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• Paired-end Whole Exome-seq analysis of the Hypermutation and Malignant Progression in Low-grade Glioma Patients

  113 DNA samples were derived from the tumors of the low grade glioma patients and sequenced using Illumina WES (exome seq) paired-end technology. Dataset contains 113 BAM files aligned to hg19 using BWA v.0.5.9. After mapping duplicated reads were removed, reads were re-aligned around InDels and read base quality score was re-calibrated.

  Dataset EGAD00001005386

• RNA-sequencing from duodenal bipsies of Celiac disease patients

  Total RNA was extracted from the PaxFPE biopsy specimens (n = 116)

  Study EGAS50000000337

• Genomic profiling of two pathogenic germline truncating variants of BRCA2 confer different haploinsufficiency phenotype

  Observation of the loss of heterozygosity of BRCA2

  Study EGAS50000000613

• Haemoglobin_E_beta_thalassaemia_in_a_patient_group_from_Sri_Lanka

  Exome sequencing of 32 patient samples from Sri Lanka with the condition haemoglobin E beta thalassaemia

  Study EGAS00001000626

• MIBS MGS

  Metagenomic sequencing of the human gut in Maastricht IBS studies, cases and controls.

  Study EGAS00001001924

• RNA-seq of human embryonic heart, lung, and cerebellum

  Characterization of cell types in the human embronic heart, lung, and cerebellum.

  Study EGAS00001004375

• BAM files ChIP-Seq

  Data from the paper Context-specific Effects of TGFβ/SMAD3 in Cancer Are Modulated by the Epigenome. Tufegdzic et al, Cell Reports 2015

  Dataset EGAD00001001669

• First in vivo investigation of the impact of PARP inhibition with rucaparib alone and in combination with atezolizumab: results of the phase Ib COUPLET clinical study in advanced gynecologic and triple-negative breast cancers

  Study EGAS00001006100

• Molecular landscape of C1498 cells

  We characterized the genomic background of C1498 cells by whole genome sequencing analysis.

  Study EGAS50000001284

• Whole Genome Sequencing of Insulinomas

  Whole Genome Sequencing of Insulinomas and paired blood controls from the same patients.

  Study EGAS50000000321

• Tumor Profiler AML Study

  Multi-omics data generated from 22 samples from the Tumor Profiler AML cohort

  Study EGAS50000000577

• Targeted_EMSeq___Development

  Development of a targeted methylation assay to determine the cell-type composition of a sample.

  Study EGAS00001007202

• Clinical Implications of Genomic Alterations in the Tumour and Circulation of Pancreatic Cancer Patients

  Clinical Implications of Genomic Alterations in the Tumour and Circulation of Pancreatic Cancer Patients

  Dataset EGAD00001001421

• Finnish - THL Psychiatric Family Collection Dataset

  The dataset encompasses 172 Runs from the WGSPD Project 3 - Genomic Strategies to Identify High-impact Psychiatric Risk Variants Project

  Dataset EGAD00001009315

• Tagomics Ltd

  The Tagomics Ltd Data Access Committee manages controlled access to datasets generated by Tagomics Ltd. The DAC evaluates applications to ensure that proposed research complies with participant consent, ethical approvals, and institutional policies.

  Dac EGAC50000000727

• MSI_Cancer_Models___RNAseq

  The study will use RNAseq to aid in define determinants of WRN dependency in MSI Cell lines.

  Study EGAS00001004180

• Single cell RNAseq of PDAC organoids

  To study the role of WNT7B, three organoid lines were sequenced using SORT-Seq

  Study EGAS50000001544

• Ni_Vanuatu_Omni2.5

  Blood DNA samples from 1,433 contemporary ni-Vanuatu were genotyped on the Illumina Infinium Omni 2.5-8 array. Genotype calling was performed using the Illumina GenomeStudio software.

  Dataset EGAD00010002344

• The landscape of cancer genes and mutational processes in breast cancer

  The landscape of cancer genes and mutational processes in breast cancer

  Dataset EGAD00001000133

• Epigenetic Intratumor Heterogeneity and Clonal Evolution in Aggressive Prostate Cancer

  Our study investigated the spatial epigenome variation within 5 aggressive prostate adenocarcinomas.

  Study EGAS00001000682

• Pilot_Fetal_Cell_Atlas_RNAseq

  As part of the Human Cell Atlas we will study fetal tissue.

