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• miRNA expression in response to LPS stimulus in macrophages

  Our lab is currently using macrophages as a model system for understanding how genetic variation modulates the response to external environmental stimulus. We want to extend this beyond regular polyadenylated RNA to small RNAs such as miRNAs. This project would cover the costs of a pilot to study miRNA response to LPS stimulus, and will be performed as part of a rotation project in the lab. We will require a small number of miRNA libraries and a single lane of MiSeq

  Dataset EGAD00001002196

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0837_SA501X2

  40 samples; filetype=bam

  Dataset EGAD00001004812

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0443_SA501X7A

  48 samples; filetype=bam

  Dataset EGAD00001004813

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0472_SA501X7A

  50 samples; filetype=bam

  Dataset EGAD00001004814

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0582_SA501X10A

  45 samples; filetype=bam

  Dataset EGAD00001004815

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0680_SA501X10A

  61 samples; filetype=bam

  Dataset EGAD00001004816

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0544_SA532X6

  68 samples; filetype=bam

  Dataset EGAD00001004817

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0650_SA532X6

  71 samples; filetype=bam

  Dataset EGAD00001004818

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0738_SA609X6

  48 samples; filetype=bam

  Dataset EGAD00001004819

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0739_SA609X6

  52 samples; filetype=bam

  Dataset EGAD00001004820

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0740_SA609X6

  60 samples; filetype=bam

  Dataset EGAD00001004821

• Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data for library px0741_SA609X6

  55 samples; filetype=bam

  Dataset EGAD00001004822

• Presentation and relapse myeloma

  Series of 56 paired presentation, relapse and control samples from newly diagnosed, uniformly treated myeloma patients. Deep of treatment response and maintenance allocation (active observation or lenaldiomide) was determined for all. All samples underwent whole exome sequencing with additional baits to cover the myc and immunoglobulin loci. There are 168 (56 presentation, 56 relapse and 56 control) samples in this study. 131 are available as part of this dataset. The remaining 37 are available with dataset accession id EGAD00001001358.

  Dataset EGAD00001004846

• Genetic vulnerability of knockout cancer lines (2019-04-01)

  Genome-wide CRISPR/Cas9 library screen was performed in isogenic cell lines. Three biological replicates were used. Cells were harvested at initiation of screen and at specific time points following cell culture. Using this approach we aim to identify genes specifically important in cell survival in engineered cell lines. Please perform 72, instead of 36, PCR reactions as the screen performed at 200x coverage. . This dataset contains all the data available for this study on 2019-04-01.

  Dataset EGAD00001004881

• unmapped Bam files from whole transcriptome RNA-seq

  In this study we characterized genomic alterations in two to five metachronous bladder tumors from 29 patients initially diagnosed with early stage disease. Fourteen patients (32 tumors) had non progressive disease (NPD) and 15 patients (34 tumors) had progressive disease (PD). Whole exome sequencing (WES, ~50x mean read depth and whole transcriptome RNA-seq was performed (RNA was not advalible for 4 tumors). Data provided here consist of 71 unmapped Bam files form whole transcriptome RNA-seq.

  Dataset EGAD00001002717

• mapped Bam files from whole transcriptome RNA-seq

  In this study we characterized genomic alterations in two to five metachronous bladder tumors from 29 patients initially diagnosed with early stage disease. Fourteen patients (32 tumors) had non progressive disease (NPD) and 15 patients (34 tumors) had progressive disease (PD). Whole exome sequencing (WES, ~50x mean read depth and whole transcriptome RNA-seq was performed (RNA was not advalible for 4 tumors). Data provided here consist of 71 mapped Bam files form whole transcriptome RNA-seq.

  Dataset EGAD00001002718

• Haplotype Reference Consortium Release 1.1

  Haplotype Reference Consortium Release 1.1 - subset for release via the EGA

  Dataset EGAD00001002729

• Exome Sequencing of Poor Prognosis Acute Myeloid Leukaemia (2019-08-19)

  We plan to sequence the exomes of 4 AML cases (tumour and germline) in an effort to discover new mutations in this disease that could improve our understanding of leukaemogenesis and guide the development of new targeted therapies. The Sanger Institute will sequence the exomes of 4 Acute Myeloid Leukaemia cases including tumour and germline DNA so that somatically-acquired, AML-specific mutations can be accurately designated. . This dataset contains all the data available for this study on 2019-08-19.

