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• Transcriptomic data from a SARS-CoV-2 human challenge study (Kelly Research Group, Arkansas Children’s Research Institute)

  This dataset contains paired-end RNA-Seq data generated from mid-turbinate nasal and throat samples collected as part of a first-in-human SARS-CoV-2 experimental challenge study conducted in the United Kingdom in 2021. Total RNA was extracted using QIAamp Viral RNA kits (Qiagen), and libraries were prepared using TruSeq RNA Exome kits (Illumina). Sequencing was performed on a NovaSeq X Plus instrument configured for 100 bp paired-end reads. The dataset includes raw FASTQ files and associated de-identified metadata.

  Dataset EGAD50000002078

• Bulk TCRseq data from 149 patients with bladder cancer

  For this dataset we performed bulk TCRseq on tumor and serial blood samples from patients with muscle invasive bladder cancer (n patients = 119, n blood = 209, n tumor = 28) or non-muscle invasive bladder cancer (n patients = 30, n blood = 56, n tumor = 19) for a total of 149 patients and 312 samples. Each sample consists of a paired fastq file. Sequenced on the Ilumina NovaSeq6000 platform using SP and S1 flow cells (v1.5, 2x101 cycles), with a mean yield of 42 million reads covering the CDR3β region.

  Dataset EGAD50000001382

• Single-cell RNA-Seq analysis of thymic ILC1 progenitors and NK cell differentiation This analysis involved a multiplexed sequencing run to study thymic innate lymphoid cells (ILCs) and NK progenitors. The generated data requires a demultiplexing file to separate and identify the individual sample tags for downstream analysis.

  This dataset contains multiplexed single-cell RNA sequencing (scRNA-seq) data from human thymic tissue, focusing on ILC1 progenitors and NK cell differentiation. The data were generated using the BD Rhapsody system and sequenced on the Illumina NovaSeq S4 platform. A demultiplexing file is required to assign sample identities.

  Dataset EGAD50000001157

• BELLINI clinical trial single-cell RNA-Seq and TCR data: cohorts A & B

  Single-cell RNA-Seq data and TCR sequencing data (both by 10X Genomics) of 51 TNBC primary tumors obtained from 29 unique patients from BELLINI clinical trial. The data includes pre- and post-treatment samples. Patients in cohort A (16 patients, 28 samples) received nivolumab for 4 weeks, patients in cohort B (13 patients, 23 samples) received nivolumab + ipilimumab for 4 weeks. The included sequencing data was generated from frozen material for cohort A and from fresh material for cohort B.

  Dataset EGAD50000000807

• Osteosarcoma WGS on multiple tissue samples from six patients

  Osteosarcoma is a primary bone tumor that exhibits a complex genome characterized by gross chromosomal abnormalities. Osteosarcoma patients often develop metastatic disease, resulting in limited therapeutic options and poor survival rates. To gain knowledge on the mechanisms underlying osteosarcoma heterogeneity and metastatic process, it is important to obtain a detailed profile of the genomic alterations that accompany osteosarcoma progression. Therefore, in this study we performed WGS on multiple tissue samples from six patients with osteosarcoma, including the treatment naïve biopsy of the primary tumor, resection of the primary tumor after neoadjuvant chemotherapy, local recurrence and distant metastases.

  Dataset EGAD50000000475

• WES data from 438 tumor/germline samples with non muscle invasive bladder cancer

  A better understanding of the molecular landscape of non-muscle-invasive bladder cancer (NMIBC) is essential to improve risk assessment and identify potential therapeutic targets. Here, we perform a comprehensive genomic analysis of patients diagnosed with NMIBC based on whole-exome- (n=438), shallow whole-genome- (n=362), and total RNA-sequencing (n=414). This dataset contains 876 BAM files corresponding to the full WES dataset. Tumor and matched germline DNA were sequenced to a mean coverage of 132x (35x-338x) and 128x (31x-302x), respectively.

  Dataset EGAD50000000730

• Single cell chromatin accessibility profiles from myelofibrosis patients

  To explore how JAK2V617F disrupts cell-fate and the regulatory chromatin landscape of HSCs, we applied GoT-ChA to CD34+ sorted progenitor cells from 21 human primary samples, comprising 18 patients with JAK2V617F-mutated MF (no additional mutations, except for Pt-08), who either had no treatment (n = 12; including three longitudinal samples from a PV patient who progressed to MF) or who were treated with ruxolitinib (n = 6), a JAK1/2 inhibitor. We included a JAK2V617F CH sample (Pt-19) to explore early epigenetic changes, before the onset of overt hematological abnormality.

  Dataset EGAD50000000234

• Amplicon-based sequencing of drug resistant lung cancer cell lines (2017-07-05)

  A EGFR mutant NSCLC cell line which is sensitive to AZD9291 inhibition was mutagenised with the chemical mutagen ENU and then drug selected using a AZD9291. Single cell derived colonies were then manually picked and expanded in drug. Resistance was confirmed in a 14 day assay and DNA was collected. These then underwent targeted amplicon-based sequencing to confirm candidate resistance effectors hypothesised from currently available literature. This dataset contains all the data available for this study on 2017-07-05.

  Dataset EGAD00001003425

• VCF file from 16 carriers of the BMPR2 p.Arg491Gln mutation in a family affected by HPAH

  VCF file from 16 carriers of the BMPR2 p.Arg491Gln mutation in a family affected by hereditary pulmonary arterial hypertension (HPAH). Whole genome sequencing of these samples was performed in an Illumina HiSeq 4000 instrument. Libraries were prepared using the Fisher PE Kit (Kapa Biosystems). BAM files were processed at the CNAG (Barcelona) with their pipeline, including GATK v3.6 for genotyping and other tools such as snpEff for annotating variants, to produce this VCF file with a total of 9,643,070 variants, out of which 7,891,370 are SNVs.

