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• Tumor Educated Platelets (TEPs) for breast cancer detection

  The TEP dataset consists of 549 Fastq samples which are divided into two experiments: a training data cohort, used to train the classifier, and a validation data cohort, used to assess classifier performance

  Dataset EGAD00001009790

• 10xscRNA sequencing of 2 samples RRMM (multiple myeloma)

  Paired scRNA sequencing using 10xgenomics library preparation and Illumina HiSeq4000 for sequencing of 2 samples RRMM (relapsed refractory multiple myeloma)

  Dataset EGAD00001009681

• Exome sequencing data

  Libraries were constructed using SureSelect HS XT Target Enrichment System v6 (Agilent). For each patient a library of CD3- cells (myeloid cells, considered tumor cells) and CD3+ cells (T cells, considered healthy) were generated.

  Dataset EGAD00001010190

• Low-pass whole-genome DNA sequencing of cohesin-mutated and wildtype adult AMLs

  Low-pass whole-genome DNA sequencing of cohesin-mutated (STAG2 or RAD21 mutations) and wildtype (CTRL-AML) adult AMLs generated generated from ultrasound-fragmented genomic DNA. Samples were only sequenced shallow (20-40 Mio reads) Used for digital karyotyping and ChIP-seq background/copy-nuber normalization/correction.

  Dataset EGAD00001011207

• Whole exome sequencing (WES) of CIMP leukemias

  Whole exome sequencing of tumor material derived from 14 mixed myeloid/lymphoid leukemias with a CpG Island Methylator Phenotype (CIMP). For 4 of these patients, normal material was also sequenced and used as control (files with the same identifiers prepended by an “h”).

  Dataset EGAD00001011053

• Human Spermatogenesis Methylome

  The dataset contains the methylome EM-sequencing raw data (fastq) of different spermatogenic cells from 5 human males (three controls and two crypotzoospermic). The datasets correspond to the following cell types: undifferentiated spermatogonia, differentiating spermatogonia, 4C spermatocytes, and 1C spermatids (this cell type only for the control individuals)

  Dataset EGAD00001011180

• Whole-genome sequencing of Himalayan populations

  Whole-genome sequencing of 60 individuals from 15 Himalayan populations using the Illumina-B HiSeq X platform. These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/.

  Dataset EGAD00001011358

• Whole-exome sequencing of additional thyroid disease cases (2017-05-11)

  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 2017-05-11.

  Dataset EGAD00001003331

• Low-coverage Whole Genome Sequencing, Colorectal advanced adenomas, NKI-AvL TGO COCOS series

  For this tissue dataset, we applied low-pass whole genome sequencing to 96 advanced adenomas. Advanced adenomas were classified as lesions with low-risk or high-risk of progression, according to the presence of specific DNA copy number changes (Carvalho et al, CancerPrevRes, 2018).

  Dataset EGAD00001004078

• KNS42 and SF188 H3K36me3 chipSeq

  Chromatin immunoprecipitation (ChIP) was carried out employing antibodies against H3K36me3 and RNA polymerase II using the HistonePath and TranscriptionPath assays by ActiveMotif. Whole genome sequencing was carried out using an Illumina HiSeq2000 and data is provided as 6 BAM files. H3K36me3 chipseq RNA polymerase II chipseq and input coverage for each cell line.

  Dataset EGAD00001004119

• Highly differentiated, fusion-negative rhabdomyosarcoma.

  Sequencing was performed using OncoPanel v.2 (OPv2), an Agilent SureSelect custom designed bait set consisting of the coding regions of 504 genes, previously linked to human cancer. Sequencing wa sperformed on an Illumina HiSeq 2500. 8 highly differentiated, fusion-negative rhabdomyosarcoma tumor samples were sequenced. BAM files are available for download.

  Dataset EGAD00001003887

• NIHR-BioResource Rare Diseases - Neurodevelopmental disorders

  This dataset contains short-read whole-genome sequencing data for individuals with neurodevelopmental disorders and their relatives from the NIHR-BioResource Rare Disease Consortium.

  Dataset EGAD00001004456

• Whole-exome sequencing of additional thyroid disease cases (2018-08-13)

  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 2018-08-13.

