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• Amplicon sequencing of long non-coding RNA associated with gastritis and gastric carcinogenesis

  This study aimed to identify dysregulations of long non-coding RNA (lncRNA) in gastric cancer, and to reveal molecular functions of lncRNAs associated with gastritis and gastric carcinogenesis. We also aimed to reveal the correlation between clinicopathological characteristics and lncRNA alterations. To this end, we will try to develop predictive markers of gastric cancer risk, which enables prevention and early detection of gastric cancer. We will also try to develop molecular markers which enable us to select treatment strategies for gastric cancer.

  Study JGAS000353

• Childhood B-cell acute lymphoblastic leukemia genomic and transcriptomic data

  The aim of the two studies was: 1) to genetically characterise childhood leukemia patients that lacked established cytogenetic abnormalities (termed B-other leukemia) and assess the clinical features of recurrent genetic abnormalities. 2) Assess the accuracy of whole genome sequencing as a diagnostic genetic test in childhood leukemia, relative to other traditional methods (karyotyping, FISH, MLPA) and whole transcriptome sequencing. As a result, this study includes targeted DNA-sequencing, whole genome sequencing and whole transcriptome sequencing data on childhood leukemia patients enrolled on UK clinical trials (UKALL2003 and UKALL2011).

  Study EGAS00001006863

• The Oral Mycobiome and Risk of Pancreatic Cancer

  The purpose of our study was to assess the influence of oral microbiota on the development of pancreatic cancer. Our preliminary case-control studies showed that oral carriage of a periodontal pathogen is related to increased risk for pancreatic cancer. We hypothesize that the oral bacteria and fungi are associated with risk of pancreatic cancer. We conducted a prospective study nested in two large well-established U.S. cohorts to determine whether the oral bacterial and fungal microbiome is associated with subsequent risk of pancreatic cancer.

  Study phs003994

• IgM heavy chain V(D)J library sequencing using varied PCR parameters

  When amplifying the rearranged V(D)J genes encoding antigen receptors during adaptive immune receptor repertoire sequencing (AIRR-seq), each cycle of the PCR can produce spurious “chimeric” hybrids of two or more different template sequences. To test the effects of PCR protocol variation on chimera formation in AIRR-seq, we produced IgM heavy chain V(D)J repertoire libraries under 8 conditions, varying the number of PCR cycles, indexing PCR template, input RNA, and extension time. Three donors were sequenced using all 8 conditions.

  Study EGAS50000001037

• Gene expression data of 2D duodenum organoids with or without continuous flow

  We developed a monolayer culture system for small intestinal organoids, and then placed the culture plate on a rotator to generate a constant flow in the overlay medium. This mechanical stimulation facilitated the formation of villus-like structures from the monolayer of small intestinal organoids. We analyzed gene expression of 2D normal duodenum organoids with or without medium rotation. Total RNA was extracted from organoids with or without a four-day medium rotation, and after 0, 1, 2 or 4 days of medium rotation, and sequenced with HiSeq X Ten (Illumina).

  Study JGAS000256

• NIBIT-EPI-MESO study samples

  Multi-omics analysis of pre-immuno checkpoint inhibitors (ICI) therapy lesions from 91 pleural mesothelioma (PM) patients enrolled in the multicenter NIBIT-EPI-MESO study. Neoplastic lesions were characterized using multiple molecular platforms, including RNA sequencing (n=82), Whole Exome Sequencing (WES) (n=87), Reduced Representation Bisulfite Sequencing (RRBS) (n=83) and cell-free methylated immunoprecipitation sequencing (cfMeDIP-seq) (n=18). Tumor samples were collected during the standard diagnostic pleuroscopy or thoracoscopy before ICI therapy. Matched Peripheral Blood Mononuclear Cells (PBMC) were collected from PM patients before ICI therapy.

  Study EGAS50000001478

• Contribution of specific cell types to the development of Barrett’s esophagus and carcinoma via germline genetic risk

  This study was designed to elucidate how individual cell types in Barrett’s esophagus (BE) and esophageal adenocarcinoma (EAC) contribute to disease development via germline genetic risk. We performed single cell RNA-sequencing (scRNA-seq) of BE, EAC and paired normal esophagus and gastric fundus tissue samples. After analyzing individual cell types, we integrated the scRNA-seq data and data of a genome-wide association study (GWAS) on BE/EAC to determine cell type-specific genetic risk. Raw data from the RNA-sequencing is provided here.

  Study EGAS50000000530

• WES of Mino-VEN-R Mantle Cell Lymphoma Cells

  This project investigates the genetic basis of therapy resistance in mantle cell lymphoma (MCL) using whole exome sequencing (WES) of the Mino_VEN_R cell line, a model of resistance to pirtobrutinib, a non-covalent BTK inhibitor. Our study suggested that drug-tolerant persister (DTP) cells evade therapy through metabolic and phenotypic reprogramming. By analyzing the exome profile of resistant cells, this study aims to identify mutations associated with treatment escape and cellular plasticity. The findings will contribute to a better understanding of resistance mechanisms and support the development of more effective therapeutic strategies.

  Study EGAS50000001088

• Whole-genome sequencing of cell-free DNA from pancreatic and breast cancer cohorts for fragmentomic and tumor fraction analysis

  This project provides whole-genome sequencing data from cell-free DNA collected from patients with pancreatic ductal adenocarcinoma and breast cancer, alongside healthy and benign controls. The study aims to identify novel liquid biopsy biomarkers by exploring the relationship between per-base quality scores and fragmentomic signals like end-motifs and fragment length. Furthermore, the data supports the development of Bayesian deep learning frameworks for the uncertainty-aware estimation of tumor fraction and ploidy in low-concentration clinical samples.

  Study EGAS50000001620

• Whole-genome methylation profiling of menstrual stem cells identifies novel biomarkers for endometriosis

  Endometriosis, despite its high prevalence, is underdiagnosed and poorly managed due to lack of clinically validated biomarkers and pathophysiological insight. Menstrual bloodderived stem cells (MenSCs) have been implicated in disease pathogenesis, but their diagnostic potential remains unexplored. We conducted a clinical study (n=42; 19 endometriosis, 23 controls) to assess whether DNA methylation profiles of freshly isolated MenSCs can identify disease-specific biomarkers. Whole-genome methylation sequencing revealed differentially methylated regions (DMRs) enriched in genes linked to hallmarks of endometriosis (e.g., inflammation, tissue remodelling, development). These DMRs robustly distinguished cases from controls, independent of technical and clinical variables. Machine learning models trained and validated on these DMRs achieved high diagnostic performance (specificity 83%, sensitivity 79%). Integration with an independent single-cell RNA sequencing dataset showed that the DMRs may modulate gene expression, further supporting their biological relevance. These findings position MenSC DNA methylation profiling as a promising, non-invasive approach for early endometriosis diagnosis and personalised care.