  Study EGAS00001002553

• 15x_WGS_HELIC_MANOLIS_

  15x whole genome sequencing in samples from the Cretan Greek isolate collection HELIC MANOLIS

  Study EGAS00001001207

• H3K27me3-mediated epigenetic repression regulates neuroblastoma development and contributes to biological heterogeneity

  Characterization of the H3K27me3 repressive landscape in neuroblastoma tumor samples.

  Study EGAS00001008225

• Genetics of male infertility in India

  The study comprises of whole exome and genome files of infertile males of Indian origin.

  Study EGAS00001008171

• Targeted deep sequencing of somatic mutations

  We used targeted deep sequencing to accurately establish the allele frequencies of the mutations identified by exome sequencing

  Dataset EGAD00001000763

• WES from two human osteosarcoma with two samples each from the corresponding cell line

  WES from two human osteosarcoma with two samples each from the corresponding cell line, BAM files

  Dataset EGAD00001005370

• WGS data set used in the study, 2 samples

  WGS data set used in the study, 2 samples

  Dataset EGAD00001007966

• HLA Genotypes

  Imputed HLA alleles and variation. Imputation was carried out using the Multi-Ethnic HLA reference panel (version 1.0 2021) available on the Michigan imputation server

  Dataset EGAD00001009965

• Bulk RNA sequencing data of high-grade serous ovarian cancer samples (set 18-19)

  The dataset contains RNA sequencing data of 66 high-grade serous carcinoma (HGSC) patients sequenced with Novoseq 6000. The 155 samples are fresh frozen tissue samples that have been collected from different tissues and time points before and during treatment. The files provided are paired fastq files.

  Dataset EGAD50000002370

• RNASeq profiles from Indian HFrEF Cohort

  The dataset contains whole transcriptomics profiling from a cohort of 49 HFrEF patients. The myocardium samples were collected from these patients during heart transplant of LVAD implantation procedure. The RNA samples were collected in RNAlater. Total transcriptome libraries were prepared using TruSeq Stranded Total RNA Library Prep with Ribo-Zero Gold kit and sequenced on Illumina HiSeq4000.

  Dataset EGAD50000001196

• Targeted DNA sequencing of 44 urothelial cancer samples from 34 Lynch syndrome patients

  Targeted Illumina sequencing of 41 tumor tissue samples and 3 urine tumor DNA samples from 34 patients with Lynch syndrome associated urothelial cancer. Target capture was performed using the UroScout hybridization capture panel targeting the coding regions of 25 urothelial cancer genes. Sequencing libraries were constructed using the Twist Biosciences Enzymatic Fragmentation DNA Library Prep kit. Sequencing was performed using an Illumina NovaSeq 6000 instrument with 2x150 bp paired sequencing.

  Dataset EGAD50000001220

• Whole Genome DNA Methylation MPI

  Whole Genome Bisulfite Sequencing on normal primary human uveal melanocytes. WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, Catalog No. 30024), the EZ DNA Methylation-Gold Kit (Zymo, D5005) and DNA Clean & Concentrator-5 (Zymo, D4013), following the instruction manual Accel-NGS® Methyl-Seq DNA Library (Revision 160510). Paired-end libraries (2 × 150 bp) were sequenced on a NovaSeq 6000 instrument.

  Dataset EGAD50000001139

• Whole Genome DNA Methylation

  Whole Genome Bisulfite Sequencing on normal primary human uveal melanocytes. WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences 30024), the EZ DNA Methylation-Gold Kit (Zymo D5005), and DNA Clean & Concentrator-5 (Zymo D4013), following the instruction manual Accel-NGS Methyl-Seq DNA Library (Revision 160510). Paired-end (2 x 150 bp) libraries were sequenced on a DNBSEQ-T7 instrument (MGI) after library conversion.

  Dataset EGAD50000000766

• WGS of low-count and high-count MBL

  The cohort consisted of individuals with low-count MBL, high-count MBL as well as patients with CLL. Whole genome sequencing was initially performed in a smaller cohort of selected, representative samples, while targeted re-sequencing of CLL putative driver genes was performed in all samples of the cohort. Besides CLL cell samples, the sequencing process was performed in paired control samples including both buccal and polymorphonuclear cell samples.

  Dataset EGAD50000000629

• Bulk RNAseq of cultured fibroblasts

  Fastq files from bulk RNAseq of fibroblasts after culture and facs sorting (N=9). Sorted FAP+ CAF cells RNAs were extracted using Qiagen miRNeasy Kit (Qiagen, #217004) according to the manufacturer's instructions. Verification of RNA integrity and quality was performed using the Agilent RNA 6000 nano Kit (Agilent Technologies, #5067-1511). cDNA libraries were prepared using the TruSeq Stranded mRNA Kit (Illumina, #20020594) followed by sequencing on NovaSeq (Illumina).