  Dataset EGAD00001004293

• Whole Exome (WE) sequencing data files for H_NO-JB001

  DNA was derived from the primary tumour, lung metastasis, and peri-aortic lymph node metastasis. DNA from the spleen was used as a normal control.For WE sequencing we user Hybrid capture (Nimblegen version 3.0) of the lymph node and lung metastases, primary tumour and spleen normal; we generated ~100-fold coverage.

  Dataset EGAD00001001252

• Low coverage WGS from plasma DNA

  Low coverage whole genome sequencing plasma DNA from 50 male, 54 female non-cancer donors. For the analysis of nucleosomal positioning all data from the non-cancer controls were merged. Furthermore, two patients with metastasized breast cancer were sequenced on a NextSeq with higher depth.

  Dataset EGAD00001002215

• Targeted Sequencing of Human Myeloid Malignancies

  This study involves targeted sequencing of samples from myeloid malignancies at different timepoints to assess clonal evolution of malignancy a. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001002225

• ETMR H3K27Ac ChIPSeq

  H3K27Ac ChIP-seq DNA libraries for 5 ETMR samples were prepared using NEBNext ChIP-seq Illumina Sequencing library preparation kit. ChIP-seqlibraries were sequenced using single-end 50 bp reads on the Illumina HiSeq 2000 platform. ChIP-seq peaks analysed was conducted as published previously(Torchia et al. 2016).

  Dataset EGAD00001004809

• Chromatin 3D interactions mediate genetic effects on gene expression (RNA-seq)

  RNA-seq data for 168 Lymphoblastoid Cell Lines (LCL) and 78 Fibroblasts (FIB) from the Gencord Cohort. This dataset was generated as part of the following study: Delaneau et al (2019). Chromatin 3D interactions mediate genetic effects on gene expression.

  Dataset EGAD00001004872

• Woodcock et al TenMenDeep Study EGA Dataset A

  Woodcock et al TenMenDeep EGA Dataset A. These are Illumina based deep sequencing data based on bait capture sequencing. See Woodcock et al methods for more detail. Note: the Amplicon sequencing data type is selected because the EGA Website currently has no option to select Bait Capture Sequencing or similar.

  Dataset EGAD00001005381

• Wilms Tumour organoid sequencing WGS (2019-09-05)

  This study investigates the genomic and transcriptomic characteristics of Wilm's tumour organoids . This dataset contains all the data available for this study on 2019-09-05.

  Dataset EGAD00001005312

• IBD-dysplasia

  This data set concerns DNA copy number alterations and mutation data from 30 IBD-associated dysplastic lesions and 13 IBD-associated cancers. DNA was isolated from formalin-fixed, paraffin-embedded material. Whole-genome shallow seq and Truseq amplicon cancer panel (Illumina) were used for detection of DNA copy number alterations and gene mutations, respectively.

  Dataset EGAD00001005196

• Woodcock et al TenMenDeep Study EGA Dataset B

  Woodcock et al TenMenDeep EGA Dataset B. These are Illumina based deep sequencing data based on bait capture sequencing. See Woodcock et al methods for more detail. Note: the Amplicon sequencing data type is selected because the EGA Website currently has no option to select Bait Capture Sequencing or similar.

  Dataset EGAD00001005382

• SF12017 scRNA-Seq Primary astrocytoma IDH mutant Male

  Single cell Primary astrocytoma G2. IDH mutant, ATRX negative. Male, 44. Single Cell RNA seq from primary astrocytoma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)

  Dataset EGAD00001005395

• SF11964 scRNA-Seq Low Grade Glioma IDHR132H mutant Male

  Single cell RNA-Seq Low Grade Astrocytoma IDHR132H mutant. Male, 64. Single Cell RNA seq from primary astrocytoma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)

  Dataset EGAD00001005396

• SF11949 scRNA-Seq primary oligodendroglioma G3 IDH1 Mutant Male

  SF11949 Primary oligodendroglioma G3 IDH1 Mutant. Male, 40 Single Cell RNA seq from primary astrocytoma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)

  Dataset EGAD00001005397

• SF10022 snRNA-Seq Primary High-grade Glioma

  SF10022 single nuclei RNA-Seq Primary High-grade glioma. gender Male Age 65. Single Nuclei RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference

  Dataset EGAD00001005409

• SF12090 snRNA-Seq IDHR132H Wild-type Primary GBM Male

  Single Nuclei RNA-Seq Primary IDHR132H Wild-type GBM. Male, 61. Single Nuclei RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference.

