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• WGS data for genomic determinants of response and resistance to inotuzumab in B-ALL

  Whole genome sequencing data for 45 samples with B-cell acute lymphoblastic leukemia

  Dataset EGAD50000000096

• EBNA2 ChIP-Re-ChIP in primary B-cells infected with EBV virus

  EBNA2 ChIP-Re-ChIP in primary bulk B cells 4 days post EBV-infection with B95-8. DNA binding elements of the viral master regulator EBNA2, EBNA2-CBF transcription factor complex or EBNA2-EBF1 transcription factor complex were analyzed to identify virally targeted genes.

  Dataset EGAD50000000301

• scRNA-seq of bronchoalveolar lavage (BAL) samples from patients with severe COVID-19 to assess dexamethasone response in the lungs

  Single-cell RNA-sequencing of bronchoalveolar lavage (BAL) samples from patients with severe COVID-19 with or without Dexamethasone treatment and for responders and non-responders was performed using 10x Genomics technology.

  Dataset EGAD50000000292

• ImmuNEO CD8 cell lines

  Paired RNA-Seq data from 16 samples of different tumors CD8+ T cells added to the study "Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification (H021)". Sequencing was performed on Illumina NextSeq 500. The sequencing was always paired

  Dataset EGAD50000000193

• Clones derived from early passage tumoroids of colorectal cancer

  We obtained different clones from early passage CRC tumoroids to study mutational signatures specific for truncal or private somatic alterations. These whole genome sequences are part of a larger study on the heterogeneity and evolution of DNA mutation rates in microsatellite-stable colorectal cancer.

  Dataset EGAD50000000152

• H3K27ac HiChIP Dataset for 19 T-ALL patients and one normal control sample

  19 H3K27ac HICHIP from T-ALL patient samples and one healthy normal control sample. Reads were aligned to HG38 reference.

  Dataset EGAD50000000023

• UK_ReplicationChip

  This dataset includes data from UK Multiple Sclerosis (MS) cases that were recruited through the University of Cambridge and included in the IMSGC Replicationchip experiment. Data from UK controls and additional UK cases that were recruited through other UK centres is available by direct application to those respective centres, as described in the original paper.

  Dataset EGAD00010002118

• A novel orthotopic patient-derived xenograft model of radiation-induced glioma following medulloblastoma

  DNA methylation arrays were performed to molecularly subtype these samples based on Capper D, Jones DTW, Sill M, et al. DNA methylation-based classification of central nervous system tumours. Nature. 2018;555(7697):469-474. doi:10.1038/nature26000

  Dataset EGAD00010002017

• UK_exomechip

  This dataset includes data from UK Multiple Sclerosis (MS) cases that were recruited through the University of Cambridge and included in the IMSGC exomechip experiment. Data from UK controls and additional UK cases that were recruited through other UK centres is available by direct application to those respective centres, as described in the original paper

  Dataset EGAD00010002019

• LITS

  Difference in gene expression values between case and control, log2 values. Blood transcriptome from women participating in the Norwegian Women and Cancer study (NOWAC) Post-genome Cohort taken up to eight years before brest cancer diagnosis. Illumina HumanWG-6 version 3 or Illumina HumanHT-12 expression bead chip, combined on identical nucleotide universal identifiers.

  Dataset EGAD00010001400

• Somatic Genetics of lesions from a POT1 patient (2017-04-27)

  In this project we will use exome sequencing to identify somatic mutations in lesions from a patient with a germline mutation in the protection of telomeres 1 gene (POT1). This dataset contains all the data available for this study on 2017-04-27.

  Dataset EGAD00001003307

• GenomeDenmark Phase 2 - variants called on chrY for 62 males.

  Variants on the Y chromosome for 62 danish males in VCF format from the GenomeDenmark Phase 2 cohort. Variants were called using reference based approaches such as the haplotype-caller module from GATK and using alignment of denovo assemblies to the reference using ASMvar.