  Dataset EGAD50000002353

• Single-nucleus RNA-seq of human fetal liver hematopoiesis

  The fetal liver is the primary haematopoietic organ during early human development, yet the timing and regulatory mechanisms governing blood formation remain incompletely understood. To define the cellular, transcriptional, and epigenetic changes underlying human fetal liver hematopoiesis over development, we generated a high-resolution, time-resolved single-nucleus multiome atlas of human fetal liver spanning 5–18 post-conception weeks (PCW) for CD45+CD235- cells. In total, 308,021 high-quality nuclei from 53 donors were profiled using paired chromatin accessibility and transcriptomic modalities. This study is for the gene expression.

  Study EGAS50000001631

• Single-nucleus ATAC-seq of human fetal liver hematopoiesis

  The fetal liver is the primary haematopoietic organ during early human development, yet the timing and regulatory mechanisms governing blood formation remain incompletely understood. To define the cellular, transcriptional, and epigenetic changes underlying human fetal liver hematopoiesis over development, we generated a high-resolution, time-resolved single-nucleus multiome atlas of human fetal liver spanning 5–18 post-conception weeks (PCW) for CD45+CD235- cells. In total, 308,021 high-quality nuclei from 53 donors were profiled using paired chromatin accessibility and transcriptomic modalities. This study is for the chromatin accessibility.

  Study EGAS50000001632

• Comparing sequencing of four proto-typical Burkitt lymphomas (BL) with IG-MYC translocation.

  By whole-genome, exome, transcriptome and methylome sequencing of four proto-typical Burkitt lymphomas (BL) with IG-MYC translocation we identified seven recurrently mutated genes including ID3. In an extended cohort, 36/53 (68%) molecularly-defined BL carried potentially damaging mutations of ID3 which were enriched at somatic hypermutation motifs. Only 6/47 (13%) other IG-MYC-positive B-cell lymphomas carried ID3 mutations suggesting cooperation of ID3 inactivation and IG-MYC translocation to be a hallmark of Burkitt lymphomagenesis.

  Study EGAS00001000271

• Whole Genome Sequences of 18th century African descended individuals from Charleston, South Carolina.

  This study presents Whole Genome Sequencing results from the Anson Street African Burial Ground Project, which is a community-based initiative aimed at understanding the histories of 37 Ancestors found during construction in Charleston, South Carolina. Here we report fastq files for all 37 Ancestors. DNA was extracted at the University of Tennessee-Knoxville following Dabney et al. 2013, and dual index libraries prepared using a modified NEBNext Ultra II kit with partial USER enzyme digestion. Libraries were then enriched for human genomic DNA (MyBaits) and sequenced on Illumina Platforms.

  Study EGAS00001006693

• Acute_Lymphoblastic_Leukemia_Exome_sequencing_2_

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 50 Acute Lymphoblastic Leukemia samples and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 100 exome libraries and mapped build 37 of the human reference genome to facilitate the identification of novel cancer genes. In addition, 500bp, NO_PCR total genomic libraries will be prepared from the same samples and five lanes of Illumina GA sequencing will be analysed to characterise genome wide, somatically acquired structural variation.

  Study EGAS00001000200

• Single cell RNA-sequencing (scRNA-seq) of the human hematopoietic stem cell compartment (CD34+CD38-CD45RA-)

  To identify a trajectory of human hematopoietic stem cell (HSC) activation single cell gene expression profiling of RNA from human HSC was performed by flow cytometry-based single cell deposition of CD34+CD38—CD45RA—cells from G-CSF-mobilized peripheral blood from 3 individual donors and 1 bone marrow donor in concert with single cell index-sorting (signals indexed: CD34, CD38, CD45RA, CD90, CD49f) and followed by SMARTseq2 based protocol. We show that INKA1 and CDK6/PAK4 expressing single cells segregate across alternative states of quiescence.

  Study EGAS00001004769

• Genomic and Epigenomic Features of Primary and Recurrent Hepatocellular Carcinomas

  Intratumor heterogeneity and divergent clonal lineages within and among primary and recurrent hepatocellular carcinomas (HCCs) produce challenges to patient management. We investigated genetic and epigenetic variations within liver tumors, among hepatic lesions, and between primary and relapsing tumors. We performed whole-genome, whole-exome, or targeted capture sequencing analyses HCC specimens collected from multiple tumor regions and matched initial and recurrent tumors to obtain a systematic evaluation of intra- and intertumor genetic heterogeneity in HCC samples and to identify genetic changes associated with tumor progression and recurrence.

  Study EGAS00001002094

• Analysis of copy number variation landscape of glioma by shallow coverage whole genome sequencing

  We reported shallow coverage whole genome sequencing (WGS) is an economic method for identification of whole genome somatic copy number variation (SCNV). Combining with a Taqman low density array (TLDA) designed for molecular subtyping of glioma, it enabled classification of glioma into biological entities with different cellular origin and genomic alterations. Further, we also showed shallow-coverage WGS enabled systematic identification of clonal and subclonal SCNV in glioma genomes and the burden and pattern of SCNV can serve as an objective marker of tumor progression and predict risk and relapse.

  Study EGAS00001003690

• Acute_Lymphoblastic_Leukemia_Exome_sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 50 Acute Lymphoblastic Leukemia samples and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 100 exome libraries and mapped build 37 of the human reference genome to facilitate the identification of novel cancer genes. In addition, 500bp, NO_PCR total genomic libraries will be prepared from the same samples and five lanes of Illumina GA sequencing will be analysed to characterise genome wide, somatically acquired structural variation.

  Study EGAS00001000201

• Identification of fusion transcripts by RNA-sequencing and Whole genome sequencing of a METABRIC patient sample

  Fusion transcripts and their exact breakpoints were identified in RNA-seq data (30X) of an ER-,HER2+ breast cancer. DNA-level breakpoints associated with the fusion events were determined by analyzing whole genome sequencing (WGS) data (30X) from the same donor. The RNA-seq and WGS data for this case were generated on the Illumina platform using standard protocols. The patient (MB-0152) derives from the METABRIC cohort for which array based copy number and gene expression data were previously described (EGAS00000000083).

