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• A95628B

  Whole genome sequencing for single cells for library A95628B 1335 samples; filetype=bam

  Dataset EGAD00001008221

• A95632D

  Whole genome sequencing for single cells for library A95632D 644 samples; filetype=bam

  Dataset EGAD00001008222

• WGS files for Genomic Landscape ALL paper

  WGS files for Genomic Landscape ALL paper titled "The genomic landscape of pediatric acute lymphoblastic leukemia"

  Dataset EGAD00001008600

• Single-cell and spatial transcriptomic profiling of hormone-naïve localised prostate cancer

  Localised prostate cancers (PCa) are heterogeneous and multifocal, with diverse outcomes. Current prognostic methods are epithelium-centric, overlooking the complex cellular landscape within the tumour microenvironment (TME), which remains incompletely characterised. We performed a comprehensive analysis of cancerous and adjacent-benign cores from 24 patients with hormone therapy-naïve localised PCa using single-cell RNA-sequencing. By integrating copy number variation and transcriptional signatures, we classified epithelial cells across a malignant spectrum, revealing widespread molecular perturbation. We found an expansion of Club cell phenotypes, suggestive of Luminal dedifferentiation. We also performed a detailed annotation of stromal phenotypes, focusing on fibroblasts, and identified a novel peri-neural fibroblast population. Spatial transcriptomics elucidated the precise anatomical distribution of CAFs within the PCa TME. This study provides a valuable foundation for advancing our understanding of PCa pathobiology and developing a comprehensive cellular model of the disease.

  Study EGAS00001008332

• Dissecting Autoimmune Cellular and Molecular Networks in Vitiligo

  This study consists of suction blister biopsies of primary human skin samples, collected from healthy patients, or patients with vitiligo. Healthy patients had healthy skin sampled. Vitiligo patients had both unaffected (non-lesional) and affected (lesional) skin sampled. The generated data consists of scRNA-seq samples generated following the inDrops method (Klein et al., 2015; PMID: 26000487).

  Study phs002455

• Gene expression in brain (Schizophrenia) study

  The study included post-mortem brain tissue samples from 68 schizophrenia patients and 44 age and sex matched control subjects. Whole transcriptome poly-A selected paired-end RNA sequencing was performed on tissue from prefrontal cortex and orbitofrontal cortex. RNA expression differences were detected between case and control individuals, focusing both on single genes and pathways.

  Study EGAS00001004199

• Profiling of H3K27ac landscape in immune cells from rheumatoid arthritis patients and healthy controls

  We collected peripheral blood mononuclear cells (PBMC) from 6 RA patients and 4 healthy controls, as well as synovial fluid from the same RA patients. We then sorted B cells, CD4+ and CD8+ T cells, regulatory T cells and monocytes using flow cytometry and profiled regions marked with H3K27ac using CUT&Tag.

  Study EGAS00001005085

• Single-cell analysis of the multicellular ecosystem in viral carcinogenesis by HTLV-1

  Single-cell RNA sequencing (scRNA-seq), antibody-derived tag sequencing (scADT-seq) and T/B-cell receptor (TCR/BCR) sequencing (scTCR/BCR-seq) on peripheral blood mononuclear cells (PBMCs) obtained from 30 ATL patients (34 samples including 4 sequential ones), 11 HTLV-1-infected asymptomatic carriers, and 4 healthy donors.

  Study EGAS00001004936

• Molecular heterogeneity and commonalities in pancreatic cancer precursors with gastric and intestinal phenotype

  Due to the limited number of modifiable risk factors, secondary prevention strategies based on early diagnosis represent the preferred route to improve the prognosis of pancreatic ductal adenocarcinoma (PDAC). Here, we provide a comparative morphogenetic analysis of PDAC precursors aiming at dissecting the process of carcinogenesis and tackling the heterogeneity of preinvasive lesions.

  Study EGAS00001006793

• Single-cell atlas of > 1.5 million PBMC with multi-layer omics data in Japanese

  Osaka Atlas of Immune Cells (OASIS) is multi-omics immune cell atlas from 235 Japanese including COVID-19 patients and healthy subjects. The 5’ single-cell transcriptomics data profiled over 1,500,000 peripheral blood mononuclear cells (PBMCs). OASIS links these single-cell transcriptomics data with host genetics, plasma proteomics, and metagenomics data.

  Study EGAS00001008016

• EM-seq data from plasma cfDNA samples of ALS patients, control and C9-carriers

  This dataset contains targeted EM-seq data from 61 plasma cfDNA samples spanning 20 sporadic ALS, 10 C9orf72-ALS, 10 asymptomatic C9orf72 expansion carriers, and 21 non-disease controls. Libraries were prepared with the NEBNext Enzymatic Methyl-seq (EM-seq) kit, captured using the Twist Human Methylome Panel (3.98 M CpGs; 123 Mb), and sequenced on Illumina NovaSeq 6000 (150 bp paired-end; ~45× on-target depth) with unmethylated lambda DNA spike-in and a 20% PhiX balance library. The dataset includes per-sample gzipped FASTQ files (R1/R2) and minimal metadata.

  Dataset EGAD50000001808

• Summarized somatic variant calls from CMMRD-associated high-grade gliomas

  This dataset contains summarized somatic variant call data derived from paired tumor–blood whole-exome sequencing of human samples. Access to the dataset is controlled and granted only upon submission and approval of a formal data access request. Requests are reviewed by the Data Access Committee led by the Principal Investigator to ensure compliance with applicable legal, ethical, and data protection requirements. Users must not attempt to re-identify study participants and must comply with all relevant confidentiality and data protection regulations. In accordance with local legal and ethical requirements, individual-level raw sequencing data are not shared.

  Dataset EGAD50000002180

• mt-scATAC-seq data and analysis

  Data and analysis of mt-scATAC-seq assay of Lin- CD34+ sorted live cells from bone marrow tissue of 4 patients with AML (before treatment with decitabine). Data files are paired-end reads in FASTQ format from the NextSeq 2000 sequencer. Analysis files are outputs from Cellranger ATAC: .h5 peak matrix file, atac_fragments.tsv.gz file and its index.

  Dataset EGAD50000001375

• Longitudinal Transcriptomic Profiling of Endothelial Progenitor Cells in Post-COVID-19 Patients: Insights at 3 and 6-Months Post-SARS-CoV-2 Infection

  Raw transcriptomic data from endothelial cells of post-COVID patients and healthy controls. Samples were collected from post-COVID patients at 3 months (n = 6) and 6 months (n = 6) post-infection, as well as from healthy control individuals (n = 5). All post-COVID patients were hospitalized during the first wave of the pandemic. Among them, half developed pulmonary embolism (TEP; n = 6), while the other half did not (no TEP; n = 6).

  Dataset EGAD50000001452

• MIBC NAC2020 cohort RNA sequencing

  The dataset contains RNA sequencing data from N=48 transurethral resections of bladder tumours (TURBTs) from N=48 patients with muscle-invasive bladder cancer who were treated with neoadjuvant chemotherapy followed by radical cystectomy. All TURBTs originate from formalin-fixed paraffin embedded tissue. We used the Illumina TruSeq RNA exome kit, previously known as the TruSeq RNA Access Library Prep Kit. This kit converts total RNA into template molecules of known strand origin, followed by sequence-specific capture of coding RNA. All samples were run in an Illumina NovaSeq6000 instrument. Paired FASTQ files from all 48 patients are provided.