  Dataset EGAD50000000323

• Whole genome sequencing data of high-grade serous ovarian cancer samples (set 12)

  The dataset contains whole genome sequencing data of 17 high-grade serous carcinoma (HGSC) patients sequenced with Novoseq 6000. The 46 samples are either fresh frozen tumour samples or blood samples. The files provided are paired fastq files.

  Dataset EGAD50000000441

• Whole genome sequencing data of high-grade serous ovarian cancer samples (set 13)

  The dataset contains whole genome sequencing data of 32 high-grade serous carcinoma (HGSC) patients sequenced with Novoseq 6000. The 82 samples are either fresh frozen tumour samples or blood samples. The files provided are paired fastq files.

  Dataset EGAD50000000442

• RNA sequencing data of pediatric BCR::ABL1 acute lymphoblastic leukemia (set 2)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one BCR::ABL1 ALL patient (ALLT-399). TruSeq Stranded Total RNA Library Prep (Illumina) kit was used in library preparation, and Novogene's internal method was utilized in rRNA removal. The diagnostic tumor sample was sequenced using Illumina Novaseq X Plus, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002580

• RNA sequencing data of pediatric KMT2A-rearranged acute lymphoblastic leukemia (set 2)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one KMT2A-r ALL patient (ALLT-355). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and Ribo-Zero Magnetic Kit (Illumina) was utilized in rRNA removal. The diagnostic tumor sample was sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002583

• RNA sequencing data of pediatric ETV6::RUNX1 acute lymphoblastic leukemia (set 3)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one ETV6::RUNX1 ALL patient (ALLT-397). TruSeq Stranded Total RNA Library Prep (Illumina) kit was used in library preparation, and Novogene's internal method was utilized in rRNA removal. The diagnostic tumor sample was sequenced using Illumina Novaseq X Plus, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002587

• RNA sequencing data of pediatric hyperdiploid acute lymphoblastic leukemia (set 2)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one hyperdiploid ALL patient (ALLT-356). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and Ribo-Zero Magnetic Kit (Illumina) was utilized in rRNA removal. The diagnostic tumor sample was sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002593

• RNA sequencing data of pediatric hyperdiploid acute lymphoblastic leukemia (set 4)

  The dataset includes RNA sequencing FASTQ files from diagnostic tumor samples of three hyperdiploid ALL patients (ALLT-382, ALLT-395, ALLK-111). TruSeq Stranded Total RNA Library Prep (Illumina) kit was used in library preparation, and Novogene's internal method was utilized in rRNA removal. The diagnostic tumor samples were sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb per sample.

  Dataset EGAD50000002596

• RNA sequencing data of pediatric B-other acute lymphoblastic leukemia (set 2)

  The dataset includes RNA sequencing FASTQ files from diagnostic tumor samples of three B-other ALL patients (ALLT-357, ALLT-361, ALLK-108). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and Ribo-Zero Magnetic Kit (Illumina) was utilized in rRNA removal. The diagnostic tumor samples were sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002597

• RNA sequencing data of pediatric B-other acute lymphoblastic leukemia (set 5)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one B-other ALL patient (ALLT-396). TruSeq Stranded Total RNA Library Prep (Illumina) kit was used in library preparation, and Novogene's internal method was utilized in rRNA removal. The diagnostic tumor sample was sequenced using Illumina Novaseq X Plus, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002601

• The Asian Diversity Project: genotyping of 37 Asian populations and ethnic groups

  The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection.

  Study EGAS00001002100

• Overactivation of the IGF signalling pathway in osteosarcoma

  Tumour samples (low coverage WGS) from 35 patients with osteosarcoma were included. All samples were re-evaluated by an experienced bone pathologist who confirmed the diagnosis and a tumour content >50% per sample. All tumours represented conventional high-grade osteosarcomas.

  Study EGAS00001004767

• Single RNA-Seq of CD11b Beads selected tumor associated macrophages (TAMs) of 3 gliomablastoma patients treated with small molecule inhibitors

  Single RNA-Seq of CD11b Beads selected tumor associated macrophages (TAMs) of 3 gliomablastoma patients treated with small molecule inhibitors. The sequencing was done on HiSeq 4000 with the SmarTer Ultra Low Input RNA v4 and NEBNext ChIP-Seq Kit. The TAMs were treated with GW2580, BLZ945 and PLX3397 and DMSO as control.