  Dataset EGAD00001005412

• SF11979 scRNA-Seq Primary GBM IDHR132H Wild-type Female

  Single Cell Prmary high grade glioma IDHR132H Wild-type Female 76 Single Cell RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference.

  Dataset EGAD00001005429

• Shallow whole genome sequencing from plasma DNA of BC, CRC and NSCLC patients

  This is the raw data obtained from shallow whole-genome sequencing of plasma DNA (plasma-Seq) for calling of somatic copy number alterations as well as focal amplifications and deletions from patients with breast, colorectal and non-small cell lung cancer.

  Dataset EGAD00001006288

• Dissecting Cell Composition and Drug Sensitivity in Human Adenoid Cystic Carcinomas (ACCs)

  The study reports the results of single-cell RNA sequencing (scRNA-seq), RNA sequencing (RNA-seq), and whole-exome sequencing (WES) experiments performed on malignant cells isolated by flow cytometry from seven patient-derived xenograft (PDX) lines established from human Adenoid Cystic Carcinomas (ACCs). Of these seven lines, five are characterized by well differentiated histology (ACCX5M1, ACCX6, ACCX14, ACCX22, SGTX6) and two by solid histology (ACCX9, ACCX11). Analysis by scRNA-seq of the well-differentiated PDX line ACCX22 led to identification of cell-surface markers (CD49f, KIT) that enabled the differential purification of the two major cellular components contained in well-differentiated ACCs: myoepithelial-like (CD49f-high/KIT-negative) and ductal-like (CD49f-low/KIT-positive) cells. The study reports the analysis by RNA-seq and WES of purified preparations of myoepithelial-like and ductal-like cells from well-differentiated PDX lines (ACCX5M1, ACCX6, ACCX14, ACCX22, SGTX6) and of ductal-like (CD49f-low/KIT-positive) cells from solid PDX lines (ACCX9, ACCX11).

  Study phs002764

• Epstein-Barr Virus status drives morphological and molecular intra-tumour heterogeneity in gastric cancer: insights from a case report and literature review

  This case report describes a rare case of bi-phenotypic gastric cancer with two distinct, but clonally related, histological components. The first component, associated with Epstein-Barr virus (EBV) infection, exhibited the morphological features of gastric carcinoma with lymphoid stroma, suggesting that EBV, as an effective immunogenic factor, may trigger a prominent immune response within the tumour microenvironment. The second component, which was EBV-negative, displayed tubular/papillary morphology and features of increased biological aggressiveness, such as high-grade areas and lymphatic invasion. Immunohistochemical and molecular studies confirmed that, despite the differing morphologies and immunophenotypes, both components were clonally related, with especially the EBV-negative area showing more complex DNA aberrations, reminiscent of Chromosomally instable (CIN) lesions. This case describes clonally related EBV-positive and negative components within a single gastric cancer, contributing to a better understanding of EBV role in tumour heterogeneity and progression and highlighting the impact of EBV loss on tumour behaviour.

  Study EGAS50000000706

• An isogenic human iPSC model unravels neurodevelopmental abnormalities in SMA

  Whether neurodevelopmental defects underlie the selective neuronal death that characterizes neurodegenerative diseases is becoming an intriguing question. To address it, we focused on the motor neuron (MN) disease Spinal Muscular Atrophy (SMA), caused by reduced levels of the ubiquitous protein SMN. Taking advantage of the first isogenic human induced pluripotent stem cell-derived SMA model that we have generated and a spinal cord organoid system, here we report that the relative and temporal expression of early neural progenitor and MN markers is altered in SMA. Furthermore, the corrected isogenic controls only partially reverse these abnormalities. These findings raise the relevant clinical implication that SMN-increasing treatments might not fully amend SMA pathological phenotypes. The approach we have taken demonstrates that the discovery of new disease mechanisms is greatly improved by using human isogenic models. Moreover, our study implies that SMA has a developmental component that might trigger the MN degeneration.

  Study EGAS00001007259

• Somatic Mutations in Variant and IGHV4-34 Expressing Hairy Cell Leukemia

  To understand the genetic mechanisms driving variant and IGHV4-34 expressing hairy-cell leukemia, we performed whole exome sequencing of tumor/normal pairs from ten patients.

