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• Enhancer plasticity in endometrial tumorigenesis demarcates non-coding driver mutations and alterations in 3D genome organization to boost oncogene expression

  Understand whether and how ERα can drive endometrial tumorigenesis. Study the mechanisms that lead to endometrial tumor progression and metastasis formation.

  Study EGAS00001007240

• Drug screen in iPSC-Neurons identifies nucleoside analogs as inhibitors of (G4C2)n expression in C9orf72 ALS/FTD

  To investigate the mode of action and potential side-effects we analyzed differential gene expression in post-mitotic C9orf72 iPSC-Neurons by RNAseq

  Study EGAS00001006138

• TB-DAR Whole Genome Sequencing Study

  116 Whole Genome Sequencing (WGS) samples from the TB-DAR study, which consists of a cohort of adult pulmonary tuberculosis patients recruited in Dar es Salaam, Tanzania.

  Study EGAS00001005850

• Dataset with genome-wide array data from Algerian Amazigh (Chaoui and Mozabite) and non-Amazigh individuals

  In this study we perform a genetic characterization of different Amazigh populations in Algeria and assess the impact of recent demography on their genomes.

  Study EGAS00001007235

• Bulk RNA-seq of stromal cells from multiple cancer types

  We sorted CD45-CD44+CD90+ stromal cells from multiple tumor types and performed bulk RNA-seq. The data allows to infer CAF programs active across indications.

  Study EGAS00001006497

• Deconvolution of bulk RNA-Seq using single cell RNA-Seq

  In this study single cell RNA-Seq data was used to train a deconvolution algorithm. The algorithm was validated on paired bulk RNA-Seq profiles.

  Study EGAS00001006723

• Targeted_NanoSeq___TwinsUK_Blood

  Utilising Targeted NanoSeq, we hope to explore the driver landscape in unprecedented detail in donors from TwinsUK. These donors have paired buccal swabs and data from this will help contextualise that work.

  Study EGAS00001007595

• Breast Cancer Sequential Sampling Targeted Capture

  This study aims to target capture sequence regions of interest from DNA derived from breast cancer patients who received neo-adjuvant chemotherapy. All patients had multiple biopsies performed before chemotherapy. Patients who had residual disease after the course of treatment underwent a further biopsy. We aim to characterise the mutations involved.

  Dataset EGAD00001000784

• Whole exome sequencing analysis on patient-derived cervical cancer tissues and respective tumoroids

  Whole exome sequencing (WES) was performed on the matched tumor and organoid pairs from 7 cervical cancer patients. The DNA was sequenced on NovaSeq6000 platform with 8Gb sequencing coverage. WES data was mapped against human reference genome GRCh38 by using BWA (v0.7.5) mapping tool.

  Dataset EGAD00001006166

• Deep targeted re-sequencing of fetal tissues

  this data set includes deep targeted re-sequencing of fetal bulk tissues of the 4 foetuses (T21=2, D21=2). The tissues include: fetal skin and intestinal organoid cultures passage 0 of all 4 fetuses, and spleen of fetus N01 (T21)

  Dataset EGAD00001008474

• Correction of a Factor VIII genomic inversion with designer recombinases

  PromethION-based whole genome sequencing of endothelial cells differentiated from patient derived induced pluripotent stem cells (iPSCs) of a hemophilic donor, transiently treated with a Cre recombinase, a RecF8 recombinase, and untreated cells. The dataset contains fastq files with all sequencing reads passing the standard quality filtering.

  Dataset EGAD00001007923

• Combined single cell immunophenotyping and genotyping of adult low hypodiploid acute lymphoblastic leukemia

  This dataset includes the Fastq files from sequencing data generate from diagnostic and remission bone marrow mononuclear cell samples using the Mission Bio Tapestri Plateform with both DNA amplicons and protein from antibody-derived tags sequencing libraries.

  Dataset EGAD00001009763

• AML-PMP miRNA-Seq

  miRNA libraries of the AML-PMP project were sequenced on the Illumina HiSeq 2000 instrument, approximately 16 samples per HiSeq lane, to a median depth of 5.7 million reads per library.

  Dataset EGAD00001009772

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

  The dataset includes fastq files from 2 LCNEC tumors and matched PDTOs. The sequencing was done with either a Nextseq 2000 or a NovaSeq 6000 instrument.

  Dataset EGAD00001009993

• Linked-Read Medulloblastoma data

  Linked-read data from 25 medulloblastomas and their matching control. Dataset consists of 25 group 4 medulloblastomas (G4) as well as 2 sonic hedgehog medulloblastomas (SHH-MB) samples and 2 group 3 medulloblastomas. The data consists of BAM files generated by the LongRanger pipeline developed by 10x Genomics

  Dataset EGAD00001010849

• Total RNA sequencing data from the Triple Negative Trial (TNT)

  BAM files from total RNA sequencing of samples from breast cancer patients in the TNT trial. Data includes 186 primary tumour samples and 13 matched recurrence samples.

  Dataset EGAD00001011141

• scRNA-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...

  Dataset EGAD00001015545

• scATAC-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...