  Dataset EGAD00001011273

• Longitudinal shotgun metagenomes of preterm infant fecal samples from the NutriBrain trial

  Metagenomic sequencing data generated from 438 fecal samples collected from preterm infants enrolled in the NutriBrain clinical trial, a study investigating the impact of early-life nutrition on gut microbiome development and neurodevelopmental outcomes.The dataset includes raw sequencing files generated on on Illumina NovaSeq 6000. Data files are provided in standard FASTQ format and support investigation of gut microbial composition and functional potential during early neonatal development.

  Dataset EGAD50000002667

• Single-cell Multi-omics Sequencing of Human Early Embryos

  The whole blood of six female volunteers and sperm from one male volunteer were used to extract genomic DNA using a DNeasy Blood & Tissue Kit (QIAGEN). 500 ng gDNA was fragmented into 300 bp by Covaris. Then, the libraries were constructed using a KAPA Hyper Prep Kit (Kapa Biosystems). In total we have 7 samples and the files we uploaded are pair-end fastq files.

  Dataset EGAD00001004108

• GoNL release 5 raw SNV calls

  These files contain a total of 20.4M SNVs and the complete information output by the GATK UnifiedGenotyper v1.4 on all 767 GoNL samples. These calls are not trio-aware and all genotypes were reported regardless of their quality. Both filtered and passing calls are reported in these files. Filtered calls include (1) calls failing our VQSR threshold and (2) calls in the GoNL inaccessible genome.

  Dataset EGAD00001000743

• Methylation profiling by MCC-Seq of visceral fat (N=199) and whole-blood (N=206) derived from IUCPQ participants

  The study includes NGS-based methylC-capture sequencing (MCC-Seq) on 199 visceral adipose tissue and 206 whole-blood DNA samples derived from obese individuals (BMI >40 kg m-2) in the IUCPQ cohort. We generated 100bp paired-end reads using the Illumina HiSeq2000 or 2500 systems.

  Dataset EGAD00001004787

• MiRNome_pituitary_adenoma

  Small RNA (<100 bases in length) were purified from total RNA using miRNeasy kit (Qiagen), then sequenced. Libraries were prepared at the Genomics Platform of the Cochin Institute, following the TruSeq small RNA protocol (Illumina), starting from 1 µg of high quality total RNA. Single read (1 × 75 bp) sequencing was performed on a Nextseq 500 platform (Illumina). FASTQ sequences were aligned on miRBase v.2052, then counted with STAR (v.2.5.2a).

  Dataset EGAD00001004998

• RNA-Seq of response to Tozinameran vaccination in individuals with KTx/dialysis or healthy controls.

  Low-input RNA-Seq (~200 cells per sample) of CD4+ T cells in patients with kidney transplants, dialysis, or healthy controls after the second dose of Tozinameran COVID-19 vaccine. RNA-Seq was performed using the Smart-Seq v4 ultra-low input protocol. The dataset includes 4 healthy control samples, 3 kidney transplant recipients, and 4 patients undergoing dialysis.

  Dataset EGAD00001007689

• low pass WGS of patient from the CN300 cohort

  We copy number profiled 688 tumor regions from 300 patients presenting with advanced prostate cancer and prospectively followed-up (median, 7 years) in the control group of the STAMPEDE trial. Patients were categorised into four metastatic states, namely high-risk non-metastatic (with or without local lymph node involvement) or metastatic (low or high volume).

  Dataset EGAD00001008800

• Paired RNA-Seq of four patients with advanced Parathyroid carcinoma (PC)

  Paired RNA-Seq of four patients with advanced Parathyroid carcinoma (PC). The library was prepared using the Illumina TruSeq stranded mRNA Kit, the sequencing was done either on an Illumina HiSeq 4000 or on Illumina NovaSeq 6000.

  Dataset EGAD00001009730

• EXPRESSION OF ANTIBODY-DRUG CONJUGATE TARGETS IN BREAST CANCER METASTASES AND NORMAL TISSUE

  Using bulk mRNA sequencing, we investigated the expression of 72 ADC targets, which are clinically approved or under investigation, in 909 samples (64 primary untreated, 749 metastatic, 96 normal) from 30 female patients from our post-mortem tissue donation program UPTIDER (NCT04531696). The study explores changes in target expression across multiple samples to identify novel targets of clinical interest and validation

  Study EGAS50000001334

• Molecular and cellular composition changes after neoadjuvant letrozole and palbociclib in early luminal breast cancer

  The NeoPAL trial compared neoadjuvant letrozole-palbociclib (LP) with chemotherapy (CT) in 103 patients with high-risk early luminal breast cancer. Deconvolution of bulk RNA-seq data revealed that myoepithelial cells, normal-like fibroblasts, FOLR2+ macrophages and SELL+ CD4+ T lymphocytes accumulated after treatment (p: 0.046 to 7.2e-07). All changes were similar between the LP and CT arms.

