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• single-cell RNA-seq profiling of 2 patient derived colorectal cancer organoids after treatment with a combination of different anticancer drugs

  This dataset consists of single-cell RNA-seq profiling of colorectal cancer organoids derived from two patients. The organoids were profiled both after 4 weeks of treatment and after a drug holiday of two weeks. There are 49 RNA sequence files generated using single cell RNA sequencing technology from 10X genomics.

  Dataset EGAD50000001495

• BAM-format HiFi whole genome sequencing reads (PacBio Revio) from stabilized human saliva

  HiFi whole‑genome sequencing data from a single human saliva sample collected and stabilized using an Oragene device. Sequencing was performed on a SMRT® Cell using PacBio Revio™ SPRQ chemistry. Sequencing produced >100 Gb of HiFi reads yielding >30× genome coverage suitable for comprehensive variant and methylation analysis. Dataset includes long‑read HiFi sequences in BAM format, containing both aligned and unaligned reads.

  Dataset EGAD50000002398

• Whole exome sequencing of virus-associated HCC

  To understand comprehensive combinations of molecular alterations and seek for potential therapeutic targets/pathways in virus-associated HCC, we have conducted a whole exome sequencing (in-solution capturing all human coding exons) of 150 pairs of HCC cases.

  Study EGAS00001000389

• Multiomic cell-free DNA profiling to inform molecular classification and immunotherapy outcomes in endometrial cancer

  This study involved a cell-free DNA (cfDNA) framework integrating genomic, transcriptomic and epigenomic profiling to investigate patient response to immune checkpoint inhibitors in advanced endometrial cancer (EC) with mismatch repair deficiency (dMMR).

  Study EGAS50000001582

• TenK10K Phase 1: Whole Genome Sequencing Alignments

  Whole genome sequencing was performed for 1,925 samples from phase 1 of the TenK10K project. Sequencing was done with Illumina 2 x 150bp chemistry on a NovaSeq 6000 instrument to achieve mean 30x coverage. Sequence reads were aligned to the GRCh38 reference assembly with a fork of DRAGMAP v1.3.1. This dataset is comprised of 1,925 alignment files in cram format, and their corresponding index files.

  Dataset EGAD50000002466

• Whole genome bisulfite sequencing of hepatitis B virus-associated hepatocellular carcinoma tumor and non-cancerous samples

  To understand comprehensive epigenetic alterations in hepatitis B virus-associated HCC, we have conducted a whole genome bisulfite sequencing of 5 tumor samples and 3 non-cancerous samples (3 pairs and 2 tumors).

  Study EGAS00001002230

• Single-cell profiling maps the spectrum of crosstalk between glioma cells and tumor associated macrophages

  Tumor associated macrophages (TAMs) are a heterogeneous glioma infiltrate, implicated in cancer progression. We performed single-cell RNA-sequencing, to survey TAM response-patterns in glioma.

  Study EGAS00001002185

• HER2_positive_Breast_Cancer_

  We propose to definitively characterise the somatic genetics of HER2+ve breast cancer through generation of comprehensive catalogues of somatic mutations in a number of cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000042

• Matched_Pair_Cell_Line_Tumour_RNAseq

  In this study we will sequence the transcriptome of Verified Matched Pair Cancer Cell line tumour samples. This will be married up to whole exome and whole genome sequencing data to establish a full catalog of the variations and mutations found.

  Study EGAS00001000434

• Genetic_factors_underlying_premature_MI_in_Greek_families_without_vessel_disease

  The study will analyse by exome sequencing 8 Greek family members with an excess of potentially damaging mutations relating to premature MI and no vessel disease, to identify genetic factors underlying this condition. This is a follow on from project GPMI-NVD

  Study EGAS00001000478

• Paroxysmal_Neurological_Disorders___rare_epilepsies

  We are sequencing the exomes of patients with paroxysmal neurological disorders mainly focusing on migraine and epilepsy. Cases are collected from performance sites of members of EuroEPINOMICS. Most cases have a strong family history. The study sample will include both cases and controls.

