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• 2 paired WGS samples of peritumour regions of colorectal cancer

  2 paired WGS samples of peritumour regions of colorectal cancer (2 patients). The library was prepared using the Illumina TruSeq Nano FFPE kit and the sequencing was done on NovaSeq6000.

  Dataset EGAD00001009714

• CITE-seq

  This dataset contains the raw sequencing data (Runs) from all of the 10x Genomics single-cell CITE-seq Experiments, as well as the demultiplexed cell-donor identities matrices which were generated with Vireo (Analysis).

  Dataset EGAD00001009820

• Data Access Committee of the Medical Faculty of the University of Basel (MF-DAC)

  Dac EGAC00001002981

• The genomic imprint of cancer therapies helps timing the formation of metastases

  Study EGAS00001003416

• DAC_For_MPN

  This is the DAC for the MPN data set from Milena Kalmer.

  Dac EGAC50000000531

• Genetic_background_for_the_major_psychiatric_disorders_in_the_general_Finnish_population

  Low coverage (4-6x) sequencing on samples from population cohorts (Finrisk, Health2000) will be done at Wellcome Trust Sanger Institute (WTSI) using Illumina HiSeq sequencing technology. We will produce 100bp paired end reads. Variants will be called using the 1000 Genomes Project pipeline. The samples have been selected from a national representative set of 8028 samples from persons of 30 years or older, which were screened for psychotic and bipolar disorders using the Composite International Diagnostic Interview, self-reported diagnoses, medical examination, and national registers.

  Study EGAS00001000162

• Investigating_the_genetics_of_immunity_against_Salmonella_in_humans

  This study entails whole genome sequencing of an interleukin (IL)-12 b-1 receptor-deficient individual who presented with a chronic systemic Salmonella Enteritidis infection that did not resolve with standard IFNg and antibiotic treatment. Whole genome sequencing of the patient’s parents are also included.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/

  Study EGAS00001001664

• 46 CLL Whole Genome Sequencing Study

  Chronic lymphocytic leukaemia (CLL) consists of two biologically and clinically distinct subtypes defined by the abundance of somatic hypermutation (SHM) affecting the Ig variable heavy-chain locus (IgHV). The molecular mechanisms underlying these subtypes are incompletely understood. Here, we present a comprehensive whole-genome sequencing analysis of somatically acquired genetic events from 46 CLL patients, including a systematic comparison of coding and non-coding single nucleotide variants, copy number variants and structural variants, regions of kataegis and mutation signatures between IgHVmut and IgHVunmut subtypes.

  Study EGAS00001003254

• USARC 10X Genomics Single Cell DNA Sequencing Data

  We investigated the impact of ploidy heterogeneity on copy number inference at a single cell level using fluorescence-activated cell sorted (FACS) nuclei from an undifferentiated soft tissue sarcoma. FACS revealed the presence of three aberrant subpopulations, including a haploid, a near diploid and a whole genome doubled population. Once sorted, single cell nuclei underwent whole genome sequencing using the chromium CNV single cell DNA library kit (10X Genomics). We sequenced single normal nuclei (2n) and single aberrant / tumour nuclei (1n, 2n and 2n+).

  Study EGAS00001006144

• De novo mutations in schizophrenia

  De novo mutations in schizophrenia

  Dataset EGAD00001000251

• WES data from 165 tumor/germline samples with muscle invasive bladder cancer.

  In this study, a total of 300 patients with MIBC receiving chemotherapy were included; 62 received NAC before cystectomy and 245 received first-line chemotherapy upon detection of locally-advanced (T4b) or metastatic disease. Treatment response, defined as pathological downstaging (< pTa,CIS,N0) after NAC or complete or partial response after first-line treatment (RECIST criteria). WES was performed using DNA from 165 tumors (76x median coverage) and associated germline DNA (46x median coverage). Data provided here consist of 5,828 fastq files for WES.

  Study EGAS00001004507

• Data Access Committee for the UCSF Chordoid Glioma of the Third Ventricle Genome Project Dataset

  Dac EGAC00001000776

• X chromosome dosage and the impact on the methylation pattern across human tissues

  Study EGAS00001007020

• Comprehensive genomic characterization of early stage bladder cancer - nanopore sequencing

  For this project about non-muscle invasive bladder cancer (NMIBC), we analysed long read sequencing data from 4 patients using the Nanopore platform. The dataset is composed of 8 BAM files: 4 tumor samples and 4 paired blood samples.