  Study EGAS00001002475

• Myeloproliferative_Disorder_Sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 50 myeloproliferative disorder samples and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 100 exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. In addition, 500bp, NO_PCR total genomic libraries will be prepared from the same samples and five lanes of Illumina GA sequencing will be analysed to characterise genome wide, somatically acquired structural variation.

  Study EGAS00001000198

• Myelodysplastic_syndrome_whole_genomes

  Wholegenome libraries will be prepared from at least two serial samples reflecting different stages of disease progression and matched constitutional DNA for 30 Myelodysplastic syndrome patient samples. Five lanes of Illumina HiSeq sequencing will be performed on each of the tumour samples and four lanes for each of the constitutional DNA. Sequencing data will mapped to build 37 of the human reference genome and analysis will be performed to characterize the spectrum of somatic variation present in these samples including single base pair mutations, insertions, deletions as well as larger structural variants and genomic rearrangements.

  Study EGAS00001000291

• Myeloproliferative_Disorder_Sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 50 myeloproliferative disorder samples and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 100 exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. In addition, 500bp, NO_PCR total genomic libraries will be prepared from the same samples and five lanes of Illumina GA sequencing will be analysed to characterise genome wide, somatically acquired structural variation.

  Study EGAS00001000199

• iNeuron_ChIPseq

  Characterisation of the chromatin status of induced neurons (iNeurons) generated by overexpression of the Ngn2 transcription factor transgenically in BOB iPS cells at the excitatory cortical neuron and iPSC stages. The aim is to understand the differentiation trajectory and characterise the chromatin status so that we can understand the impact of chromatin on gene expression during this transition. 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/

  Study EGAS00001003165

• Integrative_Oncogenomics_of_multiple_myeloma

  We used targeted capture and massively parallel sequencing of exomes of CD138 purified plasma cells and matched somatic DNA from 53 patients with Multiple Myeloma. 2281 variants were validated by 454 sequencing. The present study will validate an additional 5538 variants by targeted pull-down and sequencing. The normal and tumor samples will be indexed separately and pre-pooled in groups of 10 or 11. The sequence capture will use 5 reactions each for the normals and tumors. All normal samples will then be pooled and go thorugh one lane of HiSeq. Same for the tumors.

  Study EGAS00001000243

• Finding structural variation from the patient-derived xenografts of pediatric T-cell leukemia at the single-cell level

  In this study, we aimed to identify somatic structural variation of T-cell acute lymphoblastic leukemias (T-ALLs_ from patient-derived xenografts (PDX) at the single-cell level. For this purpose, we performed strand-specific single-cell sequencing of PDX-derived T-ALL relapse samples from two juvenile patients (P1, P33). To validate structural variation detected via scTRIP, we profiled whole exome sequencing (WES) data from P33 (samples taken during initial disease, remission, relapse), and mate-pair sequencing data from P1 (relapse).

  Study EGAS00001003365

• Acute_Lymphoblastic_Leukemia_Sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 50 Acute Lymphoblastic Leukemia samples and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 100 exome libraries and mapped build 37 of the human reference genome to facilitate the identification of novel cancer genes. In addition, 500bp, NO_PCR total genomic libraries will be prepared from the same samples and five lanes of Illumina GA sequencing will be analysed to characterise genome wide, somatically acquired structural variation.

  Study EGAS00001000058

• RNA-seq data from 121 tumor samples with muscle invasive bladder cancer.

  In this study, a total of 300 patients with MIBC receiving chemotherapy were included; 62 received NAC before cystectomy and 245 received first-line chemotherapy upon detection of locally-advanced (T4b) or metastatic disease. Treatment response, defined as pathological downstaging (< pTa,CIS,N0) after NAC or complete or partial response after first-line treatment (RECIST criteria). RNA-seq was performed using the QuantSeq kit FWD HT kit (Lexogen) using 500 ng input RNA from 121 tumor samples. Data provided here consist of 780 fastq files for RNA-seq.

  Study EGAS00001004505

• Myeloproliferative_Disease_Whole_Genomes

  Wholegenome libraries will be prepared from at least two serial samples reflecting different stages of disease progression and matched constitutional DNA for 30 Myeloproliferative Disease samples. Five lanes of Illumina HiSeq sequencing will be performed on each of the tumour samples and four lanes for each of the constitutional DNA. Sequencing data will mapped to build 37 of the human reference genome and analysis will be performed to characterize the spectrum of somatic variation present in these samples including single base pair mutations, insertions, deletions as well as larger structural variants and genomic rearrangements.

  Study EGAS00001000290

• FinHer_Breast_Cancer_Study

  The purpose of this study is to sequence 500 known cancer genes in 960 newly diagnosed high risk breast cancer patients treated with current standard of care therapies and trastuzumab, for somatic alteration and copy number changes. We will be using next gen sequencing technology to determine the prognostic relevance of these somatic genetic alterations and of teh low frequency events to determine if they are associated with trastuzumab benefit or HER2 positive breast cancer, i.e. treatment interaction. The samples will be analysed adn correlated with clinical variables including outcome.

  Study EGAS00001000648

• A single-cell atlas of human glioma

  Although tumor-propagating cells can be derived from glioblastomas (GBMs) of the proneural and mesenchymal subtypes, a glioma stem-like cell (GSC) of the classical subtype has not been identified. It is unclear if mesenchymal GSCs (mGSCs) and/or proneural GSCs (pGSCs) alone are sufficient to generate the spectrum of cellular heterogeneity observed in GBM. This study sheds light on a long-standing debate regarding lineage relationships among GSCs.

  Study EGAS00001003845

• Biological insights from the whole genome sequences of human embryonic stem cell lines

  Human embryonic stem cells (hESCs) are a powerful tool for the study of human development and can form the basis of cellular disease models or therapies. However, the genetic make-up and stability of hESCs has not been systematically studied at a genome-wide level with single nucleotide resolution. We therefore sequenced the whole genome and whole exomes of widely available hESC. This online resource will enable investigators to access raw sequencing data in order to interrogate cell lines for different disease- and trait-associated genetic variants.