  Dataset EGAD50000001025

• Single cell whole genome sequencing of luminal breast epithelial cells from wildtype and BRCA mutation carriers

  Single cell whole genome sequencing was done using DLP+ (https://doi.org/10.1016/j.cell.2019.10.026) on luminal breast epithelial cells from wildtype and BRCA mutation carriers. Each BAM file is a merged BAM from single cells from a single sample, and the cells can be uniquely identified by their @RG group. Only high quality cells were kept, thus there are large differences in BAM sizes. The same sample/patient can be found across multiple BAM files to accumulate more cells, sometimes the same patient will have multiple FACS sorted cell types also split by BAMs.

  Dataset EGAD50000000883

• Single Cell Sequencing of Medulloblastoma Samples

  This dataset contains the results of sequencing 9 samples (7 human/PDX, 2 cell lines) of medulloblastoma tumours (or 2 Neural Stem Cell lines). The data was collected to characterize the intratumour heterogeneity of chromothripsis in this tumour type. The 7 tumour samples underwent single cell DNA and RNA sequencing using the 10x CNVkit and 10xRNA protocols, and 1 of the tumour samples as well as the Neural Stem Cell lines underwent StrandSeq sequencing. All experiments were sequenced on Illumina sequencers. The provided files are paired-end fastq files from the sequencing experiments.

  Dataset EGAD50000000909

• Long-read whole-genome sequencing-based concurrent haplotype phasing and aneuploidy profiling of single cells

  This dataset contains long-read whole-genome sequencing (lrWGS) data from 14 samples. Five lrWGS data are from single-cell (sc, sc_2, sc_3), multi-cell (mc, 10 cells), and bulk samples of HG002. The remaining nine lrWGS data are from two preimplantation genetic testing (PGT) families, including four from blood bulk DNA of the parental pairs and five from trophectoderm biopsies of two embryos from one family and three embryos from another family. The data are provided in raw FASTQ format and were generated using the PromethION device from Oxford Nanopore Technologies.

  Dataset EGAD50000000787

• RNA sequecing of primary B cells infected with Epstein-Barr virus (EBV) or stimulated with heat-inactivated EBV

  Naïve (CD27-IgD+) B cells were isolated from buffy coat preparations of healthy donors using CD19 magnetic beads, followed by reals of CD19 beads and incubation with IgD-biotin and anti-biotin magnetic beads. B cells were infected with EBV by spinoculation or stimulated with heat-inactivated EBV and control cells were left uninfected. RNA was extracted immediately after isolation in un-infected B cells. From EBV-infected B cells and B cells stimulated with heat-inactivated virus, RNA was extracted 24 and 96 hours after infection / stimulation.

  Dataset EGAD50000000305

• Poland WES - The Genomic Map of Poland in Open Access

  This project used NGS (next generation sequencing), using Illumina NOVASEQ 6000 and Illumina DRAGEN aligner. The dataset includes BAM and BAM.BAI files from Whole Exome Sequencing of 450 samples (227 female, 223 male, Poland from POPULOUS collection). Library Construction Protocol: Illumina DNA Prep with Enrichment. Reference Genome: GRCh37.

  Dataset EGAD50000000130

• Single-cell RNA-seq of immune cells from human tumor fragments after 48 hour culture ex vivo (Kaptein et al., 2024)

  Single-cell RNA-seq profiling of immune cells from human ovarian carcinoma, renal carcinoma and melanoma samples after 48h of ex vivo culture using the patient-derived tumor fragment platform (5 samples total). Samples were cultured in various conditions, including: untreated, CD8-IL2v-treated, CD8-IL2v + LCKi -treated, aPD1-treated, CD8-IL2v + aPD1 -treated, Untargeted IL2-treated, aCD3-treated and aCD3 + CD8-IL2-treated . FASTQ files contain gene expression data, feature barcode antibody capture or TCR data on immune cells from all conditions combined per patient.

  Dataset EGAD50000000377

• Shallow sequencing data of samples included in the MAX-trial

  Dataset EGAD00001008280

• V2 panel bait design test

  This study comprises of three different datasets. 1) 57 samples from the 1243 canapps cell line study,2) 91 FFPE normal samples and 3) 87 samples from the SCORT WS2 dataset. The aim is to sequence these 235 samples in order to test the new V2 Colorectal bait design.

  Dataset EGAD00001003242

• Precursor lesions, clonal architecture and relapse in Wilms nephroblastoma

  Targeted resequencing at high depth (21 genes, 9 chromosomal regions): at least 4 FFPE samples per case and matched germline DNA: * 100 cases with detailed outcome data, including 15 cases with tumour relapse (515 samples) * 40 cases with matched pre-chemotherapy biopsies (240 samples) * 50 nephrogenic rests matched to above cases (50 samples) We expect a proportion (possibly 10%) of cases to be mutationally silent on the above studies, and propose to subsequently carry out integrated whole-genome, methylome and transcriptome studies on matched frozen tissue from these cases

  Dataset EGAD00001003217

• Whole-exome sequencing of 20 samples of actinic keratosis (10s) and cutaneous squamous cell carcinoma (10s)

  Whole-exome sequencing of 20 samples of actinic keratosis (10) and cutaneous squamous cell carcinoma (10) was performed to investigate a potential relationship between DNA methylation-based subtypes and genetic mutation patterns. 7 samples were shown to belong to the stem cell-like subclass (4 AK and 2 SCC), 12 - to the keratinocyte-like subtype (6 AK and 6 SCC) and one SCC sample is unclassified (was not included in the methylation analysis). Exome regions were captured using Agilent Low Input Exome-Seq Human v5 kit and sequenced on Illumina Hiseq4000 with paired-end 100-nucleotide reads.

  Dataset EGAD00001003765

• RNA-seq of iPSC-derived hepatocyte-like cells

  We performed RNA-seq on polyA-enriched mRNA isolated from the original liver biopsy tissue (Liver tissue), primary liver cells (PLC), hepatocyte-like cells (HLCs) differentiated from induced pluripotent stem cells (iPSCs), and iPSCs. RNA libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Preparation protocol (ref. RS-122-2101, Illumina, San Diego CA, US) and sequenced using the Illumina HiSeq2500 platform following the manufacturer’s protocol. Samples were sequenced in paired-end mode to a length of 2x76 base pairs. Images from the instrument were processed using the manufacturer’s software to generate FASTQ sequence files.

  Dataset EGAD00001003770

• Transposome Bisulfite Sequencing

  DNA belonging to 16 tumour/normal samples were treated with bisulfite, then up to 5 different bisulfite PCRs were performed in each one of the samples. Amplicons form the same sample were pooled and submitted to sequencing on a MiSeq platform.

  Dataset EGAD00001001028

• Human primary melanoma project

  Mutational burden and profiles to be studied in approx. 500 human primary melanomas with matched normal samples, part of the Leeds melanoma cohort. New custom design targeted capture panel covering melanoma-specific copy number alterations, promoter mutations, gene fusions, coding genes, HLA regions and IFNg/JAK/STAT pathway genes.

  Dataset EGAD00001008360

• Orthotopic murine Group 3 medulloblastoma in C57Bl/6 mice treated with saline, cyclophosphamide or gemcitabine

  Mice with medulloblastoma (Group 3) were treated with saline, cyclophosphamide, or gemcitabine as described by Abbas et al (2020). Total RNA was isolated with RNeasy Plus Mini Kit (Qiagen), library preparation (SureSelect, Agilent), rRNA depletion (Ribo-Zero Plus, Illumina) and sequencing were carried out by GenomicsWA or Australian Genome Research Facility. Libraries were sequenced on NovaSeq 6000 S1 flow cells as paired-end 150bp reads (Illumina).