  Study EGAS50000001021

• scRNA-seq data of FOXN1heterozygous patients and cord blood

  Single cell sequencing was performed from sorted CD45+ lymphocytes from two FOXN1het patients and one cord blood sample from frozen cryopreserved samples to undestand the shifts in immune cell populations in pateints with FOXN1 heterozygous deficiency. Each sorted population was labelled individually via multiplexing antibodies with subsequent Abseq staining before pooling and conducting the BD Rhapsody pipeline to generate scRNA-seq data.

  Study EGAS50000001199

• RNA-seq of CRC patient-derived xenograft tumors

  We developed a novel antibody-drug conjugate (ADC), 84-EBET. To analyze mechanism of action of 84-EBET, we obtained bulk RNA-seq data of the patient-derived xenograft (PDX) model derived from colorectal cancer (CRC) patient. The PDX model was treated with 5-fluorouracil + oxaliplatin, 84-EBET or vehicle, and then gene expression changes were analyzed with bulk RNA-seq.

  Study EGAS50000000598

• Renal Cancer Exome Sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 25 renal cancers and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 50 exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Dataset EGAD00001000014

• Familial_Thrombocytosis_germline_exome_sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 3 relatives from a family with multiple affected familial thrombocytosis (FT) patients. Germline DNA from 2-4 patients affected with FT will be used to prepare libraries and sequenced in one lane of HiSeq sequencing, mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Study EGAS00001000088

• 16S rRNA gene amplification and maternal factors

  Human breast milk contains a diverse community of bacteria but factors that produce variation in the breast milk microbiome are largely unknown. We evaluated if 1) maternal factors including breastfeeding practices modified the diversity and abundance of bacterial communities in breast milk and 2) if subclinical mastitis (SCM), an asymptomatic inflammatory condition occurring during lactation, induced a distinctive microbiota signature.

  Study EGAS00001003044

• Whole-exome sequencing of PTC, benign nodule and normal tissues in 28 patients

  In order to comprehensively investigate the genetic relationship between PTC tumors and benign nodules, we totally collected 127 fresh-frozen biopsies samples from 28 patients with concurrent thyroid benign nodule and PTC (n=20) or simple benign nodule (n=8). We carried out whole-exome sequencing on all the 127 biopsies samples and RNA-sequencing in total of 40 samples.

  Study EGAS00001002312

• Analysis of transcriptomic profiles from affected and recovered muscle biopsies from children with reversible infantile respiratory chain deficiency.

  All patients carry mitochondrial mutation m.14674T>C but not must also carry mutations in related genes such as TRMU and EARS2. Analysis compares muslce biopsies of affected patients to controls, a patient after recovery to themselves during the the disease phase, and compared patients with additional EARS2 mutations to patients without pathogenic EARS2 mutations.

  Study EGAS00001004647

• Leeds Melanoma Cohort (LMC) gene expression study

  Array-based profiling (whole genome DASL HT12.4, Illumina Inc) in over 700 FFPE tumour blocks from the population-based Leeds Melanoma cohort recruited in the North of England, with a long follow up. Data used in tumour immune micro-environment investigation (Nsengimana et al 2018, J Clin Invest doi: 10.1172/JCI95351).

  Study EGAS00001002922

• Somatic_mutation_in_skin_epidermis__SMS_

  We aim to assess the range and depth of mutations in genes linked with cancer in skin epidermis surrounding lesions which are undergoing surgical removal. Patient history will be collected to provide a detailed outline of tumour type (including histology), skin type, and sunlight exposure. We will perform ultra-deep targeted sequencing using genes implicated in cancer to try and understand the background of mutations surrounding these lesions

  Study EGAS00001002165

• Single-cell RNA sequencing on single CD45+ immune cells isolated from peripheral blood, lymphnode, ascites, tumour and adjacent normal tissues from six hepatocellular carcinoma patients.