  Study EGAS00001002400

• Identification_of_immune_mechanisms_associated_with_the_high_rate_of_relapse_in_patient_with_visceral_leishmaniasis_and_HIV_co_infection

  RNA-seq transcriptomics of whole blood samples from longitudinal follow-up of a cohort of visceral leishmaniasis (VL) patients with and without HIV coinfection, from active disease through apparent cure and potential relapse. Analysis will identify potential correlates of relapse to identify immune mechanisms underlying the high rate of relapse in HIV/VL coinfection. 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/

  Study EGAS00001003465

• RNA-sequencing of gluten-reactive and non-reactive T-cells from blood samples of treated CeD patients during a gluten-challenge

  Gluten-specific CD4+ T cells are drivers of celiac disease (CeD). Here we aimed to characterize such cells in blood of treated CeD patients during gluten challenge with comparison to similar cells of untreated disease. Treated CeD patients underwent a 3-day gluten-challenge with blood sampling at baseline and day 6 (d6). Blood cells were stained with HLA-DQ:gluten tetramers (Tetramer). CD4+, gut-homing Tetramer+ and Tetramer- effector-memory T (TEM) cells at d6 were subjected to bulk RNA-seq (n=7).

  Study EGAS00001004988

• WES data from 165 tumor/germline samples with muscle invasive bladder cancer.

  In this study, a total of 300 patients with MIBC receiving chemotherapy were included; 62 received NAC before cystectomy and 245 received first-line chemotherapy upon detection of locally-advanced (T4b) or metastatic disease. Treatment response, defined as pathological downstaging (< pTa,CIS,N0) after NAC or complete or partial response after first-line treatment (RECIST criteria). WES was performed using DNA from 165 tumors (76x median coverage) and associated germline DNA (46x median coverage). Data provided here consist of 5,828 fastq files for WES.

  Study EGAS00001004507

• Genomics of pediatric myeloid neoplasms

  Genomic profiling of pediatric myeloid tumors (AML, therapy-related myeloid neoplasms, MDS and others) has shown significant differences when compared adult myeloid neoplasms. This includes the recognition of pediatric-enriched entities including UBTF-TD and NUP98 rearranged leukemias. Collectively we have described over 23 unique molecular subtypes of pediatric AML with unique expression signatures, driver mutations, patterns of cooperating mutations and distinct outcomes. Some of the subtypes (KMT2A and NUP98, for example) have remarkable heterogeneity in fusions partners, cellular phenotypes and molecular signatures.

  Study EGAS00001005760

• scRNA-seq data of BALF and blood cells from COPD and control

  Chronic obstructive pulmonary disease (COPD) is ranked the third leading cause of death worldwide and hence constitutes a significant burden, both medically and financially. To date, the cellular mechanism underlying COPD is poorly understood and thus no effective therapy is currently available. To broaden the current knowledge of the immune landscape in the alveolar space, we performed scRNA-Seq of CD45-enriched bronchoalveolar lavage fluid (BALF) cells and isolated blood leukocytes obtained from COPD patients and healthy controls using both the Seq-Well and the Chromium (10x Genomics) technology.

  Study EGAS00001004369

• Whole genome sequencing based on short and long reads from GM09237 cell line with and without folate depletion

  To asess changes in the DNA-sequence occurring as a result of folate deprivation, DNA extracted from the GM09237 cell line grown with and without folate was sequenced using short read and long read sequencing. The DNA was extracted from cells cultured with either normal medium or medium with no folic acid for 5 days, and then sequenced by BGI PE100 platform (100 bp paired-end sequencing 60x coverage; performed by BGI), or PacBio Sequel system (SMARTbell; performed by BGI) respectively.

  Study EGAS00001005345

• A transcriptome atlas of human skeletal muscles

  We generated a large transcriptome atlas of human skeletal muscles by collecting biopsies from 6 different muscles to determine molecular signatures that may be distinct between leg muscles. The biopsies were collected from gracilis (GR), semitendinosus (ST), vastus lateralis (VL), vastus medialis (VM), rectus femoris (RF), and gastrocnemius lateralis (GL) muscles. We also investigated molecular differences within the muscle by including two biopsies from the middle and distal sides of the semitendinosus muscle (STM and STD, respectively). In total, 128 samples from 20 individuals (aged 25 ± 3.6 yr) were analyzed.

  Study EGAS00001005904

• Genomic History of the Solomon Islands

  The aim of this study was to provide for a better understanding of the genetic relationships among and between populations of Near and Remote Oceania, with a focus on the initial settlement of the Solomon Islands and their role in the first dispersal of people from Near into Remote Oceania. Irina Pugach, Ana T Duggan, D Andrew Merriwether, Françoise R Friedlaender, Jonathan S Friedlaender, Mark Stoneking, "The Gateway from Near into Remote Oceania: New Insights from Genome-Wide Data", Molecular Biology and Evolution, Volume 35, Issue 4, April 2018, Pages 871–886

  Study EGAS00001006116

• Multi-region whole-exome sequencing of 10 neuroblastoma cases

  To investigate intratumour heterogeneity and to better understand tumour evolution in neuroblastoma, we have performed a multi-region whole-exome sequencing on a total of 51 spatially separated tumor samples from 9 primary neuroblastomas (2 low-risk, 1 intermediate-risk and 6 high-risk) and 1 relapsed neuroblastoma. We also assessed the impact of chemotherapy on the clonal expansion by sequencing tumour regions from one medium risk and one high-risk tumour for which we had matched samples obtained at diagnosis and after chemotherapy.

  Study EGAS00001004735

• Gene_regulation_of_human_CD4__Treg_cells_

  This dataset maps gene expression regulation in human primary regulatory CD4+ T cells (Tregs). It includes whole genome sequence data for ChM-seq (118 H3K4me3, 118 H3K27ac and 6 inputs), ATAC-seq (114 samples) and whole transcriptome (141 samples). All individuals were genotyped (130 samples) using coreExome Illumina SNP chip array. The final quality filtered set included 123 individuals with RNA-seq data, 73 with ATAC-seq, 91 with H3K27ac ChM-seq and 88 with H3K4me3 ChM-seq data. A total of 62 individuals had QCed data for all the assays.

  Study EGAS00001003516

• Placebo-only arm transcriptomic analysis of the phase 3 PROTECT clinical trial

  It is poorly understood how the tumor immune microenvironment influences disease recurrence in localized clear cell renal cell carcinoma (ccRCC). Here we perform whole-transcriptomic profiling of 236 tumors from patients assigned to the placebo-only arm of a randomized, adjuvant clinical trial for high-risk localized ccRCC. Unbiased pathway analysis identifies myeloid-derived interleukin-6 (IL-6) as a key mediator. Furthermore, a novel myeloid gene signature strongly correlates with disease recurrence and overall survival on uni- and multivariate analysis and is linked to TP53 inactivation across multiple datasets.