  Dataset EGAD00001008511

• Transcriptome profiling of three giant cell tumour of bone (GCTB) cell lines

  This dataset contains RNA-seq data of giant cell tumour of bone (GCTB) cell lines (n=3). Cell lines consist of neoplastic "stromal" cells harboring a heterozygous H3F3A p.G34W mutation. RNA-seq was performed on the BGISEQ-500 platform (PE100) and uploaded data contains fastq files, vcf files, and gene expression values (TPM). Cell lines, data generation, and data analysis are described in the following publication: Venneker et al., Histone deacetylase inhibitors as a therapeutic strategy to eliminate neoplastic “stromal” cells from giant cell tumors of bone, 2022.

  Dataset EGAD00001009074

• IL1R1+ cancer-associated fibroblasts drive tumor development and immunosuppression in colorectal cancer

  180502: RNA-Sequencing data of cocultured matched CRC patient (P4) derived normal fibroblasts (NFs), cancer associated fibroblasts (CAFs) and tumor spheroids. 200503_coculture: RNA-Sequencing data of cocultured CRC patient derived normal fibroblasts (NFs) or cancer associated fibroblasts (CAFs) (P16, P19, P22, P32, P41, P42) and tumor spheroids (HT29). 200503_il1b: RNA-Sequencing data of IL-1β stimulated fibroblasts (NFs and CAFs) Cole: scRNA-sequencing of matched CRC tumour samples and normal tissue counterparts derived from 3 patients. 220501: RNA-Sequencing of FACS sorted IL1R1 high and IL1R1 low CT5.3 CAFs

  Dataset EGAD00001010322

• Paired RNA-Seq of 32 samples of chemo-naïve and post-chemotherapy PDAC tumors

  Paired RNA-Seq of 32 samples of chemo-naïve and post-chemotherapy PDAC tumors (HIPO_015) to define the molecular and cellular impact of neoadjuvant chemotherapy. Transcriptome analysis combined with high resolution mapping of whole tissue sections identified GATA6 (Classical), KRT17 (Basal-like) and Cytochrome P450 3A (CYP3A) co-expressing cells that were preferentially enriched in post-CTX resected samples. The sequencing was done on HiSeq2000/HiSeq2500 using the Takara_SMARTer_Ultra_Low_Input_RNA_and_NEBNext_ChIP-Seq Kit.

  Dataset EGAD00001010884

• Blood plasma and FFPE derived total RNA seq dataset from DLBCL and PMBCL patients

  Blood plasma samples (n=168) and matched diagnostic formalin-fixed paraffin-embedded (FFPE) tissue samples (n=69) of DLBCL patients, PMBCL patients and healthy controls were collected between 2016-2021. Plasma samples were collected at diagnosis, at interim evaluation, after treatment, and in case of refractory or relapsed disease. RNA was extracted from 200 µl plasma using the miRNeasy serum/plasma kit and from FFPE tissue using the miRNeasy FFPE kit. RNA was subsequently sequenced on a NovaSeq 6000 instrument using the SMARTer Stranded Total RNA-seq pico v3 library preparation kit.

  Dataset EGAD00001011679

• Epigenetic Moderators of Naltrexone Efficacy for Alcohol Use Disorder

  This study was a 16-week randomized controlled trial of oral naltrexone (50 mg daily) vs. placebo among adults with Alcohol Use Disorder. DNA was extracted from peripheral mononuclear cells isolated from a blood sample collected at baseline, prior to study medication ingestion. The Illumina MethylationEPIC BeadChip was subsequently used to analyze these extracted DNA samples.

  Study phs002424

• Gene expression analysis for nasal polyps

  The aim of the study is to identify the gene expression profile and biomarkers related with chronic rhinosinusitis with nasal polyps (CRSwNP). RNA-sequencing was performed to identify differentially expressed genes between nasal polyps (NP) and inferior turbinate mucosa from 6 patients with CRSwNP. We validated the RNA-seq results by quantitative real-time PCR.

  Study JGAS000153

• Identification of genetic mutations characteristic for recurrence and metastasis of colon and rectal cancer.

  We collected the cancerous tissues of the primary and recurrence tumors from the same patient with recurrent / metastatic colorectal cancer, and the purpose of this study is to find the characteristics of recurrent / metastatic colorectal cancers by carrying out a "molecular profiling", mainly the exome sequence analysis of these tissues.

  Study JGAS000091

• Whole exome sequencing of 49 tumor-blood pairs and transcriptome sequencing of 44 tumors for adrenocortical tumors

  Adrenal Cushing syndrome, which leads to type 2 diabetes, obesity and hypertension, is caused by ACTH-independent production of glucocorticoid by adrenocortical tumors. To investigate the genetic origins of cortisol-producing adrenocortical tumors, we performed whole exome sequencing of 49 tumor-blood pairs and transcriptome sequencing of 44 tumors

  Study EGAS00001000712

• Genomic Variant Dataset of 5,309 Jeju Residents: Integrated WGS and SNP Array Analysis

  This dataset comprises genomic data from the Jeju Genome Project (JGP). WGS libraries were prepared using TruSeq Nano DNA kits and sequenced on Illumina NovaSeq 6000, with variants called via the DRAGEN Germline pipeline (v4.0.3). Genotyping was performed using the customized Axiom_JPMI v1 Chip on the Affymetrix GeneTitan platform. Raw data were processed using APT (v2.11.4), followed by phasing with Eagle (v2.4.1) and imputation via Minimac3 (v2.0.1) using a JGP-specific reference panel to optimize accuracy for the Jeju population.

  Dataset EGAD50000002451

• Single-nuclei multiomic analysis of KOLF2.1J human induced pluripotent stem cells-derived differentiated dopaminergic neurons

  Datasets consists of 12 samples of nuclei from hIPSCs differentiated optimized protocols for generating dopaminergic neurons. 6 single nuclei (RNA-ATAC) samples of XMAS protocol with cells collected at days 0,11,16,28,42 and 56 after differentiation. 3 snRNA-seq samples from AMS protocol of cells collected at days 14,16 and 28 after differentiation and 3 snRNA-seq samples with AMS protocol until day 14 grafted and grafts processed after 5 months grafting.

  Dataset EGAD50000002054

• RNA-seq datatset of primary human thymocyte subsets

  FASTQ-files of RNA-seq experiments of 8 primary human thymocyte subsets, isolated by flow-cytometry (FACS) from neonatal thymus biopsies. All samples were sorted to be negative for the expression of the lineage surface markers CD11c, CD19, CD56, CD141 and CD303 and additionally had the following surface phenotypes: DN1 (CD4-CD8-CD7+CD1a-CD161-CD38-); DN2 (CD4-CD8-CD7+CD1a-CD161-CD38+CD3-TCRab-); DN3 (CD4-CD8-CD7+CD1a+); ISP (CD4+CD8-CD3-TCRab-CD1a+); DPE (CD4+CD8+TCRab-CD69-); DPL (CD4+CD8+TCRab+CD69+); SP4 (CD4+CD8-); SP8 (CD4-CD8+). Samples were sorted from 2-4 pediatric patients undergoing heart surgery.