  Study phs000671

• Tumor heterogeneity and acquired drug resistance in FGFR2 fusion-positive cholangiocarcinoma through rapid research autopsy

  Whole exome sequencing was performed on blood and tumor specimens (collected from biopsy or rapid research autopsy) from a patient with FGFR2 fusion positive cholangiocarcinoma.

  Study phs001830

• Test dataset from FEGA Spain

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  Dataset EGAD50000000786

• DAC of the 300BCG ATAC-seq data

  To investigate human population variation of trained immunity, we immunized healthy individuals with Bacillus Calmette-Guérin (BCG). This live attenuated vaccine induces not only an adaptive immune response against tuberculosis, but also triggers innate immune activation and memory. We established personal chromatin accessibility maps over a time course of BCG vaccination in 323 individuals using ATAC-seq.

  Dac EGAC50000000056

• MDACC Lymphoma & Myeloma scRNAseq of Plasma Cells in Multiple Myeloma

  FastQ files from Chromium single cell 5' gene expression and B-cell receptor sequencing of plasma cells from patients diagnosed with a monoclonal gammopathy of the multiple myeloma spectrum, including the precursor stages MGUS (n =13) and SMM (n = 22); newly diagnosed (n = 17); relapsed (n = 15); and plasma cell leukemia (n = 2); and 3 controls.

  Dac EGAC50000000271

• Sahel Data Access Committee

  Genome-wide genotype array data of Fulani populations presented in Fortes-Lima et al. 2025. Citation: Population History and Admixture of the Fulani People from the Sahel. Cesar A. Fortes-Lima, Mame Y. Diallo, Václav Janoušek, Viktor Černý, and Carina M. Schlebusch. American Journal of Human Genetics 112(2), February 6, 2025. doi: https://doi.org/10.1016/j.ajhg.2024.12.015

  Dac EGAC50000000290

• ABHD11 Autoimmunity Study DAC

  This DAC oversees controlled access to human RNA-seq data generated as part of the project “ABHD11 inhibition and T cell function in autoimmunity” at Swansea University. The DAC will evaluate and approve access requests based on scientific merit and alignment with participant consent. Data requests will be considered from academic researchers and healthcare professionals working on immunology or autoimmunity.

  Dac EGAC50000000750

• Building a Database of Genomic Structural Variants in Japanese population

  Purified genomic DNA was purchased from Japanese B cell DNA bank; We sequenced those genomic DNAs using PacBio and 10X Genomics sequencing technologies, and analyzed genomic structural variations.

  Study JGAS000173

• Genomic Structural Variants in Japanese Malignant mesothelioma patients

  We extracted genomic DNAs from established mesothelioma cell lines from Japanese malignant mesothelioma patients. We sequenced those genomic DNAs using 10X Genomics sequencing technologies, and analyzed genomic structural variations.

  Study JGAS000176

• Building a Database of Genomic Structural Variants in Japanese population

  Purified genomic DNA was purchased from Japanese B cell DNA bank; We sequenced those genomic DNAs using PacBio Sequel and Sequel II and analyzed genomic structural variations.

  Study JGAS000286

• RNA bulk sequencing on organoids from different organs with or without TS2/16 antibody

  RNA bulk sequencing on organoids from colon, ileum, jejunum, duodenum and pancreas duct with or without TS2/16 antibody. Also there is difference in extracellular matrix used, BME vs Colagen.

  Dataset EGAD50000001606

• Long-read Nanopore data EVOFLUx

  Bam files with all reads covering 976 fCpGs identified in Gabbutt and Duran-Ferrer 2025 to develop the EVOFLUx methodology. These include 10 samples, 6 normal B cells, and 2 CLL patients developing RT.

  Dataset EGAD50000001697

• Olink Target Protein Expression

  Olink Target 96 Inflammation panels were applied to nasal secretions (DC, CRSsNP, CRSwNP, N-ERD, n=20 each). Across both panels, 184 assays (180 unique proteins) were determined, of which 4 appeared in both panels and were measured twice (CCL11, IL10, IL5, IL-6)

  Dataset EGAD50000001328

• Distinct immune cell infiltration patterns in pancreatic ductal adenocarcinoma (PDAC) exhibit divergent immune cell selection and immunosuppressive mechanisms

  To elucidate the heterogeneity of tumour immune cell infiltration, we performed single cell RNAseq sequencing on CD45+ cells enriched from matched fresh tumour tissue following surgical resection of 12 treatment-naïve patients and matched PBMCs.

