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• Elucidation of the association of the HPV integration and oropharyngeal cancer

  Whole-genome sequencing was performed using tumor and blood samples from 14 patients with HPV-associated oropharyngeal cancer. Bulk RNA sequencing was performed using tumor samples from 19 patients with HPV-associated oropharyngeal cancer and 17 patients with non-HPV-associated oropharyngeal cancer and normal tonsil samples from 2 healthy controls.

  Study JGAS000751

• mRNA-seq data from ALL patients with NUP214::ABL1 disease

  Dataset contains mRNA-sequencing data (fastq files) from 2 patients with NUP214::ABL1 disease (one T-ALL and one B-ALL patient). Patient samples (peripheral blood or bone marrow) were taken at diagnosis (B-ALL) or relapse (T-ALL). mRNA was extracted from lymphoblasts and underwent paired-end sequencing (75bp) using the Illumina NextSeq platform. Transcriptomic data was used for identification of gene fusions, SNVs and InDels. mRNA-seq data for an additional B-ALL patient with NUP214::ABL1 disease utilised in this study has already been published (EGAS00001006460).

  Dataset EGAD50000001395

• Patients with metastatic urothelial carcinoma

  Samples from three patients with urothelial carcinoma and paired lymph node metastases and distant metastases. Patient 1: Muscle invasive tumor and lymph node metastasis. Patient 2: Muscle invasive tumor, lymph node metastasis, and distant metastasis in the small intestine. Patient 3: T1b tumor, lymph node metastasis, and distant metastasis in the lung

  Study EGAS00001002114

• Whole exome sequencing in familial Multiple Sclerosis

  The purpose of the study is to determine whether variants of genes are associated with greater risk of Multiple Sclerosis (MS). We used whole-exome sequencing in 138 individuals from 23 families including at least 2 members with MS. We compare patients with MS, patients with other autoimmune diseases (AID), and unaffected individuals.

  Study EGAS00001004204

• Whole Exome Sequencing of cohorts of Mutant Braf mouse model melanoma DNA and germline DNA.

  Whole Exome Sequencing of cohorts of Mutant Braf mouse model melanoma DNA and germline DNA. The cohorts are (1) Mutant Braf mouse model melanomas, (2) Mutant Braf mouse model melanomas from UVR exposed mice and (3) Mutant Braf mouse model melanomas from UVR exposed, sunscreen protected mice.

  Study EGAS00001000729

• Tyrol Lifestyle Atlas: Intermittent Fasting Methylation Data

  This study explored methylation, clinical, and other molecular alterations longitudinally over the course of intermittent fasting in healthy women aged 30 to 60. Here, we present methylation data from three matched sample types - buccal, cervical, and blood - longitudinally over the course of six months (baseline, month 2, month 4, and month 6).

  Study EGAS00001007840

• Tyrol Lifestyle Atlas: Smoking Cessation Methylation Data

  This study explored methylation, clinical, and other molecular alterations longitudinally over the course of smoking cessatio in healthy women aged 30 to 60. Here, we present methylation data from three matched sample types - buccal, cervical, and blood - longitudinally over the course of six months (baseline, month 2, month 4, and month 6).

  Study EGAS00001007841

• BLUEPRINT release August 2016, ChIP-Seq for effector memory CD8-positive, alpha-beta T cell, terminally differentiated, on genome GRCh38

  ChIP-Seq data for 2 effector memory CD8-positive, alpha-beta T cell, terminally differentiated sample(s). 6 run(s), 6 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002503

• scRNAseq of ALS patients

  The data set contains information from 9 individuals (5 ALS + 4 controls) using single cell RNA sequencing in combination with TCR V(D)J sequencing to study the immune profile of the central nervous compartment (CSF). Sequencing was done using 10x Genomics platform (5’ scRNAseq & V(D)J Reagent Kits v1.1). 5P and TCR libraries were then pooled and for sequencing on the NovaSeq sequencer. Provided files are in .fastq.gz format and per individual four files are available (Read 1&2 and Lane 1&2).

  Dataset EGAD00001009623

• WGS data of fetal stem cells (15x) and culture-associated mutations of iPSCs and ISC

  This data set includes WGS data of the in vivo acquired mutations in fetal ISCs and HSPCs of 4 foetuses ( T21=2, D21= 2). In addition, this data set includes sub-clonal fetal ISCs to determine the culture-associated mutations of fetal ISCs. Also, it concludes clone +subclone WGS data of iPSCs derived of the fetal ISCs

  Dataset EGAD00001008475