  Dataset EGAD50000001599

• Common origin and somatic mutation patterns of composite lymphomas and leukemias

  The dataset contains six composite lymphomas and leukemias cases (four composite B-cell lymphomas (case 1-4), and two combinations of B-cell and T-cell lymphoma (case 5+6)). Two tumor and one non-tumor (NTC) sample were sequenced from each case after library prep with NEBNext Ultra DNA Library Prep Kit, Exome capturing was done with NimbleGen SeqCap EZ Choice kit, and sequenced on a Illumina HiSeq 2000 HO and given as fastq files. WGA (Qiagen REPLI-g kit) was used for case 2 and 3. Case 1-4 were microdisected, case 5+6 were flow-sorted.

  Dataset EGAD50000001486

• Targeted Illumina sequencing of 3399 plasma cfDNA samples and 1988 leukocyte DNA samples from 1995 metastatic prostate cancer patients

  Blood samples were collected from eight clinical trials and a British Columbia-based biobank. All plasma cfDNA and leukocyte DNA samples were processed with uniform methodology, and underwent targeted sequencing using a custom hybridization capture panel and Illumina instruments. Four different generations of custom hybridization capture panel were used, all providing coverage of the complete coding regions of 72 prostate cancer genes, and later panel generations also providing exhaustive coverage of the AR locus (including introns and flanking regulatory regions), as well as a genome-wide SNP grid for copy number analysis.

  Dataset EGAD50000001594

• WES of pleomorphic lung cancer

  Pulmonary pleomorphic carcinoma (PPC) is an aggressive and highly heterogeneous non-small-cell lung carcinoma whose underlying biology is still poorly understood. Forty-two tumor areas including 39 primary tumors and 3 metastases from 20 PPC patients were microdissected and the histologically distinct components were subjected to whole exome sequencing (WES) separately. Twist Human Core Exome + RefSeq + Mito-Panel kit (Twist Bioscience) was used for the whole exome capturing according to manufacturer’s guidelines. Paired-end 100-bp reads were generated on the Illumina NovaSeq 6000. After the sequencing, reads were aligned against the reference human genome GRCh38 using Burrows-Wheeler Aligner (BWA, v0.7.12)

  Dataset EGAD50000000453

• Sequencing data for oesophageal and related samples - OACs release 4 (RNA)

  Dataset EGAD00001004021

• Warm_Autopsy_Single_Cell_X10

  Study of cell lineage and embryogenesis using biopsy samples from sites across the whole body (post mortem). Sample donors are recruited sensitively through the Phoenix study and consent to samples being taken after their death for both the Phoenix study and this WTSI study.

  Dataset EGAD00001003240

• RNA sequencing of peripheral blood samples from 17 Greenlanders

  The data contain whole deep RNA sequencing of leukocytes from 17 Greenlanders. RNA was purified from peripheral blood with the PAXGene Blood miRNA Kit (Qiagen). The RNA sequencing library was prepared following the instructions of the TruSeq RNA Sample Prep Kit v2 (Illumina). For mRNA isolation and fragmentation 200 ng of total RNA was purified by oligo-dT beads. The qualified libraries were amplified on cBot to generate the cluster on the flowcell (TruSeq PE Cluster Kit V3–cBot–HS, Illumina). The amplified flow cell was sequenced paired-end on the HiSeq 4000 System (TruSeq SBS KIT-HS V3, Illumina).

  Dataset EGAD00001003814

• Cardiogenics_Custom_Pools - Agilent SureSelect

  The Cardiogenics re-sequencing study will consist of three parts: Eight pools of 25 individuals will be sequenced using a Nimblegen hybrid-capture solution specific to miRNA sequences, 80 pools of 25 individuals will be sequenced using a custom Agilent SureSelect array covering genes associated with coronary artery disease (CAD) and myocardial infarction (MI), 10 individuals from families with a history of CAD/MI will be exome sequenced using the Sanger exome array. The experiment will use the early onset patients from the German MI cohort and the UK BHF CAD/MI cohort both of which have strong family history. For controls we will consider individuals from the UKBS and KORA cohorts.

  Dataset EGAD00001000397

• Nimblegen

  The Cardiogenics re-sequencing study will consist of three parts: Eight pools of 25 individuals will be sequenced using a Nimblegen hybrid-capture solution specific to miRNA sequences, 80 pools of 25 individuals will be sequenced using a custom Agilent SureSelect array covering genes associated with coronary artery disease (CAD) and myocardial infarction (MI), 10 individuals from families with a history of CAD/MI will be exome sequenced using the Sanger exome array. The experiment will use the early onset patients from the German MI cohort and the UK BHF CAD/MI cohort both of which have strong family history. For controls we will consider individuals from the UKBS and KORA cohorts.

  Dataset EGAD00001000398

• SCLC study George et al. - RNA-sequencing data set

  RNA-sequencing (RNA-seq) was performed with RNA extracted from fresh-frozen human tumor tissue samples. cDNA libraries were prepared from poly-A selected RNA applying the Illumina TruSeq protocol for mRNA. The libraries were then sequenced with a 2 x 100bp paired-end protocol to a minimum mean coverage of 30x of the annotated transcriptome.

  Dataset EGAD00001001244

• 4 subjects, 12 brain regions, UKBEC

  Brain samples for this dataset were provided by the Medical Research Council Sudden Death Brain and Tissue Bank (Edinburgh, UK). All four individuals sampled were of European descent, neurologically normal during life and confirmed to be neuropathologically normal by a consultant neuropathologist using histology performed on sections prepared from paraffin-embedded tissue blocks. Twelve regions of the central nervous system were sampled from each individual. The regions studied were: cerebellar cortex, frontal cortex, temporal cortex, occipital cortex, hippocampus, the inferior olivary nucleus (sub-dissected from the medulla), putamen, substantia nigra, thalamus, hypothalamus, intralobular white matter and cervical spinal cord.

  Dataset EGAD00001001274

• CITEseq data

  CITEseq data of CLL patients receiving VEN treatment for resistance study

  Dataset EGAD00001008366

• Leukemia WGS data

  Whole-genome sequencing data from 38 leukemia patients and 12 leukemia cell lines; Containing 100 fastq files; Two files for each sample.

  Dataset EGAD00001008659

• Dataset for Sarcoma-WGS linked from study EGAS00001004813

  Sequencing data of 77 sarcoma tumor and control runs, which were uploaded to EGAS00001004813. The sequencing was always paired.

  Dataset EGAD00001010257

• Organoid Derivation Project - GRCh38 - RNAseq (2023-06-22)

  Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients. . This dataset contains all the data available for this study on 2023-06-22.

  Dataset EGAD00001011092

• TXT_Cytof_15B

  Matrix of normal values from 39 marker CyTOF assay performed on longitudinal BMMC. FCS files from the CyTOF assay were normalized and concatenated using Fluidigm's CyTOF software and then de-multiplexed using Astrolabe Diagnostics, Inc., a commercial, cloud-based platform for single-cell analysis.

  Dataset EGAD00001011143

• SNF_CyTOFF_20

  Matrix of normal values from 39 marker CyTOF assay performed on baseline BMMC. FCS files from the CyTOF assay were normalized and concatenated using Fluidigm's CyTOF software and then de-multiplexed using Astrolabe Diagnostics, Inc., a commercial, cloud-based platform for single-cell analysis.

  Dataset EGAD00001011146

• Sequencing data for oesophageal and related samples - Black et al (WES)

  Data supporting: "Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett’s Oesophagus surveillance: individual-level data analysis" Black et al (WES OACs/BOs/normals)

  Dataset EGAD00001011188

• AWI-GEN 2 Microbiome Dataset

  AWI-Gen Phase 2 Microbiome Project for 1820 samples.