  Dataset EGAD50000001008

• GCP Challenges in Hepatology

  raw RNAseq data from blood plasma of patients diagnosed with liver disease. Total RNA libraries were prepared using the SMARTer Stranded Total RNA-Seq-Kit v3 - Pico Input Mammalian (Takara Bio). Libraries were paired-end sequenced (2x100) o a NovaSeq 6000 instrument using NovaSeq S2 or S1 kit (Illumina).

  Dataset EGAD50000000775

• Variants Derived From Heart Centre Biobank CHD Probands (Canada)

  Short variants identified in 731 CHD probands enrolled through the Heart Centre Biobank Registry (Canada).

  Dataset EGAD50000000838

• BELLINI clinical trial bulk WES data: cohorts A & B

  WES data of 30 breast cancer primary tumors obtained from 30 unique patients from BELLINI clinical trial (cohorts A & B) and 30 matched blood samples. The data includes pretreatment samples. The included raw WES sequencing data in fastq format was generated using Illumina NovaSeq 6000.

  Dataset EGAD50000000809

• RNA-Seq of non-canonical t(7;12) AML

  We performed WGS on AutoMACS-separated BM leukemic blasts (CD34 + CD33+) to characterize the breakpoint and genes involved in the translocation. Additionally, we performed RNA-seq of the bone marrow blast cells to explore the functional consequences of the t(7;12) translocation

  Dataset EGAD50000000268

• Whole genome sequencing of preneoplasia lung adenocarcinoma

  Whole genome sequencing of 42 pulmonary samples including lung preneoplasia atypical adenomatous hyperplasia (AAH, N=5), adenocarcinoma in situ (AIS, N=7), minimally invasive adenocarcinoma (MIA, N=6) and invasive lung adenocarcinoma (ADC, N=8) and adjacent lung tissues (Normal, N=16).

  Dataset EGAD50000000396

• RNAseq of preneoplasia lung adenocarcinoma

  RNA sequencing of 168 pulmonary samples including lung preneoplasia atypical adenomatous hyperplasia (AAH, N=38), adenocarcinoma in situ (AIS, N=22), minimally invasive adenocarcinoma (MIA, N=19) and invasive lung adenocarcinoma (ADC, N=38) and adjacent lung tissues (Normal, N=62).

  Dataset EGAD50000000395

• IMSGC and MultipleMS project MS patients from Norway

  Genotype and phenotype data on 575 MS patients from Netherlands. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002485

• IMSGC and MultipleMS project MS patients from Greece

  Genotype and phenotype data on 140 MS patients from Greece. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002493

• IMSGC and MultipleMS project MS patients from Spain

  Genotype and phenotype data on 151 MS patients from Spain. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002492

• IMSGC and MultipleMS project MS patients from UK

  Genotype and phenotype data on 943 MS patients from UK. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002491

• IMSGC and MultipleMS project MS patients from Netherlands

  Genotype and phenotype data on 209 MS patients from Netherlands. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002488

• IMSGC and MultipleMS project MS patients from Austria

  Genotype and phenotype data on 246 MS patients from Austria. All individuals were whole-genome genotyped on the Illumina Global Screening Array and files are provided in plink2 format (pgen / pvar / psam files). Provided phenotypes are sex, year of birth, age and Age Related Multiple Sclerosis Severity (ARMSS) score.

  Dataset EGAD00010002487

• Paired-end RNA-seq analysis of the 3D evolution of glioma cell populations. Part 1.

  Dataset includes 160 double-stranded RNAseq libraries collected from 16 patients with adult diffuse glioma. The majority of these samples were spatially-mapped during sample collection, enabling the genomic information derived from them to be mapped in 3D space.

  Dataset EGAD00001005222

• 1000IBD.eQTL.study.release.eQTLsummary&GeneTable

  eQTLsummary&GeneTable from eQTL study in 299 intestinal biopsy samples from IBD

  Dataset EGAD00001006789

• Whole Exome sequencing data from Shwachman-Diamond syndrome bone marrow samples

  This dataset includes paired WES from bone marrow samples of patients with SDS and paired bone marrow-derived fibroblasts as a germline reference. Some patients have multiple samples collected serially over time. There are 74 BAM files included in this dataset.