  Single-cell RNA sequencing on single CD45+ immune cells isolated from peripheral blood, lymphnode, ascites, tumour and adjacent normal tissues from six hepatocellular carcinoma patients. The transcriptional properties of these individual cells, were used to delineate the molecular subtypes, lineage, and functional properties of each cell group

  Study EGAS00001003449

• SDH_deficient_renal_tumours___WGS_

  Succinate dehydrogenase (SDH) deficient renal cancers are a rare and understudied subtype of renal cancer. As such they represent an unmet need in kidney cancer research. Here, we seek to describe the genomics and transcriptomics of SDH deficient renal cancers by sequencing five such tumours. We document their mutational burden, define driver mutations, demonstrate typical patterns of structural variants, and estimate the cell of origin and cellular composition.

  Study EGAS00001004102

• The molecular landscape of colorectal cancer reveals genetic mutations - COCA-CN

  We collected tumor samples and adjacent nomal mucosae from 46 patients with colorectal cancer in surgical operation from 2014 to 2016 in the First Affiliated Hospital of Chongqing Medical University (Chongqing, China) and the Research Institute of Surgery, Third Military Medical University (Chongqing, China). the qualified captured library of each sample was then loaded on Illumina HiSeq 2000 (Illumina, San Diego, CA) platforms and subjected to high-throughput sequencing.

  Dataset EGAD00001003304

• Role of cohesin/CTCF in human monocyte differentiation

  Here we study genome architecture in a postmitotic differentiation setting, the differentiation of human blood monocytes (MO). We profiled and compared epigenetic, transcriptome and 3D conformation landscapes during MO differentiation (either into dendritic cells or macrophages) across the genome, with and without siRNA-mediated depletion of RD21 or CTCF, and detected numerous architectural changes, ranging from higher level compartments

  Study EGAS00001005508

• Gene expression profiles of single disseminated breast cancer cells

  A set of 56 EpCAM-positive cells derived from bone marrow aspirates of breast cancer patients or patients without a cancererous disease (30 cells from 21 M0-stage and 11 cells from five M1-stage breast cancer patients, 15 cells from seven non-cancer patients serving as controls). EpCAM-positive cells from breast cancer patients were considered disseminated tumor cells as they harbored copy number alterations and showed high expression of the epithelial marker EpCAM and the mammary luminal progenitor marker KIT in comparison to EpCAM-positive bone marrow cells from non-cancer patients. Paired-end RNA-Sequencing of the samples was performed on Illumina NovaSeq6000, raw data are provided in the Fastq format.

  Dataset EGAD00001006359

• RNA-seq and scRNA/TCR-seq data for publication: "Pharmacological inhibition of nonsense-mediated mRNA decay enhances anti-tumour immunity"

  RNA-seq and scRNA/TCR-seq data from patient-derived fragments (PDFs) analysed in publication by R. Vendramin, H. Fu, S. Fernandez Patel, Y. Zhao et al.

  Study EGAS50000001208

• Bulk 3' mRNA-Sequencing of human ASC-derived kidney tubuloids

  Bulk 3' mRNA-Seq raw files (FASTQ) from human kidney tubuloids derived from 4 separate donors in collagen-based dome culture and suspension culture. Samples were collected for sequencing on day 7 of passage 3, 4, and 5. Total = 24 samples.

  Dataset EGAD50000002335

• Transcriptomics for UPST-SCCHN3 cohort

  Transcriptomics of Tumor samples on UPST-SCCHN3 cohort

  Dataset EGAD50000002179

• Metadata associated with sequencing

  Associated metadata for sequencing data.

  Dataset EGAD50000000528

• BestAgeingMiRNA

  Processed miRNA expression profiles and clinical phenotype data from patients with cardiovascular diseases (dilated cardiomyopathy, acute coronary syndrome, ischemic cardiomyopathy, and coronary artery disease) and healthy controls. MicroRNA expression was assessed using Agilent human miRNA microarrays with RMA normalization and log2 transformation. Dataset includes expression values for all detected case/control miRNAs from miRBase v21, along with clinical metadata including disease status, age, sex, and study center.

  Dataset EGAD00010002788

• FASTQ NGS dataset for EGAS00001001632:New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs

  Dataset EGAD00001001927

• Integrative modeling of tumor genomes and epigenomes for enhanced cancer diagnosis by cell-free DNA.

  3784 whole genome sequencing bam files were generated from plasma cell-free DNA of healthy individuals and patients with cancer. Paired reads were mapped to hg19 human reference genome.