  Dataset EGAD00001015449

• Whole Genome-sequencing of rhabdomyosarcoma tumour tissue (2025-09-30)

  This study investigates high-risk rhabdomyosarcoma (RMS) using multiple single-cell and spatial genomic technologies. We generated and analysed single-cell and single-nucleus RNA-sequencing, chromatin accessibility, and spatial transcriptomics data from primary tumours and validation samples. These datasets characterise cellular diversity within rhabdomyosarcoma and identify cell states associated with aggressive disease. The data support research into tumour biology, risk stratification, and therapeutic target discovery. This repository houses the whole-genome sequencing of RMS tumours data. . This dataset contains all the data available for this study on 2025-09-30.

  Dataset EGAD00001015712

• Mechanisms on relapse after allogeneic hematopoietic cell transplantation in CMML

  Disease relapse is a major cause of treatment failure after allogeneic hematopoietic cell transplantation (HCT), and mechanisms on relapse still remain to be elucidated. We experienced a patient with chronic myelomonocytic leukemia (CMML) who underwent haploidentical HCT from his daughter and developed relapse. To understand the mechanisms on relapse after HCT, we analyze blood samples at HCT and at relapse.

  Study JGAS000317

• ImmunAID Data Access Committee

  The ImmunAID Data Access Committee (DAC) oversees controlled access to cohort data and samples generated within the project. Access requests must be submitted via a standardized form and are reviewed by a Steering Committee (SC), with potential input from the External Advisory Board (EAB). Requests must include detailed scientific, ethical, and regulatory information, including data protection measures in accordance with the GDPR and French legislation. The SC evaluates proposals based on scientific merit, methodological rigor, ethical considerations, and the availability of cohort resources. Decisions are communicated within 8 weeks. Opinions can be favorable, conditional (requiring modifications), or unfavorable (with one resubmission allowed). Only academic, industrial, or project-affiliated research teams are eligible to apply.

  Dac EGAC50000000654

• Transcriptomic changes in placenta associated with anesthesia, delivery mode and maternal diabetes

  The goal of this study was to analyse the impact of maternal diabetes and other maternal factors such as birth mode and anaesthesia on placental transcriptomics. Placental tissue samples from both, the villous and the decidua were prepared and RNAseq was conducted; samples were from mothers with Type1 Diabetes or gestational diabetes or from control mothers.

  Study EGAS50000000489

• PCNSL single cell dataset

  Mononuclear cells were isolated as cell suspensions by dissociation in a BD Horizon™ Dri Tumor & Tissue Dissociation Reagent (BD Biosciences) using a gentleMACS dissociator (Miltenyi Biotec). A totalseq-C antibody cocktail (Biolegend) was used, and the cell suspensions were diluted to a concentration of 1,000 cells/μL. Library sequencing was performed using the DNBSEQ-G400 (MGI Tech), Illumina HiSeq 2000, or Illumina NovaSeq 6000 5 (Illumina). The FASTQ files were aligned to the 10x provided reference genome using 10x Genomics Cell Ranger software v7.1.0 to create unique molecular identifier count tables of gene expression of the samples.

  Dataset EGAD50000000685

• PBMC scRNA-seq data using 10X Genomics platform

  Matrices of counts from single-cell RNA-seq data and single-cell CITE-seq data collected from 16 patients enrolled in GO30103 trial, and the cell level annotation. Specifically, PBMCs at C1D1, C1D15 (2 weeks after treatment), C2D1 (3 weeks after treatment) and C4D1 (9 weeks after treatment) were collected and subject to 10x Genomics protocol. Associated metadata also included.

  Dataset EGAD50000000370

• Cityscape Serum peptide Mass Spec data

  Matrix of counts from the serum peptide mass spec data from patients enrolled in the CITYSCAPE trial, and the sample annotation. Specifically, serum samples at C1D1, C2D1, C3D1, SCRN were collected from a total of 132 patients and subject to Mass Spec at Biognosys. The current study focused on patients who have samples at both C1D1 and C2D1 (n = 64 pairs). Associated metadata also included.

  Dataset EGAD50000000369

• Single-nucleus mRNA-Sequencing of prenatal and postnatal samples from the brain and its border regions

  Single-nucleus mRNA Sequencing of prenatal and postnatal samples from the brain and its border regions. Most samples were multiplexed with several samples run in one 10X reaction. A separate immune cell dataset was combined with published data from Braun et al 2023 and Yang et al 2021 integrated using harmony is included.

  Dataset EGAD50000000044

• Inter and intra - tumor heterogeneity in Colorectal Cancer

  The dataset consists of two main sample groups. 1) The inter-tumour sample group contains a total of 97 samples from 27 patients. Each patient has a single normal and primary sample as well as one or more metastases. All samples were sequenced using IonTorrent PGM and a custom colorectal cancer (CRC) panel. 2) The intra-tumour sample group contains a total of 68 samples from a single tumour as well as a normal tissue sample. All 68 samples were sequenced using IonTorrent PGM and a custom CRC panel. Shallow whole genome sequencing was additionally applied to 10 of the samples using Illumina HiSeq 4000.

  Dataset EGAD00001003131

• GIST SSGXVIII trial targeted gene sequencing

  Targeted cancer gene sequencing of samples enrolled in the SSGXVIII trial from Finland.

  Dataset EGAD00001001427

• BLUEPRINT Whole-genome fingerprint of the DNA methylome during human B-cell differentiation

  We used whole-genome bisulfite sequencing (WGBS) to generate unbiased DNA methylation maps of six purified B-cell subpopulations: hematopoietic progenitor cells (HPC); pre-B-II cells (preB2C); naive B cells from peripheral blood (naiBC); germinal center B cells (gcBC); memory B cells from peripheral blood (memBC) and plasma cells from bone marrow (bm-PC). WGBS was performed in 2 biological replicates from each subpopulation.

  Dataset EGAD00001001304

• UMCU Molpheno Closed

  This dataset contains Whole Genome Sequencing and, if available, RNA-sequencing and/or ATAC-sequencing data obtained from PBMCs derived from blood samples of two patients with intellectual disability and/or multiple congenital anomalies and eight parents included in the University Medical Center Utrecht (The Netherlands). Data access is closed.

  Dataset EGAD00001004864

• RNA-Seq data of hepatoma (Huh7 derived) and Ph5CH cells and primary hepatocytes

  The innate immune response of cells of hepatic origin (Huh7, Huh7.5, PH5CH and primary human hepatocytes (PHH), 66 samples) was analyzed by transcriptome analysis (RNAseq) upon supernatant delivery or transfection of synthetic dsRNA (poly(I:C)). Expression of TLR3 and RIG-I was reconstituted by lentiviral transduction in Huh7 and Huh7.5 cells. The sequencing is single RNA-Seq on an Illumina HiSeq 4000 with the Illumina TruSeq stranded mRNA kit.

  Dataset EGAD00001007083

• Sequencing data associated with Smith et al, Acta Neuropathologica, 2020 (PMID: 32519082)

  The dataset includes 144 BAM files of WGS, WES, and RNA-seq data from primary and PDOX samples analyzed in Smith et al, Acta Neuropathologica, 2020 (PMID: 32519082).