  Dataset EGAD00001006815

• smRNA-seq of human post-mortem brain data of frontal lobe (Tuebingen part)

  This dataset contains smRNA-seq data from post-mortem human brain tissue of the frontal lobe of patients with FTD and healthy controls. The smRNA-sequencing was done in two parts, this dataset depicts the data generated at the DZNE Tübingen.

  Dataset EGAD00001006846

• RNA-seq cohort of normal weight women

  RNA-seq data of non-tumorous breast tissue. There are 32 samples in this cohort.

  Dataset EGAD00001007073

• Whole genome sequencing identified biomarker of response to PD1 blockade in Natural-killer/T-cell lymphoma

  WGS data of 13 and TCS data of 8 NKTCL patients. Significant association of PD-L1 rearrangements with objective response to anti-PD1 (pembrolizumab).

  Study EGAS00001002420

• WGS of off-target analysis of prime editing in organoids

  Five edited and two unedited organoid clones with one clone prior to editing were paired-end whole genome sequenced using Illumina Novaseq 6000 system. The reads were mapped to hg38 genome assembly and data is provided as BAM files.

  Dataset EGAD00001007744

• Single cell TCR Analysis of regulatory Tcells from blood, fat and skin

  Regulatory Tcells were FACS sorted and processed with 10x Genomics Chromium Next GEM SingleCell V(D)J Reagents Kits v1.1 sequencing. In total 17 samples were processed. Fastq files are supplied.

  Dataset EGAD00001007661

• Saliva microbiota and STI

  Excess sugar consumption is common among youth and can have adverse health effects. However, the relationship between saliva microbiota and sugar consumption remains sparsely studied. We aimed to explore diversity, composition and functional capacities of saliva microbiota in 11–13-year-old Finnish children with low and high sweet treat consumption.

  Dataset EGAD00001008780

• T cell receptors of pathogenic CD4 T cells isolated by using distinct phenotypic markers in celiac disease

  The dataset contains rearranged TCR‐α and TCR‐β genes of Ttet+/Tpat+, Ttet-/Tpat+ and Ttet-/Tpat- CD4+ cells from gut biopsies (exvivo) or that of T cell clones generated from gut biopsies (invitro) from 12 CeD patients.

  Dataset EGAD00001008098

• scRNA-seq of nonhematopoietic cells in human lymph nodes and lymphoma

  Single-cell count data generated by the Cellranger (10X Genomics).

  Dataset EGAD00001008311

• Mitochondria Optimized 10x data

  Optimized 10x library to increase the coverage of the mitochondrial genome from 3’ 10x gene expression data. See details of the experimental method in the methods section of the manuscript

  Dataset EGAD00001010191

• WES data of primary tumors and metastasis corresponding to three patients

  Fastq files of WES data. Primary tumor and/or metastasic samples of three chRCC patients. DNA libraries were produced using the SureSelect XT HumanAllExon V5 kit (Agilent Technologies), and sequencing was performed in a HiSeq instrument (Illumina) using a 100-bp paired-end mode.

  Dataset EGAD00001010173

• scRNAseq/snucRNAseq of human implantation sites, placenta and decidua

  This dataset is part of a study that aims to provide a spatially resolved single-cell multiomics map of human trophoblast differentiation in early pregnancy. This dataset contains snucRNAseq; from three human implantation sites (between 8 and 12 post-conceptional weeks, PCW) from medical hysterectomies.

  Dataset EGAD00001010037

• Multiomic snRNAseq/snATACseq of human implantation sites, placenta and decidua

  This dataset is part of a study that aims to provide a spatially resolved single-cell multiomics map of human trophoblast differentiation in early pregnancy. This dataset contains 10x multiome snRNA-seq/snATAC-seq from human implantation sites, decidual and placental samples from 8-9 PCW.

  Dataset EGAD00001010038

• 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

• AfricanNeo WGS aDNA Dataset

  This dataset includes WGS data of 12 ancient individuals (97–688 years BP) from Zambia and South Africa, presented in Fortes-Lima et al. Nature 2023. Further details like C14-dates and archaeological descriptions were reported elsewhere (Meyer et al. Azania 2021; Steyn et al. African Archaeological Review 2022).