  Dataset EGAD00001005758

• RNA sequencing data for Molecular Characterization of ETMRs

  The dataset contains two samples from one patient. As a representative FFPE tissue sample, ET174 was histologically iden- tified, targeted and microdissected with a puncher for nucleic acid extraction. RNA was extracted using the automated Maxwell system with the Maxwell 16 LEV RNA FFPE Kit (Promega), according to the manufacturer’s instructions. To evaluate FFPE RNA quality, we used the percentage of RNA fragments >200 nt fragment determination value (DV200). Only RNA samples with DV200 > 70% were included for sequencing on a NextSeq 500 (Illumina). Eight lanes have been sequenced resulting in 16 Fastq files (paired end).

  Dataset EGAD00001006209

• RNA of peripheral blood for pancreatic cancer and chronic pancreatitis

  Samples of nucleated cells found in peripheral blood from over 300 patients suffering from resectable pancreatic ductal adenocarcinoma, non-resectable pancreatic cancer, chronic pancreatitis, or none of these. Please cite this article when using data: Al-Fatlawi, A.; Malekian, N.; García, S.; Henschel, A.; Kim, I.; Dahl, A.; Jahnke, B.; Bailey, P.; Bolz, S.N.; Poetsch, A.R.; Mahler, S.; Grützmann, R.; Pilarsky, C.; Schroeder, M. Deep Learning Improves Pancreatic Cancer Diagnosis Using RNA-Based Variants. Cancers 2021, 13, 2654. https://doi.org/10.3390/cancers13112654

  Dataset EGAD00001006915

• Whole genome sequencing

  This dataset contains whole genome sequencing data from 22 samples of FACS-purified bone marrow CD34+ haematopoietic stem and progenitor cells and matched hair follicle controls collected from individuals undergoing hip replacement surgery. Additionally, it contains whole genome sequencing data from unseparated bone marrow mononuclear cells, CD3-CD34- bone marrow mononuclear cells, and peripheral blood granulocytes of the same 14 samples. Haematopoietic samples were sequenced to a target coverage of 90-120x; 19 of them were re-sequenced to a total target coverage of 270x. Hair follicle controls were sequenced to a target coverage of 30x.

  Dataset EGAD00001015178

• BipEx_Timpson_Bristol

  "BipEx_EGAS00001006274_Timpson_Bristol Controls Exomes. This research project was a collaboration between University of Bristol, UK and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 2,981 Control samples from collaborators in UK. Genomic DNA from each sample was sequenced to a mean depth of 20x."

  Dac EGAC50000000144

• Dac for "Development of a fully human glioblastoma-in-brain-spheroid model for accelerated translational research"

  This is the DAC for "Development of a fully human glioblastoma-in-brain-spheroid model for accelerated translational research" of Philipp Koch (philipp.koch@zi-mannheim.de), Frank Winkler (Frank.Winkler@med.uni-heidelberg.de), Moritz Mall( m.mall@dkfz-heidelberg.de)

  Dac EGAC50000000480

• Boyes Lab - DAC policy

  Access to this data is controlled. Upon request from a third party for access to the data, a separate Data Sharing Agreement would be put in place between the University of Leeds and the third party prior to EGA granting access to the data to the third party.

  Dac EGAC50000000283

• Massively Multiplex Single-Cell Hi-C of HeLa Cells

  In this study, we developed a massively multiplexed, single-cell Hi-C protocol to study the chromosomal architecture of single HeLa cells.

  Study phs001269

• NGS-based targeted exome sequencing of osteosarcoma

  The present study aimed to identify potential genomic markers for the prediction of chemosensitivity in patients with OS using a genomic approach.

  Study JGAS000282

• Semibulk RNA-seq analysis as a convenient method for measuring gene expression statuses in a local cellular environment

  For two cases of breast cancers, semibulk RNA-seq and single cell RNA-seq were performed.

  Study JGAS000387

• Plasma cell‐free transcriptome profiling in chronic liver disease

  RNAseq data from plasma samples corresponding to a Grand Challenge Programme project to find biomarkers for liver disease, including NAFLD, NASH, Cirrhosis and Hepatocelullarcarcinoma. A template of the DTA and DAA files is available in the following zenodo repository https://doi.org/10.5281/zenodo.19047046.

  Dac EGAC50000000360

• Tumor reactive γδ T cells contribute to a complete response to PD-1 blockade in a Merkel cell carcinoma patient

  Single cell RNA and TCR sequencing of γδ T cells FACS sorted from peripheral blood of two Merkel cell carcinoma patients

  Dataset EGAD50000000137

• Fungal infection in neural tissue from Amyotrophic Lateral Sclerosis

  The study shows that fungus infection, isolated from neural tissue, can be a risk factor to develop Amyothophic lateral sclerosis (ALS).

  Study EGAS00001002473

• WTCCC2 Bacteraemia Susceptibility (BS) samples

  A WTCCC2 project genome-wide association study for bacteraemia susceptibility in 4924 individuals from Kenya, genotyped on the Affymetrix 6.0 array.

  Study EGAS00001001756

• Whole-exome sequencing of Fanconi anemia

  We performed whole-exome sequencing of two Fanconi anemia patients without mutation of known FA genes, and identified a novel FA gene FANCT.

  Study EGAS00001001103

• Landscape and significance of multiple mutations in oncogenes.

  This study is a comprehensive pan-cancer study of oncogenic multiple mutations (MMs) which includes long-read whole-genome sequencing data (n = 3).

  Study EGAS00001003763

• A Hematogenous Route for Medulloblastoma Leptomeningeal Metastases

  A Hematogenous Route for Medulloblastoma Leptomeningeal Metastases

  Dataset EGAD00001003907