  Study EGAS00001006553

• MethylCap-seq based DNA methylation profiles of 65 glioblastoma and 5 non-tumoral tissues

  Data represent genome-wide DNA methylation profiles obtained by MethylCap-seq (Diagenode’s MethylCap-kit based purification followed by Illumina GAIIx sequencing), for 70 brain tissue samples, including 65 glioblastoma samples and 5 non-tumoral tissues (obtained from epilepsy surgery).

  Dataset EGAD00001001399

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - TLR_pathway_study

  upcoming publication

  Dataset EGAD00001001960

• Sequencing data for oesophageal and related samples - Mourikis et al (RNA)

  Data supporting: "Patient-specific detection of cancer genes reveals recurrently perturbed processes in esophageal adenocarcinoma." Mourikis et al. RNAseq (BAM files) 137 samples

  Dataset EGAD00001004776

• McGill EMC Community projects Release 7 for cell line "SaOS-2"

  Complete reference epigenome (as defined by IHEC) of a SaOS-2 cell line with osteosarcoma.

  Dataset EGAD00001007678

• Sequencing data for oesophageal and related samples - Ng, Contino et al (RNA)

  Data supporting: "Interplay of processes shapes structural variations undergoing selection in oesophageal adenocarcinoma" Ng, Contino et al. RNAseq (BAM files) 214 oesophageal adenocarcinoma samples

  Dataset EGAD00001007809

• Paired healthy & tumor organoid Biobank _B16PON

  Organoid cultures derived from colorectal adenomas. RNA and DNA was isolated from these cultures for genome wide profiling.

  Dataset EGAD00001008949

• Proteomic Characterization of Intrahepatic Cholangiocarcinoma Identifies Risk-Stratifying Subgroups, Proteins Associated with Time-To-Recurrence, and mTOR Effector Molecule EIF4A1 as a Druggable Therapeutic Target

  Using mass spectrometry-based proteomics, we analyzed two independent cohorts comprising 80 and 62 treatment-naive ICC tumors, 67 adjacent non-malignant tissues, and 9 patient-derived xenografts (PDX). In the first cohort, we identifed two subclusters with distinct times-to-recurrence (TTR). A 4-protein classifier trained on our data cohort accurately stratifies these ICC clusters in the Dong et al. dataset (2022) and in our independent second cohort, revealing similar associations between proteomic motifs and clinical outcomes. The Translation regulator EIF4A1 emerges as a therapeutic target, as its inhibition with novel drug eFT226 significantly reduces tumor growth in an ICC PDX model.

  Study EGAS50000001343

• Ashkenazi Jewish Leukoencephalopathy

  Genetic leukoencephalopathies (gLEs) are a group of heterogeneous disorders with white matter abnormalities in the central nervous system (CNS). Patients affected with gLEs have brain white matter defects that can be seen in MRI and exhibit variable neurologic phenotypes including motor impairment, hypotonia, pyramidal dysfunction, dystonia and/or dyskinesias, ataxia, seizures, cortical blindness, optic atrophy, and impaired cognitive development. The exact causes in half of gLEs are unknown. We studied three unrelated families affected with an undiagnosed gLE and discovered a homozygous germline mutation c.2536T>G in VPS11 by whole exome sequencing, a gene involved in membrane trafficking and fusion of the lysosomes and endosomes, as a novel cause of a new gLE syndrome.

  Study EGAS00001001767

• Reference Epigenomes and Regulatory Landscape of CLL

  Analysis of the reference epigenomes and regulatory landscape of CLL as a whole and its major clinico-biological subtypes (with mutated and unmutated IGHV) in the light of the normal B-cell differentiation. We have extensively characterized the reference epigenomes of seven primary chronic lymphocytic leukemia samples (CLLs) with mutated (n=5) and unmutated IGHV (n=2) as well as several mature B-cell subpopulations (naive B cells from blood and tonsil, germinal center B cells, memory B cells and plasma cells from tonsil) using genome-wide maps of six histone marks (H3K4me3, H3K4me1, H3K27ac, H3K36me3, H3K9me3 and H3K27me3), DNA accessibility (ATAC-seq), DNA methylation (whole-genome bisulfite sequencing) and gene expression (RNA-seq). Furthermore, we have mapped the regulatory chromatin landscape of 100 additional CLL cases using chIP-seq of H3K27ac and ATAC-seq and linked these data to additional layers of information (whole-genome and/or whole-exome sequencing (WGS/WES), RNA-seq and DNA methylation microarrays) studied in the context of the International Cancer Genome Consortium (ICGC).