  Study EGAS50000000510

• WTCCC case-control study for Bipolar Disorder - Combined Controls

  WTCCC genome-wide case-control association study for Bipolar Disorder (BD) using six disease collections together with the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000002

• 46 WES paired FASTQ germline/tumour samples from 23 early-onset prostate cancer donors from the Bob Champion Cancer Trust

  The dataset contains 46 samples: a germline and tumour sample from each of 23 donors. Donors are men diagnosed with prostate cancer at a young age, from the Bob Champion Cancer Trust. The data consists of 92 whole exome sequenced paired FASTQ files, compressed with bgzip. Exome sequences were enriched using Agilent SureSelect XT2 Human All Exon V5 baits, and sequenced with Illumina HiSeq 2500.

  Dataset EGAD50000002112

• RNA-sequencing from ALL patients treated on the Australasian Leukaemia and Lymphoma Group (ALLG) ALL06 study.

  Dataset contains RNA-sequencing data (fastq files) from 45 patients treated on the the Australasian Leukaemia and Lymphoma Group (ALLG) ALL06 study, an MRD-stratified Paediatric Protocol. Patient samples (bone marrow or peripheral blood) were taken at diagnosis. mRNA was extracted from blast cells and underwent paired-end sequencing (75bp) using the illumina NextSeq platform. Genomic data was used for identification of genomic drivers of acute lymphoblastic leukaemia (ALL).

  Dataset EGAD50000001111

• Genomic analysis of seminomas

  This study looks at the genomic landscape of seminomas, based on exome sequencing data and SNP array data. Eight seminoma tumors and their matched normal DNAs were exome sequenced on Illumina platforms. The same samples were also processed on Affymetrix SNP 6.0 arrays.

  Study EGAS00001000943

• Yemen_and_Chad_Genotyping

  HumanOmni2.5-8 data from Chad and Yemen.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/

  Study EGAS00001001231

• Somatic_Variation_Angiosarcoma

  Through whole genome sequencing, this study will explore the mutational profiles and signatures within an angiosarcoma tumour from a patient with xeroderma pimentosum. Very little information is known about this tumour type and it has not previously been studied within the context of xerogerma pigmentosum.

  Study EGAS00001002610

• Cell types of the human retina and its organoids at single-cell resolution. Cowan et al

  Human organoids recapitulating the cell-type diversity and function of their target organ are valuable for basic and translational research. We developed light-sensitive human retinal organoids with multiple nuclear and synaptic layers, and functional synapses. We sequenced the RNA of 285,441 single cells from these organoids at seven developmental time points and from the periphery, fovea, pigment epithelium and choroid of light-responsive adult human retinas.

  Dataset EGAD00001006350

• Metagenomic sequences from human stool samples

  ​DNA extraction from human stool samples was performed at the Center for Microbiome Innovation (CMI) at University of California, San Diego. DNA sequencing libraries were prepared using Nextera XT (Illumina). Shotgun DNA sequencing was performed on the Illumina HiSeq4000 platform. Raw fastq reads were quality-checked. Skewer (version 0.2.2) was utilized with the paired-end mode. Human reads were identified and removed by Bowtie2 mapping against the human genome reference (hg19), followed by bam2fastq with --unaligned --no-aligned --force options.

  Dataset EGAD00001006364

• Single-cell RNA sequencing of erythroid and megakaryocytic acute myeloid leukemia patient cells

  Single-cell RNA sequencing was performed on bone marrow mononuclear cells of a patient with acute myeloid leukemia with erythroid differentiation of the blasts and on peripheral blood mononuclear cells of a patient with acute myeloid leukemia with megakaryocytic differentiation of the blasts. The dataset contains raw fastq files of these two samples with single-cell RNA sequencing performed using the 10x Genomics platform.

  Dataset EGAD00001009865

• WGS patient 130

  Whole genome sequencing on DNA from snap frozen tumour sample and matched whole blood of patient #130. Analysis used the QIAamp DNA Mini Kit. Libraries were prepared using the Illumina TruSeq Nano library method using 200ng of DNA. Extracted DNA was sheared using the Covaris M220 Focused-ultrasonicator with a target fragment length of 550bp through bead size selection. The libraries were sequenced at depth of 40x for germline DNA and 80-100x for tumour DNA using paired 150bp reads.

  Dataset EGAD00001011271

• The WID-EC test for the detection and risk prediction of endometrial cancer

  Study EGAS00001005033