  Dataset EGAD00001005265

• A96146A

  Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96146A 1195 samples; filetype=bam

  Dataset EGAD00001005338

• A96172B

  Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96172B 1694 samples; filetype=bam

  Dataset EGAD00001005340

• A96226B

  Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96226B 1274 samples; filetype=bam

  Dataset EGAD00001005345

• A96193B

  Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96193B 2410 samples; filetype=bam

  Dataset EGAD00001005347

• A96199A

  Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96199A 843 samples; filetype=bam

  Dataset EGAD00001005348

• A96199B

  Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96199B 1170 samples; filetype=bam

  Dataset EGAD00001005353

• A96211C

  Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96211C 1397 samples; filetype=bam

  Dataset EGAD00001005354

• A96225C

  Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96225C 1034 samples; filetype=bam

  Dataset EGAD00001005355

• Non-invasive prenatal diagnosis by genome-wide haplotyping of cell-free plasma DNA

  This dataset contains a total of 10 families and 51 samples presented in 'Non-invasive prenatal diagnosis by genome-wide haplotyping of cell-free plasma DNA' study, in which 9 of them are cfDNA samples and the rest of samples are gDNA samples. All the samples are targeted sequencing data with a custom 45Mb capture library . Raw pair-end fastq files for each sample is available.

  Dataset EGAD00001004989

• Melanoma post mortem analysis

  Despite multiple large-scale sequencing studies offering substantial insight into the genomic landscape of cutaneous melanoma, the molecular events surrounding disease progression and the resulting molecular heterogeneity between metastases have not been fully elucidated. We have been applying whole genome and transcriptome sequencing across metastases collected during post mortem. Herein we show the findings for the first such patient. This is a targeted pulldown validation in support of the whole-genome sequencing analysis of the metastatic tumours and targeted pulldown of the primary tumour.

  Dataset EGAD00001005073

• NIHR BioResource Rare Diseases WGS project - Leber Hereditary Optic Neuropathy (LHON) Rare Disease domain

  Short read whole genome sequencing (WGS) CRAM files for the NIHR BioResource Rare Diseases WGS project – Participants from the Leber Hereditary Optic Neuropathy (LHON) Rare Disease domain

  Dataset EGAD00001005122

• Childhood arthritis DNA (2020-01-15)

  The aim of this study is to describe the transcriptome of single arthritic cells. . This dataset contains all the data available for this study on 2020-01-15.

  Dataset EGAD00001005785

• Whole exome sequencing of an alveolar rhabdomyosarcoma patient with RET germline mutation

  Whole exome sequencing of an alveolar rhabdomyosarcoma patient with RET germline mutation and subsequent analysis of potential therapeutic mechanisms associated with the patient's rare germline mutation. Patient sampels were sequenced from an initial biopsy and from a relapse biopsy, in addition to normal blood as the matched normal DNA. RNA sequencing was performed on the relapse sample as initial sample was unable to produce usable RNA for analysis.

  Dataset EGAD00001006125

• Processed RNA-seq data for clinical efficacy and biomarker analysis of neoadjuvant atezolizumab in operable urothelial carcinoma in the ABACUS trial

  ABACUS is a single arm phase 2 study that investigated 2 cycles of atezolizumab (1200mg Q3) prior to cystectomy in 95 patients with muscle invasive transitional cell cancer (T2-4N0M0). Pathological complete response (pCR) occurring in ≥20% of patients was the primary endpoint. Biomarker analysis on sequential tissue was a co-primary endpoint. This dataset includes the TPM and raw counts tables.

  Dataset EGAD00001006199

• Raw RNA-seq data for clinical efficacy and biomarker analysis of neoadjuvant atezolizumab in operable urothelial carcinoma in the ABACUS trial

  ABACUS is a single arm phase 2 study that investigated 2 cycles of atezolizumab (1200mg Q3) prior to cystectomy in 95 patients with muscle invasive transitional cell cancer (T2-4N0M0). Pathological complete response (pCR) occurring in ≥20% of patients was the primary endpoint. Biomarker analysis on sequential tissue was a co-primary endpoint. This dataset includes the raw RNA-seq data.