  Dataset EGAD00001007980

• Mutation and Microsatellite Burden Predict Response to PD-1 Inhibition in Children with Germline DNA Replication Repair Deficiency: An Observational Registry Study

  This dataset contains raw data from polyA RNAseq, hybrid capture target TCR panel data, and bam files from whole exome sequencing on 39 tumors with matched germline blood.

  Dataset EGAD00001008036

• Whole genome and RNA-sequencing in T-cell acute lymphoblastic leukemia

  Dataset includes whole genome and transcriptomic sequencing data from five T-cell acute lymphoblastic leukemia (T-ALL) patients. Whole genome sequencing has performed from both diagnostic (T-ALL sample) and control (remission sample) samples. RNA-sequencing has performed from diagnostic samples. Samples has been taken from the bone marrow or peripheral blood.

  Dataset EGAD00001008658

• Orthotopic murine Group 3 medulloblastoma in C57Bl/6 mice treated with sham or craniospinal irradiation

  Mice with medulloblastoma (Group 3) were treated with sham (isofluorane and imaging xray) or CSI as described by Abbas et al (2022). Total RNA was isolated with RNeasy Plus Mini Kit (Qiagen), library preparation (SureSelect, Agilent), rRNA depletion (Ribo-Zero Plus, Illumina) and sequencing were carried out by GenomicsWA or Australian Genome Research Facility. Libraries were sequenced on NovaSeq 6000 S1 flow cells as paired-end 150bp reads (Illumina).

  Dataset EGAD00001008510

• Genetic architecture of autism spectrum disorder in India

  The dataset consists of whole exome sequencing data (fastq format) of 100 non-syndromic autism spectrum disorder patients from India. Whole exome sequencing data is generated using Agilent SureSelect v6 capture kit and Illumina HiSeq sequencing platform. Paired end fastq files are available.

  Dataset EGAD00001008621

• Targeted DNA sequencing

  Targeted DNA sequencing of high-grade serous ovarian cancer (HGSC) tumour and normal samples from 15 patients with homologous recombination deficiencies. The dataset includes fastq files from 243 HGSC tumours (15 primary, 3 relapse, 225 end-stage) and 15 normals from 15 HGSC patients. Following target hybrid capture of 63 genes involved in DNA repair and response to treatment with an Agilent SureSelect XT panel, sequencing libraries were generated using the SureSelect XT Low Input Target Enrichment System (Agilent) as per the manufacturer's protocol. Libraries were sequenced on an Illumina NextSeq 500 at the Peter MacCallum Cancer Centre (Melbourne, Australia).

  Dataset EGAD00001009747

• COVID-19 progression and resolution in common variable immunodeficiency patients

  116,958 single-cell transcriptomes from samples of peripheral blood mononuclear cells (PBMCs) from five CVID patients at three distinct stages of the SARS-CoV-2 infection: 1) baseline, before viral infection, 2) progression, during viral infection, and 3) convalescence, once the viral infection had been resolved and the patient was PCR negative. CVID patients were under regular immunoglobulin replacement therapy and displayed only mild symptoms during SARS-CoV-2 infection.

  Dataset EGAD00001009773

• Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time

  A key characteristic of osteosarcoma is extensive and complex genomic rearrangements. However, published models explaining how these genomic rearrangements occur disagree about if these rearrangements occur early in tumor progression and then are stable afterwards, or if there is ongoing genomic instability. Previous studies have employed bulk sequencing technologies to characterize genomic alterations. A limitation of this approach is that it averages all changes within the bulk sample, essentially masking intra-sample heterogeneity and making evaluation of ongoing genomic instability difficult. To overcome this limitation and compliment previous work, we utilized single-cell whole genome sequencing to quantify somatic copy number alterations (SCNA). By interrogating individual cells within a sample, we were able to examine intra-sample heterogeneity. We found that the SCNA patterns between cells within a single sample were remarkably consistent, which supports the concept that the genomes of osteosarcoma tumors are relatively stable after early genome fragmentation events.

  Study phs003209

• Spatial Dynamics of the Developing Heart (single-cell)

  Heart development relies on a topologically defined interplay between diverse cardiac cells. We finely curated spatial and single-cell measurements with high-resolution imaging-based transcriptomics validation to explore spatial dynamics during early human cardiogenesis. Analyzing almost 80,000 individual cells and 70,000 spatially barcoded tissue regions between the 5.5th and 14th postconceptional weeks, we identified 31 coarse- and 72 fine-grained cell states and mapped them to highly resolved cardiac cellular niches. We provide novel insight into the development of the cardiac pacemaker-conduction system, heart valves, and atrial septum, and decipher heterogeneity of the hitherto elusive cardiac fibroblast population. Furthermore, we describe the formation of the cardiac autonomic innervation and present the first spatial account of chromaffin cells in the fetal human heart. Our study, supported by an open-access, spatially centric interactive viewer, delineates the cellular and molecular architecture of the developing heart, offering links to genetic causes of heart disease.

  Study EGAS50000001029

• High-grade B-cell lymphoma, not otherwise specified: an LLMPP study

  Molecular characterization of high-grade B-cell lymphoma, not otherwise specified (HGBCL-NOS), is hindered by its rarity, evolving definition, and poor diagnostic reproducibility. To address this challenge, we analyzed 92 HGBCL-NOS tumors collected across Lymphoma/Leukemia Molecular Profiling Project sites. These tumors were profiled using whole-genome sequencing (WGS) or whole-exome sequencing (WES) to identify somatic mutations, WGS or low-pass WGS to detect copy number alterations, targeted capture sequencing to assess MYC and BCL2 structural variants, and RNA sequencing. The genetic features of HGBCL-NOS were compared to those of diffuse large B-cell lymphoma (DLBCL-NOS) and EBV-negative adult Burkitt lymphoma (BL). DLBCL-NOS tumors underwent targeted capture sequencing using a panel of 125 genes recurrently mutated in aggressive B-cell lymphomas. BL biopsies were drawn from the Burkitt Lymphoma Genome Sequencing Project and had available WGS (dbGaP Study Accession: phs000527.v18.p6).

  Study EGAS50000000932

• Spatial Dynamics of the Developing Human Heart

  Heart development relies on a topologically defined interplay between diverse cardiac cells. We finely curated spatial and single-cell measurements with high-resolution imaging-based transcriptomics validation to explore spatial dynamics during early human cardiogenesis. Analyzing almost 80,000 individual cells and 70,000 spatially barcoded tissue regions between the 5.5th and 14th postconceptional weeks, we identified 31 coarse- and 72 fine-grained cell states and mapped them to highly resolved cardiac cellular niches. We provide novel insight into the development of the cardiac pacemaker-conduction system, heart valves, and atrial septum, and decipher heterogeneity of the hitherto elusive cardiac fibroblast population. Furthermore, we describe the formation of the cardiac autonomic innervation and present the first spatial account of chromaffin cells in the fetal human heart. Our study, supported by an open-access, spatially centric interactive viewer, delineates the cellular and molecular architecture of the developing heart, offering links to genetic causes of heart disease.