  Study EGAS00001006344

• Single-cell RNA and ATAC sequencing data analysis of human postmenopausal fallopian tube and ovary

  In this study, we used a combination of technologies, including Drop-seq, 10X single-cell RNA-seq (scRNA-seq), and single-cell assay on transposase accessible chromatin (scATAC-seq) to generate  a high-quality cell atlas that consists of four tissue sites from the reproductive tract of postmenopausal women. This atlas, by far the most comprehensive map of the postmenopausal female reproductive system to date, will pave the way to a better understanding of the pathophysiology of many diseases affecting older women.

  Study EGAS00001006780

• FASTQ files of the polyA+ (oligo-dT) RNA-Seq dataset from the POPS SGA (Small for Gestational Age) samples and their matched controls.

  FASTQ files of the polyA+ (oligo-dT) RNA-Seq dataset from the POPS SGA (Small for Gestational Age) samples and their matched controls. The POP study placental biopsies were collected within 30 minutes of birth and flash frozen in RNAlater (ThermoFisher). For each biopsy, total placental RNA was extracted from approximately 5 mg of tissue using the “mirVana miRNA Isolation Kit” (Ambion) followed by DNase treatment (“DNA-free DNA Removal Kit”, Ambion). RNA quality was assessed with the Agilent Bioanalyzer and all the samples with RIN values ≥ 7.0 were used in the downstream experiments. RNA-libraries were prepared from 1g of total placental RNA with the TruSeq Stranded mRNA Library Prep Kit (Illumina) which captures polyA-tailed transcripts by oligo-dT beads, then pooled and sequenced (single-end, 50bp) using a Single End V4 cluster kit and Illumina HiSeq2500

  Dataset EGAD00001006304

• Precise reconstruction of the tumor microenvironment using bulk RNA-seq and a unique machine learning-based algorithm trained on artificial transcriptomes

  Cellular deconvolution algorithms virtually reconstruct tissue composition by analyzing the gene expression of complex tissues. Here, we present the decision tree machine learning algorithm, Kassandra, trained on a broad collection of > 9,400 tissue and blood sorted cell RNA profiles to accurately reconstruct the tumor microenvironment (TME). Bioinformatic correction for technical and biological variability, aberrant cancer cell expression inclusion, and the accurate quantification and normalization of transcript expression increased the stability and robustness of Kassandra. Performance was validated on over 4,000 H&E tissue slides and more than 1,000 normal and tumor tissues by comparison with cytometric, immunohistochemical or single-cell RNA-seq measurements. Kassandra accurately deconvolved stromal and immune elements of blood and tumors, revealing the role of the TME in tumor pathogenesis. Digital TME reconstruction revealed that the presence of PD1-positive CD8+ T cells strongly correlated with immunotherapy response and increased the predictive potential of established biomarkers, indicating that Kassandra could potentially be utilized in future clinical applications.

  Dataset EGAD00001008776

• RNAseq of circulating monocytes of familial hypercholesterolaemia (FH) patients before and after treatment, and healthy controls.

  RNAseq of circulating monocytes of familial hypercholesterolaemia (FH) patients before and after treatment, and healthy controls. Please cite original paper: Monocyte and macrophage lipid accumulation results in downregulated type-I interferon responses. Willemsen et al. Frontiers in Cardiovascular Medicine (2022) Familial hypercholesterolemic patients (n=10) and healthy subjects (n=9): the study population, design, and further processing of these human study subjects and their samples have been extensively described (Stiekema et al., 2021). Briefly, untreated FH patients who indicated to start lipid-lowering therapy (statin, PCSK9 antibody, and/or ezetimibe) according to their treating physician were included. The healthy controls were age, sex, and body mass index (BMI) matched with the FH patients. After inclusion, FH patients fasted for at least 9 hours before blood samples were drawn for lipid measurements and monocyte isolation. This was repeated after 12 weeks of lipid-lowering therapy. RNA-seq was performed on circulating monocytes. V1 = visit 1. V2 = visit 2.

  Dataset EGAD00001008967

• Myeloid-specific KDM6B inhibition sensitizes Glioblastoma to PD1 blockade

  This data set include FASTQ files for five experiments: Human scRNA-Seq data (6 samples), Human Visium spatial transcriptomic data (3 samples), Mouse scRNA-seq data (4 samples), Mouse scATAC-seq data (2 samples), Mouse ChIP-seq data (8 samples). For the mouse scATAC-seq data (2 samples), there are originally three FASTQ files, R1, R2 and R3 files. The R1 and R2 FASTQ files were merged into one larger file ("R1R2") per sample for submission as paired-end sequencing setting to follow the EGA guidelines. They can be split into individual R1 and R2 files in order to be processed by Cell Ranger software. The files with IC1 suffix are CHIP-seq Input control for anti-KDM6B antibody pull down experiments and the files with IC2 suffix are CHIP-seq Input control for anti-H3K27ME3 antibody pull down experiments in murine model.

  Dataset EGAD00001010073

• DRIP-seq data for Molecular Characterization of ETMRs

  This dataset contains DRIP-seq data from 2 patients. DNA–RNA hybrids were extracted from tissue derived from ETMR patient-derived xenograft (PDX) models (BT183) that were treated using topotecan or saline as described previously27. Tumours were subsequently frozen and pelleted using ultracentrifugation. DNA–RNA hybrids were extracted as described previously using the same protocol that is applied for cultured cells21. DNA was extracted using proteinase K followed by phenol–chloroform extraction and ethanol precipitation. Subsequently the DNA was fragmented using the restriction enzymes HindIII, EcoRI, BsrGI, XbaI and SspI (New England Biolabs). Digested DNA was subsequently incubated with the anti-DNA–RNA hybrid anti- body S9.6 (Merck, MABE1095) and immunoprecipitated using agarose beads. Bound DNA–RNA hybrids were eluted and incubated with pro- teinase K and cleaned with an additional phenol–chloroform–ethanol extraction. The DNA was subsequently sonicated and sequenced using a Hiseq 2000 machine with a 50-bp single-read protocol. Each treat- ment condition was performed in duplicate and both RNase H and the input was included as negative controls resulting in 10 Fastq files.

  Dataset EGAD00001006219

• A developmental cell atlas of the human thyroid gland - WGS

  The thyroid gland produces hormones essential for health from embryogenesis to adulthood. Thyroid disorders, including congenital hypothyroidism and thyroid carcinoma, are prevalent and pose significant health challenges. Congenital hypothyroidism often results from thyroid dysgenesis or impaired hormone synthesis, is particularly prevalent in trisomy 21 (T21), while thyroid carcinoma is the most frequent endocrine malignancy, affecting both paediatric and adult populations. Understanding the molecular basis of these conditions requires deeper insights into fetal thyroid development. We generated a spatiotemporal atlas of the human thyroid during early pregnancy, revealing key cell types, including hormone-producing thyrocytes. Thyroid follicular cells are heterogeneous, with two functional cell states (fTFC1, fTFC2) that persist into adulthood, with fTFC2 characterised by elevated PAX8 expression. We demonstrated that T21 thyroids displayed dysgenesis with disrupted follicular morphology, and altered extracellular matrix interactions, and that the fTFC2 signature was enriched in paediatric papillary thyroid cancer compared to adults. These findings uncover thyrocyte heterogeneity across the lifespan, advancing understanding of thyroid development and disease.