  Dataset EGAD00001006205

• Whole exome sequencing data for Molecular Characterization of ETMRs

  This dataset contains exome sequencing data from 21 samples. Sequencing of samples using whole-exome sequencing was per- formed by creating libraries using the IlluminaTruSeq exome enrich- ment kit following the manufacturer’s instructions after size selection. Size selection was performed by fractionation using a Covaris ultra- sonicator and subsequent selection was performed using a 1.5% gel Pippin Prep cassette (Sage Science). One lane per sample has been sequenced resulting in 42 Fastq files (paired end).

  Dataset EGAD00001006210

• Sequencing data for ICGC / OCCAMS samples - Perner et al (WGS, sWGS, WES, mutREAD)

  Data supporting: "The mutREAD method detects mutational signatures from low quantities of cancer DNA." Perner et al. WGS, sWGS, WES, and reduced representation sequencing data tumour and normal samples BAM files

  Dataset EGAD00001006170

• 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

• RRBS profiling for a cohort including 88 precancer specimens from 62 resected lung nodules from 39 patients including atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA), and invasive adenocarcinoma (ADC) and 39 matched normal lung tissues.

  To study the evolution of DNA methylation at genome level and methylation intra-tumor heterogeneity (ITH) during early lung carcinogenesis, we performed multiregional reduced representation bisulfite sequencing (RRBS) of 127 resected lung samples from 39 patients using single end library Hiseq3000.

  Dataset EGAD00001006367

• McGill EMC Community projects Release 7 for cell line "lung epithelial"

  Complete reference epigenome (as defined by IHEC) of a lung epithelial cell line with non-small Cell Lung Adenocarcinoma

  Dataset EGAD00001007679

• The Xq22.3 contiguous gene deletion syndrome (ATS-ID): from genotype to further delineation of the phenotype

  Approximately 200 ng of high-quality of genomic DNA samples were used for library preparation. DNA libraries were prepared using the Human Core Exome Kit according to manufacturer’s recommendations (Twist Bioscience, San Francisco, CA, USA) and then sequenced on Illumina NovaSeq 6000 (Illumina, Inc., san Diego, CA, USA). Detailed protocol of WES data processing and variant analysis are available in Supplementary data.

  Dataset EGAD00001007740

• LSC RNA-Sequencing

  To infer the proteomic Mito signature in the LSC subcompartiment, myeloid blasts for 10 patients from the discovery cohort were FACS-sorted into CD34-GPR56+NKG2DLigands- (CD34-), alias 61dc5fb798e2520001702c03 CD34+GPR56+NKG2DLigands- (CD34+), alias 61dc5fb798e2520001702c03 Detailed gating strategy will be described in Donato, Correia, Andresen and Trumpp et al., (manuscript in preparation)

  Dataset EGAD00001008488

• Drug-induced epigenomic plasticity reprograms circadian rhythm regulation to drive prostate cancer towards androgen-independence

  ChIP-seq for AR, FOXA1 and H3K27ac in primary prostate tumors before and after 3 months of neoadjuvant enzalutamide treatment. RNA-seq expression data of primary prostate tumors before and after 3 months of neoadjuvant enzalutamide treatment.

  Dataset EGAD00001008562

• Fastq and reference alignment of 19 samples for defining structural variation associated with breast cancer susceptibility by long-read genome sequencing

  Long-read genome sequencing performed on the Oxford Nanopore Technologies' PromethION to resolve variants underlying breast cancer susceptibility in sixteen individuals with pathogenic germline SVs in BRCA1, BRCA2, CHEK2 or PALB2.

  Dataset EGAD00001008690

• Stromal and dendritic cells from lymph nodes: single-cell RNA-seq

  Although cross-species transcriptional analysis has been generated for DCs, transcriptomic conservation between mouse and human FRCs at single-cell resolution has been unclear. To test whether GREM1+ FRCs might also play a role in DC homeostasis in humans, we performed scRNA-seq of CD45–PDPN+ stromal cells, as well as CD45+CD11c+ immune cells from healthy human LNs of three human donors. Data was generated using the 10x platform.

  Dataset EGAD00001008731

• Whole genome sequencing of multifocal ileal neuroendocrine tumors

  This dataset includes whole genome sequences of 75 synchronous primary tumors, 15 metastases, and corresponding normal samples from 13 patients with multifocal ileal neuroendocrine tumors. The whole genomes were sequenced on Illumina HiSeq X Ten to generate 151-bp paired-end reads, which were aligned to GRCh38/hg38 reference assembly using BWA–MEM and duplicate-marked with Picard tools. GATK was utilized for base score recalibration and local indel re-alignments. The whole genomes are provided as CRAM files.