  Study EGAS50000001122

• Integrated genomic characterization of IDH1 mutant Glioma malignant progression

  Gliomas represent approximately 30% of all central nervous system tumors, and 80% of malignant brain tumors. To understand the molecular mechanisms underlying the malignant progression of low-grade Isocitrate Dehydrogenase 1 (IDH1) mutant gliomas, we studied paired tumor samples from 41 patients, comparing higher-grade, progressed samples to their lower-grade counterparts. Integrated genomic analyses, including whole-exome sequencing, copy number, gene expression and DNA methylation profiling, demonstrated non-linear clonal expansion of the original tumors and identified oncogenic pathways driving progression. These include activation of the MYC and RTK-RAS-PI3K pathways, up-regulation of the FOXM1- and E2F2-mediated cell cycle transition genes, as well as epigenetic silencing of developmental transcriptional factors bound by Polycomb repressive complex 2 in human embryonic stem cells. Our results not only provide mechanistic insight into the genetic and epigenetic mechanisms driving glioma progression but also identify inhibition of the bromodomain and extra-terminal (BET) family as a potential therapeutic approach.

  Study EGAS00001001588

• Elucidating the genomic architecture of Asian EGFR-mutant lung adenocarcinoma through multi-region exome sequencing

  EGFR-mutant lung adenocarcinomas (LUAD) display diverse clinical trajectories and are characterized by rapid but short-lived responses to EGFR tyrosine kinase inhibitors (TKIs). Through sequencing of 79 spatially distinct regions from 16 early stage tumors, we show that despite low mutation burdens, EGFR-mutant Asian LUADs unexpectedly exhibit a complex genomic landscape with frequent and early whole genome doubling, aneuploidy and high clonal diversity. Multiple truncal alterations, including TP53 mutations and loss of CDKN2A and RB1, converge on cell cycle dysregulation, with late sector-specific high amplitude amplifications and deletions that potentially beget drug resistant clones. We highlight the association between genomic architecture and clinical phenotypes, such as co-occurring truncal drivers and primary TKI resistance. Through comparative analysis with published smoking-related LUAD, we postulate that the high intra-tumor heterogeneity observed in Asian EGFR-mutant LUAD may be contributed by an early dominant driver, genomic instability and low background mutation rates.

  Study EGAS00001001736

• UK renal cancer samples genotyped on Illumina OmniExpress BeadChip

  Renal cell carcinoma (RCC) cases comprised adult patients with histologically proven RCC were collected through two sources within the UK. First, 856 cases from SORCE, a MRC collection of surgically treated RCC cases ascertained through UK clinical oncology centres. Second, 189 RCC cases collected through the ICR and Royal Marsden NHS Hospitals Trust. Cases included 590 clear cell carcinomas (CCCs), 42 papillary carcinomas (PCs), 33 chromophobe carcinomas (CCs) and 19 mixed or other histological subtypes. DNA was extracted from EDTA-venous blood samples using the conventional methods and quantified using PicoGreen (Invitrogen). Cases were genotyped using the Human OmniExpress-12 BeadChip according to the manufacturer's recommendations (Illumina Inc, San Diego, CA, USA). After strict QC, 944 cases were retained. Data provided in plink format. Controls used were data from the Wellcome Trust Case Control Consortium 2 (WTCCC2) 1958 birth cohort and the UK Blood Service Control Group (available as EGAS00000000028).

  Study EGAS00001002336

• Multiome_HB

  Hepatoblastoma (HB) cells display strong phenotypic heterogeneity with a major impact on drug response, but the underlying mechanisms are poorly understood. Here, we use a single-cell multi-omic strategy to unravel the molecular determinants of this plasticity. HB display a continuum of single-cell states between hepatocytic (scH), liver progenitor (scLP) and mesenchymal (scM) differentiation poles, with an intermediate scH/LP population bordering scLP and scH areas in spatial transcriptomics. Chromatin accessibility landscapes reveal the gene regulatory networks of each differentiation pole, and the sequence of transcription factor activation underlying cell state transitions. Single-cell mapping of somatic alterations reveals the clonal architecture of each tumor, showing that each genetic subclone displays its own range of cellular plasticity across differentiation poles. The most scLP subclones, overexpressing stem cell and DNA repair genes, proliferate faster after neo-adjuvant chemotherapy. These results highlight how the interplay of clonal evolution and epigenetic plasticity shapes the potential of HB subclones to respond to chemotherapy.

  Study EGAS00001006932

• The genetic history of the southern Andes from present-day Mapuche ancestry

  We generate genome-wide data from 64 participants from three Mapuche populations in Southern Chile: Pehuenche, Lafkenche, and Huilliche. Broadly, we describe three main ancestry blocks with a common origin, which characterize the Southern Cone, the Central Andes, and Amazonia. Within the Southern Cone, ancestors of the Mapuche lineages differentiated from those of the Far South during the Middle Holocene, and did not experience further migration waves from the north. We find that the deep genetic split between the Central and Southern Andes is followed by instances of gene flow, which may have accompanied the southward spread of cultural traits from the Central Andes, including crops and loanwords from Quechua into Mapudungun (the language of the Mapuche). Our findings add new perspectives on the genetic (pre)history of South America, from first settlement through to the present-day indigenous presence. Follow-up fieldwork took these results back to the indigenous communities to contextualize the genetic narrative alongside indigenous knowledge and perspectives.

  Study EGAS00001007200

• A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories.

  Background: Atypical teratoid rhabdoid tumors (ATRTs), characterized by the loss of SMARCB1, are among the most lethal pediatric central nervous system (CNS) tumors. Three molecular subtypes have been identified, each defined by distinct molecular and clinical features. No subtype-specific treatments are available, highlighting the necessity to better understand inter- and intra-subtype heterogeneity. Methods: We generated a single-nucleus transcriptome atlas of ATRTs, validated by single-cell ATAC-seq and spatial transcriptomics, to study subtype-specific differentiation trajectories. Results: We identified brain progenitor-like expression profiles within unique subtype-specific differentiation lineages. A shared cycling, progenitor-like cell population, interspersed throughout tumors, was observed across all ATRT samples. Moreover, we demonstrate that subtype-specific differentiation trajectories can be induced pharmacologically in ATRT tumoroids directing tumor cells towards a non-proliferative, mature phenotype. Conclusions: Our study reveals that ATRT subtypes exhibit signaling trajectories mirroring normal fetal brain development, enabling the development of maturation therapies tailored towards ATRTs.

  Study EGAS00001008108

• Molecular and clinical diversity in primary central nervous system lymphoma: a LOC network multi-omic PCNSL study

  Primary central nervous system lymphoma (PCNSL) is a distinct extranodal lymphoma presenting with limited stage disease but variable response rates to treatment despite homogenous pathological presentation. The likely underlying molecular heterogeneity and its clinical impact is poorly understood. The present dataset contents paired-ended whole-exome sequencing information (n=115; HyperExome Kapa hyperprep), paired-ended RNA-seq information (n=123; KAPA mRNA HyperPrep Kits), and paired-ended bisulfite sequencing (n=64; TruSeq Methyl Capture EPIC) from fresh-frozen tumor tissue immunocompetent, treatment naïve PCNSL patients. Additionally, the dataset includes single-ended RNA-seq (n=93; QuantSeq 3’ mRNA-Seq Library Prep Kit) from formalin-fixed, paraffin-embedded tissue of immunocompetent, treatment naïve PCNSL patients. All samples were sequenced in an Illumina NovaSeq 6000 instrument.