  Dataset EGAD00001015546

• Whole-Genome Sequences from five human populations of Sudan

  This dataset provides the first high-coverage (~30X) whole-genome sequencing (WGS) data from Sudan, encompassing 125 individuals from five ethnolinguistic groups: Copts, Beja, Fulani, Fur, and Mahas. These populations represent three major linguistic families: Afro-Asiatic, Nilo-Saharan, and Niger-Congo, offering a detailed view of the country’s genetic diversity.

  Dataset EGAD00001015636

• The cellular immune and airway epithelial profile throughout childhood and in response to COVID-19 at multi-omic single cell level.

  Single-cell data gene expression data set (5’Chromium 10X) of healthy paediatric volunteers, and paediatric and adult COVID-19 patients. Gene expression was determined from samples of nasal, tracheal and bronchial brushings and blood (PBMCs). In addition to gene expression, PBMC’s were assayed by CITE-seq. A subset of samples have VDJ sequencing data for T cell receptors (TCR) and B cell receptors (BCR).

  Dataset EGAD00001007718

• Dataset for hepatopancreaticobiliary_malignancy-RNA

  Rare cancer sequencing data of 119 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008863

• The ACS study

  Dac EGAC00001002140

• Genomic Characterization of HPV+ Oropharyngeal Tumors

  Archived surgical samples from HPV positive oropharynx patients were identified and sequenced through the UNC/UTHSC NCTN Integrated Translational Science Center. DNA targeted panel sequencing data will be available through dbGaP.

  Study phs003925

• Comprehensive molecular profiling with whole-exome sequencing (WES) and RNA sequencing (RNA-seq) of PDX tumors

  To identify biomarkers of the antitumor efficacy of molecular targeted therapies, patient-derived xenograft (PDX) mouse models established from 52 patients with solid tumors were treated.

  Study JGAS000707

• Whole genome sequencing of chondrosarcoma

  Massive parallel sequencing of 10 chondrosarcoma genomes was conducted to identify somatic mutations, structural alterations including fusion genes and mutation signatures that may help to comprehensively characterize the molecular features.

  Study EGAS00001000505

• Whole Exome Sequencing Data of indolent primary renal B-Cell lymphomas

  We used sequenced 34 iNHL samples using whole exome sequencing (WES) data to evaluate possible mutational signatures and driver mutations associated with the patient’s clinical and cytogenetic characteristics.

  Study EGAS50000000774

• Circulating Tumor DNA analysis in Relapsed/Refractory Germ Cell Tumors Treated with Salvage High-Dose Chemotherapy - IGG-04 Study

  Shallow whole genome analysis of circulating tumor DNA detected in the plasma of Relapsed/Refractory germ cell tumors treated with high dose chemotherapy

  Study EGAS50000001510

• Breast cancer risk SNPs converge on estrogen receptor binding sites commonly shared between breast tumors to locally alter estrogen signalling output

  Evaluate the biology underlying inter-tumor cistromic heterogeneity of ER-alpha, in relation to genomic locations and germline variations between breast cancer tumors

  Study EGAS50000000008

• Whole-genome sequencing of primary mediastinal large B-cell lymphoma

  To understand the molecular pathogenesis of Primary mediastinal large B-cell lymphoma (PMBCL), we performed whole-genome sequencing of 10 PMBCLs from 8 patients including 2 relapsed tumors.

  Study EGAS50000000340

• Small RNA sequencing of human oocytes and early embryos

  This study looks at small RNA expression in human oocytes (n=12), zygotes (n=5), and embryos (n=10). The sample preparation and sequencing were done in two batches.

  Study EGAS50000000157

• Variant calling dataset from the whole-exome study of sepsis and acute distress respiratory syndrome in Spain

  Whole-exome sequence reads were obtained from a set of 934 unrelated individuals from the study of sepsis and acute distress respiratory syndrome in Spain (GEN-SEP study), using Illumina paired-end reads.

  Dataset EGAD50000001613

• CHIP panel sequencing of rheumatoid arthritis patients

  Targeted NGS sequencing data (bam and index files aligned to hg38) a total of 573 newly diagnosed, untreated RA patients and 163 healthy controls. The sequencing panel included 65 genes recurrently mutated in myeloid malignancies, to capture clonal hematopoiesis of indeterminate potential (CHIP) mutations. The median target coverage was 1700x across samples.

  Dataset EGAD50000001300

• mUM patient biopsies pre and post treatment with tebentafusp

  The dataset includes 141 RNA-seq samples form mUM patietns. Tumour biopsies were obtained from uveal melanoma patients pre and post treatment with tebentafusp. Biopsies, which were either snap frozen or put in RNA later, were analysed by bulk RNA sequencing (50 million reads per sample) using the Illumina NovaSeq system.

  Dataset EGAD50000001258

• SNP_array

  33 ETMR samples were genotyped using Illumina HumanOmni2.5M array. Hybridization and scanning was done according to the manufacturer's instructions (Illumina). Copy number (Log R) and B allele frequency estimates were obtained sing the Genotyping module (v1.9.4) in GenomeStudio v2011.1 (Illumina). Normalized and log2-transformed copy number measurements were imported from genomestudio and analysed using R package CopyNumber to identify segments with similar copy number.