  Dataset EGAD00001008831

• Whole exome data from PMID27216186

  This dataset comprises complete exome data from from the study PMID27216186 (Harbst & Lauss et al, Cancer Research 2016). These data are from 49 samples (tumor and matched normal) from 8 patients representing multi-region sequencing of human melanoma. Files are in the BAM format and contain aligned and processed data used for e.g. somatic variant calling. The sequencing libraries were constructed using SureSelect target enrichment with Clinical Research Exome Panel (Agilent) and sequenced on a HiSeq2500 (Illumina).

  Dataset EGAD00001008149

• Multi-region sequencing of 10 neuroblastoma cases

  To investigate intratumour heterogeneity and to better understand tumour evolution in neuroblastoma, we have performed a multi-region whole-exome sequencing on a total of 51 spatially separated tumor samples from 9 primary neuroblastomas (2 low-risk, 1 intermediate-risk and 6 high-risk) and 1 relapsed neuroblastoma. We also assessed the impact of chemotherapy on the clonal expansion by sequencing tumour regions from one medium risk and one high-risk tumour for which we had matched samples obtained at diagnosis and after chemotherapy.

  Dataset EGAD00001008020

• Paired-WGS Sequencing of Primary lymphomas of the central nervous system (PCNSL)

  Paired WGS samples, 24 tumor/control pairs of primary CNS lymphoma, sequenced on HiSeq X Ten using Illumina TruSeq Nano DNA for library preparation.

  Dataset EGAD00001007810

• ATAC-seq of metastatic prostate tumors

  This dataset includes Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data, in FASTQ format, from 70 metastatic castration-resistant prostate cancer tumor samples from the SU2C/PCF West Coast Dream Team (WCDT) project. The sequencing data is paired-end, 150 bp sequencing data from an Illumina NovaSeq 6000 machine. ATAC-seq libraries were prepared following the protocol described in Buenrostro et al. Nature Methods. 2013 (PMID: 24097267) and Corces et al. Nature Methods. 2017 (PMID: 28846090).

  Dataset EGAD00001009654

• Single-cell RNA and TCR sequencing of BALF from 11 ICI-pneumonitis patients and 6 controls

  Dataset containing the FASTQ files of RNA (scr*) and TCR (vdj*) sequencing of 17 bronchoalveolar lavage fluid samples collected from ICI pneumonitis (n=11) and control (n=6) patients. To comply with GDPR regulations, please note that individual sample identifiers used for this data deposit (alphabetical ID) are different from and cannot be traced back to the patient identifiers used throughout the manuscript (numerical ID).

  Dataset EGAD00001009723

• Papua New Guinean Genome Altitude Project Dataset 2

  The PGAP dataset 2 includes 82 whole genome sequences for Papua New Guinean individuals sampled in Daru (N=1), Port Moresby (N=64) and Mount Wilhelm (N=17). DNA was extracted from saliva samples (Oragen kit). Sequencing libraries were prepared using the TruSeq DNA PCR-Free HT kit. 150 bp paired-end sequencing was performed on the Illumina HiSeq X5 sequencer. The PGAP dataset provides Fastq, mapped cram files (GRCh38) and phenotype measurements.

  Dataset EGAD00001010142

• WGS data from LCNEC patient derived tumor organoids (PDTOs) and matched parental tumors - SA

  The dataset includes cram files from WGS of 2 LCNEC tumors and matched PDTOs. For all tumors, cram files from WGS of matched normal tissue derived organoids from the corresponding patients is included. Analysis VCF files are also included in the dataset. The sequencing was done with a NovaSeq 6000 instrument.

  Dataset EGAD00001009990

• DLP+ Single Cell Genomic Library A98167

  DLP+ Single Cell Genomic Library A98167 for Diffuse large B-cell lymphoma patient sample TFRIPAIR4_DLBCL

  Dataset EGAD00001010249

• 10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0198_004A

  10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0198_004A for Lymph node patient sample RLN_02_5Prime

  Dataset EGAD00001010237

• 10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0198_005A

  10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0198_005A for Lymph node patient sample RLN_03_5Prime

  Dataset EGAD00001010238

• DLP+ Single Cell Genomic Library 98211

  DLP+ Single Cell Genomic Library 98211 for Diffuse large B-cell lymphoma patient sample TFRIPAIR11_DLBCL