  Dataset EGAD00001008706

• Systemic mutagen exposures reported by normal kidney cell genomes - matched normal samples (whole-genome sequencing)

  Lifestyle, environmental and other exposures to exogenous mutagens generate somatic mutations in normal human cells in vivo and increase cancer risk. However, the global repertoire of exogenous mutagen exposures is uncertain. Using single-molecule duplex sequencing of normal kidney (n=319) and blood (n=272) samples from 10 countries, we show that kidney proximal tubule cells exhibit higher mutation rates than most normal cell types despite low cell division rates. Compared to cells from kidney glomeruli, medulla, distal tubules, or peripheral blood, proximal tubule cells show marked enrichment of mutational signatures due to the exogenous carcinogenic mutagens, aristolochic acids, and of several signatures of unknown causes. The results suggest the existence of multiple, common, systemically circulated mutagens affecting human populations and indicate that the genomes of kidney proximal tubule cells report such exposures with high sensitivity.

  Dataset EGAD00001015828

• Characterizing the immune and genome landscapes for osteosarcoma

  Osteosarcoma have heavily rearranged genomes and moderate tumor mutation burden, which suggests that the patients may express neoantigens that could be targeted by immune cells. To characterize the immunogenomic landscape of this disease, we performed genome, transcriptome, immune and proteomic profiling of 48 patients comprised largely of relapsed and metastatic cases from both pediatric and adult patients.

  Study EGAS00001003247

• WES Profiles from the CheckMate-577 Clinical Trial

  The dataset contains WES profiles of 396 patients from the CheckMate-577 (CA209-577) clinical trial whose ICF allows data deposition into a public repository. The Allprep DNA/RNA FFPE kit was used to simultaneously purify genomic DNA and total RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections. DNA was analyzed by Whole Exome Sequencing using Swift Biosciences Accel-NGS 2S Hyb DNA Library Kit for library preparation and hybridization using Agilent SureSelect All Exon v6, followed by sequencing on the Illumina NovaSeq platform with a 100bp paired-end strategy and a target read depth of 100M per tumor sample. Fastq files are included.

  Dataset EGAD50000002395

• 10X CD4 auto-antigens

  Ex vivo CD4 T-cells from 4 donors were stimulated with antigen-coupled beads to aCD3, ABD, EBNA1, ANO2 or CRYAB and the LiveCD3+CD4+CFSEdim cells were sorted by flow cytometry. Cells were labelled with barcoded antibodies to identify the original stimulus. All stimulations from each donor were pooled into four reactions, i.e. one reaction per donor. Libraries were assembled with the 10X Chromium Next GEM Single Cell 5’ Kit for TCR and transcriptome with feature barcodes. Dataset contains raw fastq reads as well as supplementary information needed to link fastq files to modality, i.e. gene-expression, protein or VDJ, and includes supplementary information to de-multiplex the reactions by stimulation condition.

  Dataset EGAD50000002201

• RNAseq and T cell receptor (TCR) profiling of PBMC cells 3 months post Omicron exposure

  This dataset contains RNA-seq and T cell receptor (TCR) sequencing files from a cohort (n=20) 3 months post positive PCR for SARS-CoV-2. A total of 10 hospitalised (samples H1-10) and 10 non-hospitalised (samples NH1-10) are contained within this dataset. RNA sequencing was performed using the Illumina Stranded mRNA Prep Ligation kit to investigate the protein coding transcriptome of PBMC cells. T cell receptor (TCR) repertoire profiling was performed with the TakaraBio SMART-Seq Human TCR (with UMIs) on PBMC cells to investigate the depth and persistence of SARS-CoV-2 targeting TCRs.

  Dataset EGAD50000001356

• Single cell RNA-seq of 24 samples from 13 individual human embryonic meninges of PCW 5.0-13.0 using 10X chromium technology

  A total of 24 samples of meninges from 13 normal human embryos of post-conceptional week (PCW) 5.0-13.0 were dissected and subject to 10Xgenomics chromium single cell RNA sequencing with the purpose of identifying cell types and gene expression programs for normal meninges development. All libraries were sequenced on an Illumina NovaSeq 6000 using S4 to a target sequencing depth of 100,000 reads/cell. Final data after processing with STARSolo 2.7.10a, using human genome GRCh38.p12 and transcript annotations from ENSEMBL release 93 from reference package GRCh38-3.0.0 as available from 10Xgenomics, consists of 24 BAM files.

  Dataset EGAD50000001434

• Sequence data to study genomic CNVs that drive apoptotic resistance and relapses on immune checkpoint inhibitors

  The dataset consists of bulk whole exome sequencing (WES) and whole genome sequencing (WGS) data from baseline and disease-progressed tumors after immune checkpoint inhibitor (ICI) treatment, derived from patients, human cell lines, and mouse models. Whole exome sequencing includes 17 clinical cases and one human cell line model with parental and acquired resistant cell lines (n = 5). Whole genome sequencing encompasses the YUMMER mouse model, including vehicle-treated controls (n = 2) and acquired resistant tumors (n = 3). The sequence reads have been aligned to hg19 and mm9 reference genomes, with mapped files (BAM) made available for analysis.

  Dataset EGAD50000001537

• GSA pilot raw data

  Unfiltered genotype data for a pilot study (Batch 1) of 1,140 DDD Study participants (and 12 "Empty" samples). Samples include 380 mothers, 382 fathers and 378 probands, and form 376 trios. Most of the probands have been previously genoyped on the llumina HumanCoreExome BeadChip (EGAD00010001598) or the Illumina InfiniumCoreExome Beadchip (EGAD00010001600). All samples were genotyped on the Illumina Global Screening Array.

  Dataset EGAD00010002567

• InterPregGen-GWAS-KAZ-3

  Preeclampsia (PE) is a syndrome affecting pregnant mothers and fetus/babies characterised by hypertension and proteinuria, and is a leading cause of maternal and fetal death and of premature births worldwide. The InterPregGen Consortium was funded by a European Framework 7 (FP7) grant and grew out of the WTCCC3 GWAS comparing ~2000 UK PE mothers with ~6000 common UK controls. This dataset includes Infinium GSA genotyping of maternal, paternal and fetal PE cases and controls from Kazakhstan. This study is one component of the InterPregGen FP7 project. DNA samples for this component were collected by InterPregGen Consortium collaborators at the Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Kazakhstan (Gulnara Svyatova, Principal Investigator).

  Dataset EGAD00010001949

• InterPregGen-GWAS-KAZ-2

  Preeclampsia (PE) is a syndrome affecting pregnant mothers and fetus/babies characterised by hypertension and proteinuria, and is a leading cause of maternal and fetal death and of premature births worldwide. The InterPregGen Consortium was funded by a European Framework 7 (FP7) grant and grew out of the WTCCC3 GWAS comparing ~2000 UK PE mothers with ~6000 common UK controls. This dataset includes OmniExpress genotyping of maternal and fetal PE cases and controls from Kazakhstan. This study is one component of the InterPregGen FP7 project. DNA samples for this component were collected by InterPregGen Consortium collaborators at the Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Kazakhstan (Gulnara Svyatova, Principal Investigator).

  Dataset EGAD00010001947

• InterPregGen-GWAS-KAZ-1

  Preeclampsia (PE) is a syndrome affecting pregnant mothers and fetus/babies characterised by hypertension and proteinuria, and is a leading cause of maternal and fetal death and of premature births worldwide. The InterPregGen Consortium was funded by a European Framework 7 (FP7) grant and grew out of the WTCCC3 GWAS comparing ~2000 UK PE mothers with ~6000 common UK controls. This dataset includes lllumina 2.5-8 genotyping of maternal and fetal PE cases and controls from Kazakhstan. This study is one component of the InterPregGen FP7 project. DNA samples for this component were collected by InterPregGen Consortium collaborators at the Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Kazakhstan (Gulnara Svyatova, Principal Investigator).

  Dataset EGAD00010001945