  Dataset EGAD00001011320

• Sequencing Data of Leukemic Samples

  Sequencing data of leukemic samples included in study. Including WES, WGS and targeted sequencing files from patients at diagnosis, remission and at relapse. The dataset includes samples from 52 pediatric patients, totaling 311 samples.

  Dataset EGAD00001015662

• Single cell mRNA sequencing of primary GBM - SF 10592

  We collected fresh tissue from an untreated GBM (SF10592) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

  Dataset EGAD00001003112

• Single cell mRNA sequencing of primary GBM - SF 10679

  We collected fresh tissue from an untreated GBM (SF10679) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

  Dataset EGAD00001003113

• Single cell mRNA sequencing of primary GBM - SF 10281

  We collected fresh tissue from an untreated GBM (SF10281) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

  Dataset EGAD00001003114

• Whole Genome Sequencing of Mutifocal HCC tisue

  The differentiation of distinct multifocal hepatocellular carcinoma (HCC): multicentric disease vs. intrahepatic metastases, in which the management and prognosis varies substantively, remains problematic. We aim to stratify multifocal HCC and identify novel diagnostic and prognostic biomarkers by performing whole genome and transcriptome sequencing, as part of a multi-omics strategy.

  Dataset EGAD00001003348

• The British Autozygosity Populations BioResource

  This data set contains whole exome sequences of individuals with self-stated parental relatedness from the East London Genes & Health cohort. Rare frequency functional variants in these healthy individuals will be studied with respect to the genetic health of the participants and loss-of-function analysis of human genes.

  Dataset EGAD00001003215

• Whole-genome, whole-exome and transcriptome sequencing of pancreatic ductal adenocarcinomas from young adults (NCT MASTER)

  Whole-genome, whole-exome and transcriptome sequencing of pancreatic ductal adenocarcinomas from young adults reveals recurrent NRG1-fusions in KRAS wild-type tumors.

  Dataset EGAD00001004068

• 16S sequencing from feces

  Sequencing of V4 hypervariable region of 16S gene of microbiota present in feces of IBD patients

  Dataset EGAD00001003935

• 16S sequencing of intestinal biopsies

  Sequencing of V4 hypervariable region of 16S gene from microbiota present in intestinal biopsies of IBD patients

  Dataset EGAD00001003936

• Whole genome shotgun sequencing and somatic mutations data in Hepatocellular carcinoma

  There are 88 paired samples from HCC patients including tumors and matched adjacent normal tissues which were sequencing by Illumina HiSeq 2000 platform.

  Dataset EGAD00001003760

• Sequencing data of primary uveal melanomas and their matched metastases

  We performed targeted DNA sequencing of primary uveal melanomas and their matched metastases from 35 patients, analyzing a total of 124 tissues. Sequencing was performed on an Illumina HiSeq 2500 instrument using a panel of 538 genes commonly involved in cancer. 124 BAM files were generated.

  Dataset EGAD00001004453

• FFPE CPA Accreditation Study

  FFPE CPA accreditation of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using targeted pulldown capture prior to Illumina sequencing.

  Dataset EGAD00001000678

• A comprehensive characterisation and analysis of human breast cancers through whole-genome sequencing

  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.

  Dataset EGAD00001002740

• WGS of human colorectal cancer organoid exposed to genotoxic pks+ E. coli

  Organoid cultures were exposed to two different E.Coli strains and a dye control with three biological duplicates. Their original culture was harvested as a control. In total 10 organoid cultures were whole-genome sequenced using the Novaseq6000 platforms. The data is deposited as .bam format.

  Dataset EGAD00001005416

• WGS from PDAC samples

  Bam files from WGS of PDAC samples used in the PCSI mismatch repair study

  Dataset EGAD00001006262

• WGS paired B-Cell lymphoma cells sorted according to CD48

  paired WGS data of one tumor of one patient with nodal B-cell lymphoma. Tumor cells were sorted according to CD48 expression in a high and low fraction. Library preparation with TruSeq Nano and sequencing on Hiseq XTen.