  Dataset EGAD00001010239

• DLP+ Single Cell Genomic Library A98180

  DLP+ Single Cell Genomic Library A98180 for Diffuse large B-cell lymphoma patient sample TFRI_Pair_13_DLBCL

  Dataset EGAD00001010240

• DLP+ Single Cell Genomic Library A98193

  DLP+ Single Cell Genomic Library A98193 for Follicular lymphoma patient sample TFRI_Pair_6_FL

  Dataset EGAD00001010241

• DLP+ Single Cell Genomic Library A98203

  DLP+ Single Cell Genomic Library A98203 for Diffuse large B-cell lymphoma patient sample TFRIPAIR8_DLBCL

  Dataset EGAD00001010242

• DLP+ Single Cell Genomic Library A98205

  DLP+ Single Cell Genomic Library A98205 for Follicular lymphoma patient sample TFRIPAIR9_FL

  Dataset EGAD00001010243

• DLP+ Single Cell Genomic Library A98208

  DLP+ Single Cell Genomic Library A98208 for Diffuse large B-cell lymphoma patient sample TFRIPAIR10_DLBCL

  Dataset EGAD00001010244

• DLP+ Single Cell Genomic Library A98221A

  DLP+ Single Cell Genomic Library A98221A for Follicular lymphoma patient sample TFRIPAIR5_FL

  Dataset EGAD00001010245

• DLP+ Single Cell Genomic Library A98225

  DLP+ Single Cell Genomic Library A98225 for Diffuse large B-cell lymphoma patient sample TFRIPAIR12_DLBCL_rel

  Dataset EGAD00001010246

• DLP+ Single Cell Genomic Library A98288

  DLP+ Single Cell Genomic Library A98288 for Follicular lymphoma patient sample TFRIPAIR2_FL

  Dataset EGAD00001010247

• DLP+ Single Cell Genomic Library A98297

  DLP+ Single Cell Genomic Library A98297 for Follicular lymphoma patient sample TFRIPAIR3_FL

  Dataset EGAD00001010248

• Bulk RNA-Seq

  Human data for transcriptome (bulk RNA-Seq) in eight B-cell precursors: HSC, CLP, pro-B, pre-B, Immature B, Transitional B, Naive B CD5-, Naive B CD5+ cells

  Dataset EGAD00001010906

• Bulk ATAC-Seq Illumina NextSeq 500 (10M reads)

  Human data for chromatin accessibility (ATAC-Seq) in eight B-cell precursors: HSC, CLP, pro-B, pre-B, Immature B, Transitional B, Naive B CD5-, Naive B CD5+ cells

  Dataset EGAD00001010908

• Spectrum of Response to Platinum and PARP Inhibitors in Germline BRCA Associated Pancreatic Cancer in the Clinical and Pre-clinical Setting

  Whole genome sequencing data for germline BRCA pancreatic cancer

  Dataset EGAD00001011129

• scRNA-seq

  This dataset gather scRNAseq data performed for MM.1S cell line in control and dex conditions at 4h and 24h

  Dataset EGAD00001011139

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0076_000

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0076_000 for Triple negative breast cancer sample SA1035X5XB03021

  Dataset EGAD00001011240

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0142_004

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0142_004 for Triple negative breast cancer sample SA1035X6XB03209

  Dataset EGAD00001011243

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0162_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0162_002 for Triple negative breast cancer sample SA1035X7XB03502

  Dataset EGAD00001011246

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0162_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0162_001 for Triple negative breast cancer sample SA1035X8XB03420

  Dataset EGAD00001011248

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0164_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0164_002 for Triple negative breast cancer sample SA530X3XB03295

  Dataset EGAD00001011250

• 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

• Extended screen by deep amplicon sequencing

  The whole study comprises of two patient cohorts. Screening cohort: 40 patients of Germany; validation cohort: 40 patients from Asia. Further, bile duct and CCA cell lines have been analyzed. This dataset contains targeted DNA sequencing data of 40 tumor/normal pairs from the validation cohort plus 10 tumor/normal pairs of patients from the screening cohort for technical validation. Data was generated on Illumina HiSeq 2000 device in paired-end mode and is stored in BAM file format.

