  Dataset EGAD00001008985

• SNF_OLINK_20

  Matrix of normalized values from Olink assay performed on baseline BM Plasma. The Olink Immuno-Oncology multiplex proteomic Panel included 92 proteins associated with human inflammatory conditions. Data is analyzed using real-time PCR analysis software via the Ct method and Normalized Protein Expression (NPX) manager. Data were normalized using internal controls in every single sample, inter-plate controls, negative controls and a correction factor and expressed as Log2 scale, which was proportional to the protein concentration. One NPX difference equals the doubling of the protein concentration.

  Dataset EGAD00001011147

• 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

• RNA-seq dataset of patient and healthy donors

  RNA-seq dataset on a patient (P) presenting with defects of immunity and three healthy donors (C1, C5, C6). This dataset contains raw and processed files from RNA-seq transcriptome analysis performed according to the Smart-seq2. There are 24 single-read (50 bp) fastq files, 6 per patient/donor consisting of 2 cell types and 3 replicates per cell type. There is one count matrix file generated using featureCounts against Ensembl v98 gene models.

  Dataset EGAD00001008371

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

  Data supporting: "Esophageal adenocarcinoma organoid cultures recapitulate human disease heterogeneity and provide a model for clonality studies and precision therapeutics." Li et al. WGS (BAM files) RNAseq (BAM files) Tumours, organoids, normals

  Dataset EGAD00001004007

• PGDx elio™ plasma resolve assay: targeted sequencing analyses of WBC DNA

  The dataset "PGDx elio™ plasma resolve assay: targeted sequencing analyses of WBC DNA" includes paired end FASTQ reads of 49 white blood cell (WBC) genomic DNA samples from metastatic colorectal cancer patients. Sequencing was performed using a panel consisting of 33 genes, covering over 237,000 bp, targeting 25,000x depth across the targeted regions.

  Dataset EGAD00001009721

• Tapestri snDNA-seq data along with matched bulk data for validation

  Files from Tapestri snDNA-seq of archival tissue samples from 16 pancreatic ductal adenocarcinoma (PDAC) patients. Matched bulk sequencing (whole-exome, whole-genome, MSK-IMPACT) data are attached for a subset of the patients.

  Dataset EGAD00001009735

• 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

• PGDx elio™ plasma resolve assay: targeted sequencing analyses of plasma cfDNA

  The dataset "PGDx elio™ plasma resolve assay: targeted sequencing analyses of plasma cfDNA" includes paired end FASTQ reads of 183 cfDNA samples from metastatic colorectal cancer patients. Sequencing was performed using a panel consisting of 33 genes, covering over 237,000 bp, targeting 25,000x depth across the targeted regions.

  Dataset EGAD00001009719

• Pseudotime ordering of cell cycle state (2020-01-29)

  We will be using G&T method to sequence single cell genome and transcriptome derived from FS13B iPSCs cell line. The cell cycle state of each of the single cells is known. Hence, we will be analysing the genome and transcriptome of single cells from each of the cell cycle state to generate a copy number profile and transcriptome profile per given cell cycle stage: G1, S, G2, S. . This dataset contains all the data available for this study on 2020-01-29.

  Dataset EGAD00001005919

• Evolutionary Genome Analysis of Transformation into Small Cell Carcinomas from Lung Adenocarcinomas

  This dataset includes the high-throughput sequencing data from a study entitled "Clonal History and Genetic Predictors of Transformation into Small Cell Carcinomas from Lung Adenocarcinomas". Whole-genome sequencing libraries were generated by PCR-free methods, and sequencing run was made in HiSeq X or HiSeq 2500 machines. PCR duplicates-marked, indel-realigned, and base-recalibrarted BAM files are provided in our dataset.

  Dataset EGAD00001003315

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

  Data supporting: "Genomic and epidemiological similarities between phenotypically distinct esophageal adenocarcinoma suggest a single entity" Zamani et al

  Dataset EGAD00001015435

• The impact of the human leukaemia virus HTLV-1 on host gene expression

  PBMCs were purified from blood samples of 8 HTLV-1 infected individuals, and cryo-preserved in fetal calf serum containing 10% DMSO. DNA from each samples was extracted using Qiagen Blood & Tissue kit according to the manufacturer's protocol. 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 please see http://www.sanger.ac.uk/datasharing/ .

  Dataset EGAD00001004169

• Prevalence of transthyretin amyloidosis in patients with heart failure and no left ventricular hypertrophy

  The study prospectively enrolled patients admitted for HF with LV ejection fraction (LVEF) ≥ 50% and LV wall thickness <12 mm. TTR cardiac amyloidosis was diagnosed according to accepted criteria, which include positive cardiac 99-Tc-DPD scintigraphy in the absence of monoclonal protein expansion in blood. In a cohort of patients with HFpEF without LVH, the prevalence of TTR cardiac amyloidosis was 5%. Transthyretin gene sequencing was performed in positive patients.

  Dataset EGAD00001007787

• Single-Cell RNA Sequencing of Terminal Ileal Biopsies Identifies Signatures of Crohn’s Disease Pathogenesis

  Biopsies from the terminal ileum of healthy individuals and terminal ileum of 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 EGAD00001015692

• Validation of SNVs found by Exome-seq in S2-SF1, -SF5 and -SF9 hiPSCs

  PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. 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 EGAD00001000631

• Multiple Myeloma Diagnosis to Relapse study samples (2016-01-27)

  The study will investigate serial samples from the same patient taken at the time of MGUS or SMM diagnosis, and later at the time of evolution towards MM. Samples will be sequenced by whole genome along with a matched normal to obtain the highest possible amount of information toinvestigate genomic changes at disease evolution. This dataset contains all the data available for this study on 2016-01-27.

  Dataset EGAD00001001898

• Comparison of protocols for deriving pancreatic progenitors from hPSCs (ATAC-seq)

  This dataset contains 27 mapped bam files. The samples were generated with 3 different protocols for deriving pancreatic progenitors from hPSC. Three parallel differentiations were performed, all done in a hPSC NKX6.1-GFP reporter line. For each protocol there are three cellular populations: total (presort), GFP+ and GFP- . In summary: 3 differentiations x 3 protocols x 3 cellular populations. We prepared ATAC-seq libraries for the 27 samples, and sequenced them on Illumina HiSeq4000.

  Dataset EGAD00001004824

• Healthy human B-lymphopoiesis RNA-Seq reference using FACS sorted bone marrow aspirates

  To define a transcriptomic reference of human B lymphopoiesis, bone marrow aspirates were obtained from n=4 healthy donors (study registration DRKS00023583). After immunodensity cell separation, samples were FACS-sorted into 7 established lymphopoietic differentiation stages. RNA was extracted from 5,000-320,000 cells per differentiation stage and subjected to ultra-low-input RNA sequencing after generation of stranded sequencing libraries.

  Dataset EGAD00001010917

• Targeted resequencing of Acute Myeloid Leukemia patients with an acquired inv(3)(q21q26) or t(3;3)(q21;q26).

  Targeted resequencing on the specific regions chr3:126036241-130672290 and chr3:157712147-175694147 in hg19 centered on the chromosomal regions 3q21 and 3q26 respectively. The focus lies on the detection of the exact breakpoints in Acute Myeloid Leukemia (AML) patients having acquired a inv(3)(q21q26) or t(3;3)(q21;q26). This dataset contains all information to detect all structural variants contained within these regions, including the 3q-aberrations inducing the overexpression of the proto-oncogene EVI1.

  Dataset EGAD00001000727