  Study EGAS00001000421

• The Asian Diversity Project: genotyping of 37 Asian populations and ethnic groups

  The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection.

  Study EGAS00001002100

• Balanced_Brain_Tumour_Whole_Genome_Sequencing

  We propose to definitively characterise the somatic genetics of a number of pediatric malignant tumours including ependymoma, high grade glioma and central nervous system primitive neurectodermal tumours through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.

  Study EGAS00001000360

• 560 whole-genome sequenced breast cancers

  A comprehensive characterisation and analysis of 560 human breast cancers through genome-wide approaches including genomics, transcriptomics and epigenomics.

  Study EGAS00001001178

• IBDCA_Edinburgh

  In this experiment we have sequenced tumour normal pairs from patients presenting with CRC who have a prior history of inflammatory bowel disease. The idea is to identify driver mutations, new genes and novel pathways associated with the development of these malignancies.

  Study EGAS00001001129

• Predictor_RIO_TNBC

  In this study, samples fom a window study of the PARP inhibitor rucaparib in patients with primary triple negative or BRCA1/2 related breast cancer (RIO trial) will be investigated. Samples will undergo whole genome sequence and analysis, including use of HR Predict.

  Study EGAS00001002805

• Triple_Negative_Breast_Cancer_sequencing

  We propose to definitively characterise the somatic genetics of triple-ve breast cancer through generation of comprehensive catalogues of somatic mutations in a number of cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Study EGAS00001000161

• Genomic landscape of IG-MYC positive Burkitt lymphoma with precursor B-cell immunophenotype.

  As part of the ICGC, the ICGC MMML-Seq project performed whole genome sequencing of a rare Burkitt lymphoma subtype with precursor B-cell immunophenotype. Analysis were performed in concordance with the guidelines of the ICGC.

  Study EGAS00001002968

• Whole genome amplification and whole genome sequencing of human single cells

  Human single fibroblasts and T-lymphocytes were amplified using multiple annealing and looping-based amplification and multiple displacement amplification. Amplified products were next subjected to whole genome sequencing with the goal of performing a genetic variant analysis.

  Study EGAS00001003108

• HCA_Heart_Disease_BHF_DZHK_RNA_

  Cell Atlas of the diseased human heart. 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 EGAS00001004566

• All available datasets of DEEP

  All available datasets of DEEP. There are several Reference Epigenomes available. For metadata check out www.deep.dkfz.de One reference epigenome represents a set of 6 ChIP-Seqs, WGBS, RNA-Seq, smallRNA-Seq and sometimes DNase1 and/or NOME-Seq.

  Study EGAS00001001608

• Chromatin run-on and RNA sequencing of fibrolamellar carcinoma

  Fibrolamellar carcinoma (FLC) is a rare, therapeutically intractable liver cancer that disproportionately affects youth. Here we used chromatin run-on sequencing to characterize the enhancer landscape in FLC and RNA sequencing to identify dysregulated genes in FLC.

  Study EGAS00001004169

• Whole Exome Sequencing of healthy Spanish individuals

  The need for a detailed catalogue of local variability for the study of rare diseases within the context of the Medical Genome Project motivated the whole exome sequencing of 267 unrelated individuals, representative of the healthy Spanish population.

  Study EGAS00001000938

• Transposome_Bisulfite_Sequencing

  DNA belonging to 16 tumour/normal samples were treated with bisulfite, then up to 5 different bisulfite PCRs were performed in each one of the samples. Amplicons form the same sample were pooled and submitted to sequencing on a MiSeq platform.

  Study EGAS00001000751

• Uterine leiomyoma: DNA methylation, chromatin activity and gene expression

  In this study, we observed the effects of different uterine leiomyoma driver mutations to tumor DNA methylation, chromatin activity and gene expression, to form a comprehensive view on the epigenetic consequences of the mutations.

  Study EGAS00001004499