  Dataset EGAD00001006058

• Single cell RNAseq of PBMC from bladder cancer patients

  This dataset contains single cell RNA sequencing data of PBMC samples from 20 bladder cancer patients. cDNAs and single cell RNA libraries were prepared following manufacturer’s user guide (10x Genomics). Each library was sequenced in HiSeq4000 (Illumina) to achieve ~300 million reads following manufacturer’s sequencing specification.

  Dataset EGAD00001006182

• Single-Nuclei RNA-seq of healthy (post-mortem) and temporal lobe epilepsy (biopsy) subjects.

  To identify dysfunctional neuronal subtypes underlying seizure activity in the human brain, we have performed single-nucleus transcriptomics analysis of >110,000 neuronal transcriptomes derived from temporal cortex samples of multiple temporal lobe epilepsy and non-epileptic subjects.

  Dataset EGAD00001006575

• Structural variant analysis of homologous recombination-deficient genomes

  Homologous recombination (HR) deficiency causes DNA breaks and cytogenetic aberrations. Paradoxically, the types of DNA rearrangements specifically associated with HR-deficient cancers only minimally impact chromosomal structure. Addressing this, we combined a genome graph analysis of short-read whole genome sequencing (WGS) profiles across thousands of tumors with deep linked-read (LR) WGS of 46 BRCA1 or BRCA2 mutant breast cancers to discover a distinct class of HR deficiency-enriched rearrangements called reciprocal pairs. LR WGS showed that reciprocal pairs with identical rearrangement orientations gave rise to one of two distinct chromosomal outcomes, distinguishable only with long molecule data. While one (cis) outcome corresponded to the copy and pasting of a small segment to a distant site, a second (trans) outcome was a quasi-balanced translocation or multi-megabase inversion with substantial (10kb) duplications at each junction. The full spectrum of reciprocal pair outcomes could be explained by an HR-independent replication restart repair mechanism. LR WGS additionally identified single-strand annealing (SSA) as a BRCA2-deficiency specific repair pathway in human cancers. Replication restart- and SSA-associated SVs improved BRCA1- vs. BRCA2- deficiency classification and identified metastatic cancer cases with favorable chemotherapy responses. Our data reveal classes of BRCA1- and BRCA2-deficiency specific rearrangements as drivers of cytogenetic aberrations in HR deficient cells.

  Study EGAS00001007186

• Dataset for neuroendocrine_adrenal_tumor-RNA

  Rare cancer sequencing data of 145 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008862

• DAC of "Gene expression adaptation of metastases to their host tissue"

  The DAC consists of Prof. Axel Hillmer, University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany, e-mail: ahillmer@uni-koeln.de and Prof. Andreas Beyer, University of Cologne, Faculty of Mathematics and Natural Sciences, Cologne Excellence Cluster for Aging and Aging-Associated Diseases (CECAD), Cologne, Germany, e-mail: andreas.beyer@uni-koeln.de

  Dac EGAC50000000514

• Scalable ultra-high-throughput multiplexed single-cell chromatin and RNA profiling reveals gene regulatory dynamics during stimulation time courses and CRISPR perturbation screens

  Data for 1) hiPSC-derived macrophages across a polarization time course from the naive M0-state to the M1- and M2-states, 2) Primary T-cells differentiated to helper subtypes, and 3) spontaneous differentiation of hiPSCs upon perturbation of GATA2, NR4A2 or SOX17

  Dac EGAC50000000485

• Single-cell RNA-sequencing for peripheral blood mononuclear cells and plasma proteomics data from COVID-19 patients and healthy controls of Japanese

  We performed single-cell RNA-sequencing of peripheral blood mononuclear cells and measured plasma protein expression from COVID-19 patients and healthy controls.

  Study JGAS000783

• WTCCC case-control study for T1D and RA - combined cases

  WTCCC genome-wide case-control association study using two disease collections together with the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000013

• Integrated whole-genome and transcriptome sequencing reveals divergent evolutionary processes across biliary tract cancer subtypes (WGS data from biliary tract cancer molecular subtype study)

  WGS data for biliary tract cancer samples (Consensus molecular subtypes define distinct evolutionary trajectories of biliary tract cancers). The dataset includes tumour bam files sequenced on Illumina HiSeq/NovaSeq and aligned against GRCh38 (n=97 tumour normal pairs)

  Dataset EGAD50000002530