  Dataset EGAD00010001667

• Whole exome and transcriptome sequencing of biliary tract cancer

  To uncover the full repertoire of genetic and transcriptomic landscape of biliary tract cancer (BTC), we molecularly characterized BTC based on genetic and transcriptomic alteration profiles.

  Study EGAS00001000950

• Testing_the_feasibility_of_genome_scale_sequencing_in_routinely_collected_FFPE_cancer_specimens_versus_matched_fresh_frozen_samples

  Testing the feasibility of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using whole exome and targeted exome capture prior to Illumina sequencing.

  Study EGAS00001000173

• Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing

  We applied multi-region exome sequencing to 10 clear cell renal carcinomas to resolve the genetic architecture, intra tumour heterogeneity and evolutionary histories of these tumours.

  Study EGAS00001000667

• Sequencing_melanoma_germlines

  In this project we performed targeted sequencing of around 50 candidate melanoma genes in the germline of melanoma patients and matched controls. Our aim was to identify variants that contribute to melanoma susceptibility.

  Study EGAS00001002081

• Genome-wide characterization of Arabian Peninsula populations

  The screening of 741,000 variants in 420 individuals from Arabian Peninsula (100 from Saudi Arabia, 100 from Yemen, 100 from Oman and 120 from UAE) and 80 individuals from Iran.

  Study EGAS00001003335

• RNASeq of PAX4 KO vs WT in 7 stages of differentiation from human iPSCs to BLC

  Transcriptomes were profiled along with the differentiation from human induced pluripotent stem cell (iPSC) to beta-like cell (BLC) with PAX4 knocked out or not.

  Study EGAS00001006036

• Single cell RNA sequencing of colorectal cancer patients (CRC-SG1)

  Fresh single-cell suspensions were loaded into the Chromium system (10x Genomics) targeting 5,000 cells per well. Barcoded sequencing libraries were generated using 3’v3 Reagent kit.

  Study EGAS00001006013

• GWAS of SJS/TEN in Thai population

  This study looks at the Phenytoin-Induced SJS/TEN development based on SNP genotyping data of 1965 individuals from Thailand. Their normal DNAs were genotyped on Illumina HumanOmniExpressExome-8 v1.2 array.

  Study EGAS00001008316

• PhIP-Seq LLD

  Bacteriophage Immunoprecipitation Sequencing (PhIP-Seq) of LLD participants. Libraries and protocol were developed in the Weizmann Institute of Science. Two different libraries were used, containing microbial and other immunological peptides respectively.

  Study EGAS00001006999

• Whole genome sequencing of paediatric glioblastoma in the ICGC PedBrain project

  Whole genome sequencing of paediatric glioblastoma in the ICGC PedBrain project

  Dataset EGAD00001002006

• The transcriptome and DNA methylome profiling of the early human post-implantation embryos

  whole genome sequencing data of parent blood samples. Single cell full-length RNA-seq and PBAT-Seq data of in vitro culture D6 to D14 human embryo.

  Dataset EGAD00001005137

• Exome_pituitary_adenoma

  Whole‐exome sequencing was performed using NimbleGen MedExome capture (Roche NimbleGen, Madison, WI, USA) from 1 μg of high quality genomic DNA, followed by sequencing of libraries using paired-end mode (2x 75bp) on a Nextseq 500 platform (Illumina, San Diego, CA, USA), at the Genomics Platform of the Cochin Institute. Reads were aligned on hg19 (GRCh37) using BWA V0.7.17.

  Dataset EGAD00001004997

• Genomic profiling of patient-derived xenograft models of myxoid liposarcoma either sensitive or resistant to trabectedin

  The dataset consists of two patient-derived xenograft model of myxoid liposarcoma one sensitive and one resistant to trabectedin. Both models underwent the same treatment schedule with trabectedin (tree time points and one treatment with doxorubicin). We performed genomic profiling using Agilent OneSeq assay.

  Dataset EGAD00001005099

• LBC1921 VCF

  LBC1921 and LBC1936 GVCFs called with GATK's HaplotypeCaller were combined and subject to variant quality score recalibration. This VCF contains the subset of samples (n = 296) from the LBC1921 cohort.

  Dataset EGAD00001005477

• Whole Exome Sequencing of 5 FFPE prostate samples (normal and tumour pairs) to identify mutations

  Whole Exome Sequencing was performed on radical prostatectomy formalin-fixed paraffin-embedded sample pairs (n = 6). Library prep was done by exon capture using the Illumina Truseq Exome kit and sequenced as 75bp paired end on Illumina NextSeq 500. Sequences were aligned to the human genome (hg38) using BWA.

  Dataset EGAD00001006107

• sWGS of matched patient and PDX ovarian tumour tissues

  This dataset contains 8 .bam files of shallow WGS (~0.1×) from fresh frozen tumour tissues of four matched patients and first generation PDX models. Sequencing reads were aligned to the 1000 Genomes Project GRCh37-derived reference genome using the BWA aligner (v.0.07.17; CRUK-CI alignment pipeline).

  Dataset EGAD00001008650