  Dataset EGAD00001003186

• ICR_RNASeq_pHGG

  RNA sequencing of paediatric high grade gliomas and diffuse intrinsic pontine gliomas. RNA was sequenced from fresh frozen surgical material or from primary cells cultured under stem cell conditions. RNA was subjected to Illumina whole transcriptome paired end sequencing. Data is provided as paired-end FASTQ files

  Dataset EGAD00001004116

• Exome sequencing files for "A single mutant clone populates the pancreatic ductal system to generate coexisting neoplastic lesions"

  Files from whole exome sequencing of eight tumors from eight pancreatic cancer patients along with matched PanIN precursor lesion(s) and a matched normal tissue.

  Dataset EGAD00001004044

• Verification of BCR reconstruction from single-cell RNA-seq using BraCeR

  This dataset was made to verify the computational reconstruction of B cell reseptors from single-cell RNA-seq using BraCeR. The dataset contains BCR-derived reads from single-cell RNA-seq from 13 cells using the Smart-seq2 protocol, as well as targeted BCR-sequencing data from the same cells.

  Dataset EGAD00001004199

• Exome sequencing in patients with Oliver McFarlane Syndrome

  In this work, using exome sequencing, we identified biallelic PNLPA6 mutations in patients with childhood blindness due to severe photoreceptor death and clinical features of Leber congenital amaurosis (LCA) and, interestingly, also of the rare Oliver McFarlane Syndrome

  Dataset EGAD00001001042

• TRACERx esophageal adenocarcinoma multi-region NGS

  This dataset contains whole exome data from 8 esophageal adenocarcinoma tumors, that has been subjected to multiregion sequencing, ranging from 3-8 regions per tumor. In total, 40 tumor samples and 8 normal blood samples have been sequenced on Illumina HiSeq 2500 at a median dept of 90x.

  Dataset EGAD00001001364

• Whole-exome sequencing of additional thyroid disease cases (2015-08-05)

  Whole-exome sequencing of a cohort of families (probands and affected/unaffected relatives) suffering from one of two rare thyroid disorders: congenital hypothyroidism (CH) and resistance to thyroid hormone (RTH). This dataset contains all the data available for this study on 2015-08-05.

  Dataset EGAD00001001460

• BASIS BC WGS Dataset

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

  Dataset EGAD00001001337

• Papuan Genomes: high depth (30x) whole genome sequence data

  This dataset includes the whole genomes, sequenced to high depth (30x) of 25 individuals from Papua New Guinea. The individuals were chosen from several geographically distinct Papuan groups, focusing on the highland regions: Bundi, Kundiawa, Mendi, Marawaka and Tari.

  Dataset EGAD00001001634

• Somatic Genetics of lesions from a POT1 patient (2016-04-20)

  In this project we will use exome sequencing to identify somatic mutations in lesions from a patient with a germline mutation in the protection of telomeres 1 gene (POT1). This dataset contains all the data available for this study on 2016-04-20.

  Dataset EGAD00001002050

• Transcriptome profiling for Korean Early Onset Gastric Cancer

  To identify transcriptome profile in this unique subset of gastric cancers, RNA-seq analyses were performed using frozen cancer tissue. Adjacent normal tissue of the same patients were used in differently expressed gene selection and fusion gene prediction.

  Dataset EGAD00001002187

• Single-cell Transcriptome for glioblastoma intra-tumoral heterogeneity

  Single-Cell RNA Sequencing of 355 cells isolated from 7 tissue fragments of 3 patients corresponding to locally adjacent tumor, multifocal with recurrence and sections segregated by a marker of tumor cellularity (5-ALA).

  Dataset EGAD00001002249

• Whole genome sequencing of matched esophageal tumor-normal samples

  The dataset includes whole genome sequencing (WGS) data on ten matched esophageal tumor-normal pairs. WGS was performed by the cancer sequencing service of CG with an average read coverage of approximately 50-fold. Illumina HiSeq2000 instrument was used to perform the sequencing.

  Dataset EGAD00001004832

• Immunoglobulin sequences of self-reactive plasma cells in celiac disease

  Paired immunoglobulin heavy and light chain sequences were obtained from 803 single IgA plasma cells isolated from duodenal biopsies of five celiac disease patients. The cells were specific to discrete antigenic regions of the enzyme TG2, which is the main autoantigen in celiac disease.

  Dataset EGAD00001005029