  Dataset EGAD00001015447

• Co-amplification of MYC and CCNE1 in aggressive childhood osteosarcoma

  Osteosarcoma, the most common primary malignant tumour of bone, affects children and adults alike. No fundamental biological differences between paediatric and adult osteosarcoma are known. Here, we apply multi-region whole genome sequencing to an index case of a four-year old child whose aggressive tumour harboured high level, focal amplifications of MYC and CCNE1 connected by translocations. We re-analysed copy number readouts of 258 cases of high-grade osteosarcoma from three different cohorts and identified an additional three cases with MYC and CCNE1 co-amplification, confined to children and associated with aggressive disease. Examining the age distribution of MYC and CCNE1 amplicons across all cases revealed a significant enrichment of focal MYC amplification in children, whereas CCNE1 amplification is not strictly restricted to children. Our findings indicate that amplification of the MYC oncogene, known to be associated with a poor outcome, delineates a variant of osteosarcoma specific to childhood. When co-amplified with CCNE1, it may herald an aggressive disease course.

  Dataset EGAD00001006859

• Tagged-amplicon deep sequencing

  This dataset contains a collection of tumour samples from high grade serous ovarian carcinoma patients with recurrent disease collected near the point of diagnosis as well as tumour samples collected after patient relapse upon or some time after study entry. Whole blood samples were also collected from patients at study entry for the purpose of germline variant detection. The majority of diagnosis samples were preserved in neutral buffered formalin whereas the majority of post-relapse samples were preserved in universal molecular fixative (UMFIX, Sakura Finetek USA, Inc). DNA was extracted and the tagged-amplicon deep sequencing assay was applied (TAm-Seq, Forshew et al. 2002, Sci Transl Med) with the aid of fluidigm access array technology. Targeted loci were sequenced at very high depths (typically >100X) for the detection of both somatic and germline variants. Sequenced reads were aligned to the GRCh37 reference genome (release hs37d5).

  Dataset EGAD00001011058

• Genomics of acral lentiginous melanoma

  Melanoma is the most aggressive type of skin cancer, causing about 75% of dermatological cancer deaths. Acral lentiginous melanoma (ALM) is the most common subtype of melanoma in admixed Latin American populations, but very few tumour genomes and exomes, all from European-descent individuals, have been analysed across several studies. Because of this, the genomic landscape of ALM is mostly unknown. Our aim in this project is to define this landscape and identify driver somatic alterations by whole-exome sequencing a collection of ALM germline/tumour paired FFPE samples from the National Cancer Institute of Mexico. . This dataset contains all the data available for this study on 2023-03-09.

  Dataset EGAD00001010126

• NEOPREDICT-Lung: longitudinal whole exome sequencing of non-small cell lung cancers under immunotherapy

  In 43 patients pretreatment tumor biopsies, resected tumors and normal tissue of sufficient quality and quantity were obtained to longitudinally explore the mutational profiles of a comprehensive set of cancer-related genes. For tumor samples, one to four FFPE sections (10 µm thickness, number depending on sample size) were lysed for genomic DNA isolation. Isolation was performed semi-automatically on the Maxwell purification system (Maxwell RSC DNA FFPE Kit, AS1450, Promega) as specified by the manufacturer. DNA was eluted in 50 µl RNase-free water and quantified fluorescently for library preparation using a Qubit 2.0 fluorometer (Life Technology) with its appertaining DNA broad-range assay. Corresponding normal DNA was isolated from blood or PBMCs using routinely available QIAGEN technology. DNA was stored at -20°C before use. Whole-exome sequencing (WES) was performed using the Twist Human Core + RefSeq + Mitochondrial Panel (Twist Bioscience), and 2 x 100 bp fragment sizes were sequenced using a NovaSeq6000 (Illumina). Demultiplexing of sequenced reads was achieved using bcl2fastq (version 2.2).

  Dataset EGAD00001015362

• The scRNA dataset for TIGIT in MCL with CART

  We collected longitudinal samples from 15 patients with MCL at various clinical time points before and after CAT-T therapy brexucabtagene autoleucel (BA) infusion. The patients were grouped into three categories based on their clinical responses after BA treatment: 1) responsive (n = 9), 2) relapsed (n = 5), and 3) refractory (n = 1). All patients in category #1 and #2 had initially attained a complete response (CR) after BA therapy. The responsive group maintained CR with no relapse at the time of last follow up, while the relapsed group achieved initial CR but eventually relapsed. The 10x Chromium™ Single-Cell 5′ Reagent Kit v2 (PN-1000190, 10x GENOMICS) and Chromium Single-Cell Human TCR amplification Kit (PN-1000252, 10x GENOMICS) were used to perform single-cell separation, cDNA amplification, and library construction for gene expression and TCR repertoire following the manufacturer’s guidelines. Thirty-nine samples passed quality control and underwent single-cell transcriptome profiling with simultaneous single-cell T-cell receptor (TCR) repertoire analysis.

  Dataset EGAD00001010180

• RNA sequencing in primary inflammatory (TPP) macrophages following deletion of a disease-associated gene desert at chr21q22, disruption of ETS2, or treatment of ETS2-edited macrophages with a HIF1α stabiliser.

  This dataset comprises raw RNA sequencing data (FASTQs) from primary inflammatory (TPP) macrophages that were unedited (non-targeting control, NTC), edited to delete the disease-associated chr21q22 enhancer region (n=5), or edited to disrupt ETS2 with 1 of 2 independent gRNAs (n=9). We also performed RNA-sequencing in NTC or ETS2-edited TPP macrophages that were treated for 12 hours with vehicle (DMSO) or roxadustat (30 uM, n=3). Macrophages were detached using Accutase and lysed. RNA was extracted from cell lysates using an AllPrep DNA/RNA Mini Kit (Qiagen). Sequencing libraries were prepared from 10ng RNA using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara) following the manufacturer’s instructions. The quality and molarity of all libraries was assessed using a BioAnalyzer 2100 and the libraries were sequenced on a NextSeq500. Raw data are provided as 50 bp paired-end Illumina reads.