  Dataset EGAD00001011323

• Fusion gene analysis using multiplex single primer extension-based RNA-sequencing

  The whole study comprises of two patient cohorts. Screening cohort: 40 patients of Germany; validation cohort: 40 patients from Asia. Further, bile duct and CCA cell lines have been analyzed. This dataset contains fusion gene analysis using multiplex single primer extension-based RNA-sequencing for a subset of 25 patients of the screening cohort. Data was generated on Illumina NexSeq 550 device in paired-end mode and is stored in compressed FASTQ file format.

  Dataset EGAD00001011326

• RNAseq in pleural mesothelioma primary cell lines

  Pleural mesothelioma (PM) requires new treatments. Drug repurposing offers a potential approach to finding effective therapies. This study aimed to explore new therapeutic options for PM using RNA sequencing. RNA sequencing was performed on 58 patient-derived PM cell lines. Drug screening of over 1300 compounds was conducted on 11 lines, with further testing of selected drugs on 48 lines. Top candidates were validated in 3D culture and mouse models.

  Dataset EGAD00001015408

• RNA-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 EGAD00001011819

• CUT&RUN/ChIP-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 EGAD00001011821

• Single-cell Transcriptomic and Immune Receptor Profiling of PBMCs from Dengue-Infected Individuals with Varying Disease Severities

  This dataset comprises single-cell RNA sequencing (scRNA-seq) and immune receptor (TCR/BCR) profiling of peripheral blood mononuclear cells (PBMCs) collected from individuals infected with dengue virus (DENV) exhibiting different clinical severities: asymptomatic dengue (AD), dengue fever (DF), and dengue hemorrhagic fever (DHF). PBMCs were collected during the acute phase and, in some cases, during convalescence. The data provide a resource for understanding protective versus pathogenic immune responses in dengue infection.

  Dataset EGAD00001015634

• TenK10K Phase 1: Whole Genome Sequencing tandem repeats multi-sample VCFs

  Tandem repeat variants were called for 1,925 samples from phase 1 of the TenK10K project. Variant calling from WGS alignments to the GRCh38 reference assembly was completed with ExpansionHunter v5. This dataset is comprised of autosomal tandem repeat variants provided as multisample compressed VCF format files. SNV-derived principal component scores used in the manuscript (Tanudisastro et al.) are also provided in this dataset.

  Dataset EGAD50000002378

• 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

• BLUEPRINT September 2016, RNA-Seq Acute Lymphocytic Leukemia from bone marrow, on Genome GRCh38

  RNA-Seq data for 1 sample(s) Acute Lymphocytic Leukemia from bone marrow, on Genome GRCh38. 1 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001002954

• BLUEPRINT September 2016, RNA-Seq Acute Myeloid Leukemia from venous blood, on Genome GRCh38

  RNA-Seq data for 1 sample(s) Acute Myeloid Leukemia from venous blood, on Genome GRCh38. 1 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001002958

• BLUEPRINT September 2016, ChIPmentation T-cell Acute Lymphocytic Leukemia from capillary blood, on Genome GRCh38

  ChIPmentation data for 2 sample(s) T-cell Acute Lymphocytic Leukemia from capillary blood, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002938

• Dataset for linked files from Master-RNA

  RNA sequencing data of thymic epithelias tumors (TETs), 23 runs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001009096

• Clonal expansion of mutated cell population in bladder urothelium

  1cm biospies of from patients undergoing bladder cystectomy will be collected. The underlying muscle and stroma will be removed and the remaining epithelia dissected into small sequential areas which will be sent for ultra-deep exome sequencing using a panel of known cancer and viral genes. Sequence analysis using similar methods to Martincorena I et al (Science 2015, 348:880) will provide an idea of the somatic mutational landscape in these patient samples. Individual patient muscle samples will also be sequenced as a reference.

  Dataset EGAD00001003250

• WGS data for medulloblastoma samples (ICGC)

  WGS data of medulloblastoma tumor/control pairs.

  Dataset EGAD00001003127

• The spatial organization of intratumor heterogeneity and evolutionary trajectories of metastasis in hepatocellular carcinoma

  A dataset consisting of Multi-regional Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS) data for 54 samples from 9 patients with hepatocellular carcinoma. The dataset includes 45 tumor samples and 9 normal blood samples. Selected somatic variants were validated by Sequenom. Patients covered are: Patient 1, Patient 2, Patient 3, Patient 4, Patient 5, Patient 6, Patient 7, Patient 8, Patient 9 and Patient 10.