  Dataset EGAD00001004046

• Analysis of the co-occurrence of LOY and CHIP in Alzheimer's disease patients and control individuals using whole-exome sequencing (WES)

  We performed deep whole-exome sequencing of FACS-isolated CD4+ T lymphocytes, NK and myeloid cells from men with AD and controls exhibiting either LOY or retention of Y chromosome (ROY). We found 39 sequence variants in known (canonical) myeloid driver genes of clonal hematopoiesis (MD-CH) and known lymphoid driver genes (LD-CH), and maximally 14 (35%) of these could co-exist with LOY within the same clone. We further describe 192 unknown drivers of clonal hematopoiesis (UD-CH), which were markedly enriched in AD-LOY individuals (odds ratio=4.8, Benjamini-Hochberg-adjusted p=0.041), and over 20% of these variants were protein-truncating. In myeloid cells, the total burden of all detected drivers correlated with the percentage of LOY cells (Spearman ρ=0.52, adjusted p=0.00041).

  Study EGAS00001008234

• Transgenerational transmission of reproductive and metabolic dysfunction in the male progeny of polycystic ovary syndrome

  The transgenerational maternal effects of PCOS in female progeny have been revealed. As there are evidence that a male equivalent of PCOS may exist, we asked whether sons born to mother with PCOS (PCOS-sons) transmit reproductive and metabolic phenotypes to their male progeny. Here, in a Swedish nationwide register-based cohort and a clinical case-control study from Chile we found that PCOS-sons are more often obese and dyslipidemic. Their serum miRNAs are found to potentially regulate PCOS-risk genes. Our prenatal androgenized PCOS-like mouse model with or without diet-induced obesity confirmed that reproductive and metabolic dysfunctions in F1 male offspring are passed down to F3. Small non-coding RNAs (sncRNAs) sequencing of F1-F3 sperm revealed distinct differentially expressed (DE) sncRNAs across generations in the androgenized, obese, and obese and androgenized lineages, respectively. Notably, common targets between transgenerational DEsncRNAs in mouse sperm and in PCOS-sons serum indicate similar effects of maternal hyperandrogenism. These findings strengthen the translational relevance highlighting a previously underappreciated risk of reproductive and metabolic dysfunction via the male germline transmission and potential molecular markers to study in future generations.

  Study EGAS00001007079

• RISE-UP Cohort

  The RISE-UP study contains raw metagenomic sequencing data of Crohn's disease patients. Paired-end sequencing was performed using the Illumina HiSeq 2000 platform.

  Dataset EGAD50000001436

• Transcriptomic characterization of the histopathological growth patterns in breast cancer liver metastases

  20 fastq files of RNA-sequencing of the 2 main histopathological grow patterns observed in liver metastases.

  Dataset EGAD50000000331

• bulk TCR seq

  bulk TCR-seq data IMCISION on the PBMCs of responding patients bulkTCR-seq data generated with the immunoSEQ platform (Adaptive Biotechnologies) on PBMCs of responding patients, pre- and post-treatment.

  Dataset EGAD00010002546

• Angiosarcoma follow up study

  A bespoke targeted pulldown experiment will be performed on patients with Angiosarcoma. the resulting products will be sequenced to determine the prevalence of previously found mutations in these patients.

  Dataset EGAD00001000620

• GWAS study on arsenic-exposed population

  Genetic analysis of women from the Andes Mountains that are exposed to arsenic in drinking water.

  Study EGAS00001001168

• Pulldown_cytosine_deaminases

  We are looking at the causal factors behind hyper-mutator phenotypes found in previous Breast Cancer sequencing studies.

  Study EGAS00001000233

• Use_of_deep_sequencing_to_detect_clonal_mutations_in_sun_exposed_human_epidermis___whole_genome

  Deep sequencing of two skin biopsies to study the landscape of somatic mutations in human adult tissues.

  Study EGAS00001000860

• Characterising the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER

  Characterising the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER

  Dataset EGAD00001015411

• Germline sequencing

  Detection of SNVs/indels in the germline of pediatric cancer patients with a focus on CHEK2 germline variants.

  Study EGAS00001006254

• Germline sequencing

  Detection of SNVs/ indels in the germline of pediatric cancer patients with a focus on CHEK2 germline variants

  Study EGAS00001006705

• HCA_Immune_Adult_CIDP_RNA_Managed_Access

  Leveraging single-cell sequencing technologies to shed light on the immune aetiology of chronic inflammatory demyelinating polyradiculoneuropathy (CIDP)

  Study EGAS00001007419