  Dataset EGAD00001011338

• A developmental cell atlas of the human thyroid gland - RNA

  The thyroid gland produces hormones essential for health from embryogenesis to adulthood. Thyroid disorders, including congenital hypothyroidism and thyroid carcinoma, are prevalent and pose significant health challenges. Congenital hypothyroidism often results from thyroid dysgenesis or impaired hormone synthesis, is particularly prevalent in trisomy 21 (T21), while thyroid carcinoma is the most frequent endocrine malignancy, affecting both paediatric and adult populations. Understanding the molecular basis of these conditions requires deeper insights into fetal thyroid development. We generated a spatiotemporal atlas of the human thyroid during early pregnancy, revealing key cell types, including hormone-producing thyrocytes. Thyroid follicular cells are heterogeneous, with two functional cell states (fTFC1, fTFC2) that persist into adulthood, with fTFC2 characterised by elevated PAX8 expression. We demonstrated that T21 thyroids displayed dysgenesis with disrupted follicular morphology, and altered extracellular matrix interactions, and that the fTFC2 signature was enriched in paediatric papillary thyroid cancer compared to adults. These findings uncover thyrocyte heterogeneity across the lifespan, advancing understanding of thyroid development and disease.

  Dataset EGAD00001015448

• Whole-genome sequence data for The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer

  Each tumor sample was cut into three pieces, yielding two end-pieces for cryovials and a middle portion placed in 10% buffered formalin. End pieces were homogenized manually and with a paddle blender (Stomacher). All paraffin-embedded blocks, including formalin-fixed tumor samples and molecular-fixed fallopian tubes, were sectioned and stained with hematoxylin and eosin prior to expert histopathological review to confirm the presence of high grade serous carcinoma. Homogenized end pieces were then flash frozen and later used for WGS. For all tumor and matched normal (peripheral blood) samples, DNA was extracted with the Qiagen AllPrep DNA/RNA kit (tumor samples from patients 25,26,28-32) or the Qiagen Blood and Tissue Extraction Kit (tumor samples from patients 1-4,7,9-17, and all blood samples). For all tumor and normal samples, DNA extraction was followed by library construction and sequencing using Illumina HiSeq2500 whole genome shotgun v4 chemistry with paired-end 125bp reads.

  Dataset EGAD00001003984

• Mechanisms of patient response to Dabrafenib in Melanoma

  Samples will be from the BRF113683 (BREAK-3) study which is a Phase III Randomized, Open-label Study Comparing GSK2118436 to Dacarbazine (DTIC) in Previously Untreated Subjects With BRAF Mutation Positive Advanced (Stage III) or Metastatic (Stage IV) Melanoma (n=250 enrolled)*NGS [Agilent capture (Sanger V2 panel): 360 genes and 20 gene fusions; Illumina HiSEQ Sequencing]*CNV: [via NGS or Affy SNP 6.0 or Illumina Omni (TBD)]Bioinformatics: Analysis will be performed using core Sanger informatics pipelines similar to those previously described (Papaemmanuil E et al. (2013) Blood. 22:3616 -3627). Briefly, copy number analysis will be performed using the ASCAT algorithm, and base substitutions, small insertions and deletions using the CAVEMAN and Pindel algorithms, respectively. Statistical approaches including generalized linear models will be used to predict clinical variables such as maximum clinical response and duration of response using genetic data. Sanger and EBI to conduct analysis; Raw data and correlation with clinical endpoints to be analyzed by both EBI/Sanger and GSK (unique pipeline analyses to increase call confidence)

  Dataset EGAD00001001375

• Direct transcriptional consequences of somatic mutation in breast cancer

  The disordered transcriptomes of cancer encompass direct effects of somatic mutation on transcription; co-ordinated secondary alterations in transcriptional pathways; and increased transcriptional noise. To catalogue the rules governing how somatic mutation Overall, 59% of 6980 exonic substitutions were expressed. Compared to other classes, nonsense mutations showed lower expression levels than expected with patterns characteristic of nonsense-mediated decay. 14% of 4234 genomic rearrangements caused transcriptional abnormalities, including exon skips, exon reusage, fusion transcripts and premature poly-adenylation. We found productive, stable transcription from sense-to-antisense gene fusions and gene-to-intergenic rearrangements, suggesting that these mutation classes may drive more transcriptional disruption than previously suspected. Systematic integration of transcriptome with genome data therefore reveals the rules by which transcriptional machinery interprets somatic mutation.

  Dataset EGAD00001002237

• Whole Genome sequencing of Angolan and Mozambican individuals

  To support the continued discovery and cataloguing of genomic variation in human populations and to further our understanding of the Bantu Expansion, we sequenced the genomes of 291 individuals from Cabinda, a northern exclave of Angola, and 49 individuals from Maputo, the capital of Mozambique. Utilising the power and flexibility of these whole-genome sequencing datasets, we discover rare variation, fine-scale population structure, and perform analyses using haplotype-based inference tools and our own model-based simulation framework to reconstruct complex dispersals of Bantu speak-ing populations across sub-Saharan Africa.

  Study EGAS00001007458

• EGAD00010000766

  We have established a mechanism for the collection of postal DNA samples from consenting National Joint Registry for England and Wales (NJR) patients and have carried out genotyping genome-wide in 903 patients with the condition Developmental Dysplasia of the Hip (DDH) on the Illumina CoreExome array

  Dataset EGAD00010000766

• Tcells_CD_scRNAseq

  This set features unfiltered, aligned, UMI-based single cell RNA sequencing count data for 5290 Blood, intraepithelial ileum (IEL) and lamina propria ileum (LPL) T cells from Crohn's disease patients as published in Uniken Venema et al, Gastroenterology 2019

  Dataset EGAD00010001649

• Whole-exome sequencing and microRNA profiling predicted relapse risk of stage I lung adenocarcinomas for the study and all the datasets.

  This dataset contains CEL files and rma normalized expression value for microarray of stage I lung adenocarcinomas from Asian patients. In total, there are 69 patients and 138 samples, including 69 tumor samples and 69 adjacent normal samples.

  Dataset EGAD00010001901

• methylation_bc_buccal

  Raw methylation data from buccal samples in individuals with breast cancer.

  Dataset EGAD00010002082

• methylation_ctrl_buccal

  Raw methylation data from cervical samples in controls.

  Dataset EGAD00010002080

• methylation_ctrl_cervix

  Raw methylation data from cervical samples in controls.