  Dataset EGAD00001003138

• RNAseq - Colorectal organoids and tumoroids (2017-05-04)

  Transcriptome sequencing of tumour tissue, adjacent normal tissue and derived organoids/tumoroids from colorectal cancer This dataset contains all the data available for this study on 2017-05-04.

  Dataset EGAD00001003320

• Mutational Analysis of Colorectal PDX models (2017-05-11)

  Targeted exome sequencing of patient derived xenografts from primary colorectal tumours and liver metastases. This dataset contains all the data available for this study on 2017-05-11.

  Dataset EGAD00001003334

• Pairs of whole genome sequencing repeated measurement sample pairs

  This dataset includes 186 whole genome sequencing samples which combine to create 93 pairs. Each pair is comprised of two sequencing experiments carried out on the same donor to the NIHR BioResource Rare Disease cohort. These samples have been used to validate the Telomerecat method (a method for estimating telomere length from whole genome sequencing).

  Dataset EGAD00001003809

• Cancer gene panel (T200.1) sequencing analysis of adult type ovarian granulosa cell tumors (Validation cohort from Hillman, et al)

  Cancer gene panel (T200.1) sequencing data from tumor/normal pairs for adult type ovarian granulosa cell tumor sequencing project. This data set contains 55 tumor panel sequencing data and 44 matched normal panel sequencing data generated using the MD Anderson Cancer Center T200.1 cancer gene hybrid capture platform, with sequencing performed on an Illumina HiSeq 2000. This dataset contains BAM files generated by aligning paired-end reads to the hg19 reference genome.

  Dataset EGAD00001004091

• Clinical sequencing in multiple myeloma

  DNA (n=1281) and RNA (n=767) were extracted from bone marrow aspirates where CD138+ selection had been performed to enrich plasma cells from patients with monoclonal gammopathy of undetermined significance (MGUS), smoldering multiple myeloma (SMM), or multiple myeloma (MM). DNA and/or RNA were sent to Foundation Medicine where targeted sequencing was performed using their Foundation 1 Heme panel. Resulting BAM files were returned along with annotations for somatic events including single nucleotide mutations, indels and structural rearrangements.

  Dataset EGAD00001004113

• Dataset of PGD PGS study in CITIC Xiangya and BGI

  A total of 395 couples were subjected to IVF-PGD treatment, including 129 couples with NGS-based test and 266 couples with SNP array based test for the detection of embryonic chromosomal abnormalities. The NGS test was performed using low coverage whole genome sequencing with HiSeq 2000 platform. And the SNP array test was using Affymetrix Gene Chip Mapping Nsp I 262K. The average age of patients was 32.1 years (age range 20-44 years).

  Dataset EGAD00001001037

• Targeted sequencing of cell-free DNA and white blood cells from 24 men with metastatic prostate cancer

  This dataset consists of aligned DNA sequencing data in BAM file format from cell-free DNA and white blood cells from 24 men with metastatic prostate cancer. One cell-free DNA sample and one white blood cell sample is available for each patient, resulting in 48 total BAM files in this dataset. The sequencing was performed using a hybrid capture-based targeted panel of 73 prostate cancer driver genes.

  Dataset EGAD00001004486

• Sequencing data for oesophageal and related samples - Abujudeh et al (WGS, fastSeq)

  Data supporting: "Low-cost and clinically applicable copy number profiling using repeat DNA." Abujudeh et al. DNA WGS (BAM files) DNA fastSeq (fastq files) Tumours, Barrett's, normals.

  Dataset EGAD00001004289

• Whole genome and RNA sequencing of cutaneous melanoma metastases

  Whole genome sequencing of cutaneous melanoma skin and brain metastases and matched normal DNA, as well as RNA sequencing of material from the skin and brain metastases. In addition, RNA sequencing was performed for Dabrafenib and Trametinib treated patient-derived xenografts, together with untreated and vehicle treated controls.

  Dataset EGAD00001004130

• Variant Calling used in ABB project

  This dataset has two Variants Files in VCF format used in ABB project (https://github.com/Francesc-Muyas/ABB). One has the variants found in a Rare Variant Association Study performed in CLL patients. This has 1217 samples represented. The other variant file has 209 SNPs predicted in 10 samples by GATK HaplotypeCaller and selected for Sanger Sequencing Validation. Raw reads were aligned against the Human Reference genome (Hg19) with BWA mem and variants were obtained using GATK HaplotypeCaller.

  Dataset EGAD00001004132