  Dataset EGAD00010002079

• ChIP-seq ERa in primary breast cancer tissues

  ChIP-seq has been perfomed on 5 tumor fresh-frozen primary breast cancer tissues from female patients. Immunoprecipitation has been performed for ERa (SC-543, Santa Cruz). Raw single-end fastq data have been aligned using bwa-mem using Hg19 genome assebly as reference. Unfiltered aligment bam files are provided.

  Dataset EGAD50000000014

• Single-cell RNA-sequencing of peritoneal fluid from patients with achalasia

  The data published here contains single-cell RNA-sequencing (scRNAseq) data as obtained using the 3' scRNAseq using Chromium Single Cell 3’ Reagent from 10X Genomics on peritoneal fluid (PF) from patients with achalasia. Sequencing was performed in a paired-ended fashion on the NovaSeq6000.

  Dataset EGAD50000000251

• University of Bergen Rare Monogenic Autoimmune Syndrome (APS-1) Data Access Committee

  This is the DAC appointed by the University of Bergen for the datasets related to the study of APS-1 in the Department of Clinical Sciences . These data are from single cell transcriptomic analysis of expanded Tregs from patients with the rare monogenic autoimmune syndrome “APS-1” compared to healthy donors.

  Dac EGAC50000000081

• Exome sequencing for heterogeneity and evolution of DNA mutation rates

  Dataset comprising 27 pairs of high-depth (300x) WES results obtained from 54 PDXs derived from primary CRCs resected synchronously with their corresponding metastases. These exoms sequences are part of a larger study on the heterogeneity and evolution of DNA mutation rates in microsatellite-stable colorectal cancer.

  Dataset EGAD50000000208

• Whole exome sequencing of preneoplasia lung adenocarcinoma

  Multi-region exome sequencing of 271 pulmonary nodules and matched adjacent lung tissue including lung preneoplasia atypical adenomatous hyperplasia (AAH, N=49), adenocarcinoma in situ (AIS, N=42), minimally invasive adenocarcinoma (MIA, N=37), invasive lung adenocarcinoma (ADC, N=86) and adjacent lung tissues (Normal, N=57).

  Dataset EGAD50000000397

• Tumor heterogeneity and immune-evasive microenvironment in T follicular helper cell lymphomas

  Single-cell analysis data for tumor and immune cells from lymph node and peripheral blood samples of 14 patients with T follicular helper cell lymphomas

  Study EGAS50000000275

• 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

• ctDNA diva aggregate data

  ctDNA biomarker and relevant clinical data for divarasib phase I GO42144 study, including tumor type, KRAS G12C mutation detectability in plasma at baseline, baseline SLD, sites of metastasis, lines of therapy, best response, confirmed best response, PFS, ctDNA tumor fraction and KRAS G12C VAF at baseline/C1D15/C3D1.

  Dataset EGAD50000000454

• IMSGC and MultipleMS project MS patients from Germany, Mainz

  Genotype and phenotype data on 301 MS patients from Germany, Mainz. 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 EGAD00010002484

• IMSGC and MultipleMS project MS patients from Italy, OSR

  Genotype and phenotype data on 538 MS patients from Italy, OSR. 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 EGAD00010002486

• IMSGC and MultipleMS project MS patients from Germany, TUM

  Genotype and phenotype data on 683 MS patients from Germany, TUM. 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 EGAD00010002489

• IMSGC and MultipleMS project MS patients from Italy, Piedmont

  Genotype and phenotype data on 1067 MS patients from Italy, Piedmont. 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 EGAD00010002490

• ERa ChIP-seq in breast healthy, primary cancer and metastatic tissues

  ChIP-seq has been perfomed on fresh-frozen tissue derived from healthy breast (HB), primary breast cancer (PB), BCa-derived liver metastasis (LM). Immunoprecipitation has been performed for ERa (sc-542, SantaCruz). Raw paired-end fastq.gz files are provided for both immunoprecipitated DNA and input samples.

  Dataset EGAD50000000642

• Prognostic whole-genome and transcriptome signatures in colorectal cancers

  This dataset consists of RNA-seq CRAM raw-data files of 1063 primary colorectal cancer and 120 adjacent normal tissue samples. The expression profiles for these samples can be found at the ArrayExpress with accession number E-MTAB-12862.

  Dataset EGAD50000000169

• Test dataset from FEGA Spain

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  Dataset EGAD50000000786

• 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

• 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

• Targeted deep sequencing data of 386 T-ALL patients

  Targeted deep sequencing data of 386 T-ALL patients in several high-risk T-ALL genes. Samples were prepared according to Agilent's HaloPlex HS Target Enrichment Protocol and sequenced as 75bp paired-end reads. Data is available as paired-end FASTQ files for each sample.

  Dataset EGAD50000001168

• 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

• 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

• 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

• Immunophenotype data for a subset of NSCLC cases in OAK

  The investigators would like to correlate NGS data from OAK to immunophenotype designation performed manually based on a panCK/CD8 immunohistochemistry stain for a subset of squamous cell carcinomas.

  Dataset EGAD50000001253

• CHIP panel sequencing of rheumatoid arthritis patients

  Targeted NGS sequencing data (bam and index files aligned to hg38) a total of 573 newly diagnosed, untreated RA patients and 163 healthy controls. The sequencing panel included 65 genes recurrently mutated in myeloid malignancies, to capture clonal hematopoiesis of indeterminate potential (CHIP) mutations. The median target coverage was 1700x across samples.

  Dataset EGAD50000001300

• Cell-free DNA methylation profiling of sepsis patients

  This data set contains paired-end NGS files (in FASTQ format) generated from a methylation profiling experiment of cell-free DNA derived from the plasma of sepsis patients and healthy controls. Methylation profiling was performed using the TET-assisted pyridine borane sequencing (TAPS) protocol.

  Dataset EGAD50000001505

• Targeted DNA sequence

  Targeted DNA sequencing files that were used in our study. The cohort was composed of 36 cases of tumor-only targeted DNA sequencing data. All files are UMI processed. The panel is designed with Agilent Sure Select and the sequence was performed using DNBSEQ sequencer.

  Dataset EGAD50000000972

• 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

• 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

• 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

• WES dataset used for the study "Longitudinal Multi-Omics Study Reveals Molecular Drivers and Tumor Microenvironment in Extramedullary Multiple Myeloma"

  This dataset contains 72 paired fastq files of raw Whole exome sequencing data from 14 patients with Extramedullary myeloma, 8 paired samples from the same patients at the time of Newly diagnosed myeloma, and the corresponding normal samples

  Dataset EGAD50000000052

• 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