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• Germline WES-data of pediatric cancer patients with variants in HBOC-related genes

  This study focused on the identification of (likely) pathogenic germline variants (LP/PV) in 25 adult-onset HBOC-related genes in a cohort of 372 pediatric cancer patients. The cohort was sequenced on Illumina platforms. The files uploaded here belong to the 27 individuals with such a LP/PV.

  Study EGAS50000001073

• Chordoma_Exome_Sequencing

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

  Study EGAS00001000188

• Single-cell RNA sequencing of metastatic colorectal cancer patient-derived xenografts treated with cetuximab

  Single-cell RNA sequencing was performed on a cetuximab-sensitive metastatic colorectal cancer (mCRC) patient-derived xenograft (PDX) model. The objective of this analysis was to assess whether the transcriptional patterns identified in the single-cell RNA-seq data of matched organoids were preserved in the in vivo context.

  Study EGAS50000001459

• Renal_Matched_Pair_Cell_Line_Exome_Sequencing

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

  Study EGAS00001000179

• Kaposi_sarcoma_exome

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from Kaposi sarcoma cancer and matched normal DNA from the same patients. Next Generation sequencing will be performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes

  Study EGAS00001000032

• Chondrosarcoma_Exome_

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from Chondrosarcoma cancer and matched normal DNA from the same patients. Next Generation sequencing will be performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes

  Study EGAS00001000038

• RNA-seq analysis of midbrain dopaminergic neurons following ZFHX4 knockdown.

  We performed RNA-seq analysis on midbrain dopaminergic neurons derived from induced pluripotent stem cells following lentiviral-mediated knockdown of the transcription factor ZFHX4. Transcriptomic analysis enabled the identification of potential ZFHX4 target genes. Enrichment analysis of the differentially expressed genes was conducted to assess the biological pathways regulated by ZFHX4.

  Study EGAS50000001111

• Meningioma_Exome

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

  Study EGAS00001000177

• Identifying mutations in patient-derived melanoma DCC lines

  To identify mutations that cause resistance, we analyzed two patient-derived cell lines: Mel-DCC-11 (the parental line, sensitive to the BRAF inhibitor) and Mel-DCC-11-R (resistant to the BRAF inhibitor). We employed targeted-panel sequencing to examine the coding sequences of 410 cancer-associated target genes.

  Study EGAS50000001225

• The Genetics of Food Cue Reactivity in Children

  This study aimed to investigate genetic factors related to appetite, eating in the absence of hunger and brain reward response to food cues in a convenience sample of pre-adolescent children taken through two studies (A and B). The study involved genome-wide genotyping using the Illumina Global Screening Array. The study found an obesity polygenic risk score related to parent-reported appetitive traits in children, The study also found that FTO was related to eating in the absence of hunger and brain reward response to food cues. Available data include genotypes, measured height and weight, appetitive traits, consumption, brain reward response to food cues, and sociodemographic variables.

  Study phs003550

• KIR imputation panel

  Construction of the KIR variant imputation panel in the Japanese population

  Study JGAS000314

• Improving Transcriptome Fidelity Following Synovial Tissue Disaggregation

  Synovial tissue was collected at the time of arthroplasty from rheumatoid and osteoarthritis arthroplasty. Tissues were left intact or disaggregated with different methods to evaluate the effect on the transcriptome.

  Study phs002991

• SCANDARE HNSCC

  Prospective biobanking study in SCANDARE HNSCC (Head and Neck Squamous Cell Carcinoma) patients aiming at better understand the link between the molecular alterations of the tumor itself, its microenvironment and immune response.

  Study EGAS50000001158

• Papua New Guinean Genome Diversity Project

  Papua New Guinean populations have one of the highest genetic diversity of the world. Our dataset provides genomic data covering most of the Papua New Guinean territory (n=58).

  Study EGAS00001005393

• STAT1 AM RNAseq

  The transcriptome of peripheral blood cells (PBMCs) from control or patients with an activation mutation on the STAT1 gene was analyzed. This analysis aimed to identify the major changes in the circulating immune cells of patients with STAT1 mutation and compare this with the result of the perturbation prediction tool huva (human variation, R).

  Dataset EGAD00001006962

• We performed whole-exome sequencing and whole epigenome sequencing (RRBS) of samples collected from different time points during radiotherapy from thirty-four ESCC patients. We compared the genetic and epigenetic features of the different time biopsy samples to reveal the changes in ESCC received radiotherapy.

  We performed whole-exome sequencing and whole epigenome sequencing (RRBS) of samples collected from different time points during radiotherapy from thirty-four ESCC patients. We compared the genetic and epigenetic features of the different time biopsy samples to reveal the changes in ESCC received radiotherapy.

  Study EGAS00001002718

• We performed whole-exome sequencing and whole epigenome sequencing (RRBS) of samples collected from different time points during radiotherapy from thirty-four ESCC patients. We compared the genetic and epigenetic features of the different time biopsy samples to reveal the changes in ESCC received radiotherapy.

  We performed whole-exome sequencing and whole epigenome sequencing (RRBS) of samples collected from different time points during radiotherapy from thirty-four ESCC patients. We compared the genetic and epigenetic features of the different time biopsy samples to reveal the changes in ESCC received radiotherapy.

  Study EGAS00001002719

• Novel APC Promoter and Exon 1B Deletion and Allelic Silencing in Three Mutation-Negative Classic Familial Adenomatous Polyposis Families

  The ~80% of individuals with classic familial adenomatous polyposis (FAP) have detectable mutations in the coding sequence of the adenomatous polyposis coli (APC) gene. To investigate the 20% of families without detectable causative mutations, we used exome sequencing and second-generation sequencing of the APC locus including non-coding regions. We identified a novel ~11kb deletion 44kb upstream of APC that was present only in affected individuals of three kindreds. SNP analysis showed that this ~11kb deletion was accompanied by silencing of one of the APC alleles in blood-derived RNA of affected individuals.

  Study phs000904

• Whole exome sequencing and RNA sequencing of cervical cancer

  We designed this study to identify molecular markers involved in the development and prognosis of cervical adenocarcinoma. In this study, we would like to elucidate the molecular biological characteristics of cervical adenocarcinoma in relation to the carcinogenesis of other cervical cancers (squamous cell carcinoma), vaginal and vulvar cancers. In addition, some squamous cell carcinomas of the cervix develop at a young age and have a poor prognosis. Furthermore, small cell carcinoma of the cervix also progresses rapidly and has a poor prognosis, making the establishment of diagnostic and therapeutic methods an urgent task.

  Study JGAS000586

• Whole exome sequencing and RNA sequencing of cervical cancer

  We designed this study to identify molecular markers involved in the development and prognosis of cervical adenocarcinoma. In this study, we would like to elucidate the molecular biological characteristics of cervical adenocarcinoma in relation to the carcinogenesis of other cervical cancers (squamous cell carcinoma), vaginal and vulvar cancers. In addition, some squamous cell carcinomas of the cervix develop at a young age and have a poor prognosis. Furthermore, small cell carcinoma of the cervix also progresses rapidly and has a poor prognosis, making the establishment of diagnostic and therapeutic methods an urgent task.

  Study JGAS000582

• Single-cell proteogenomics of MDS upon AZA

  To study the evolution of the clonal molecular and cellular architecture of MDS upon the treatment with AZA, we performed scDNA-seq of an amplicon panel of 53 genes recurrently mutated in myeloid malignancies, as well as typically lost or gain DNA regions, and scProt-seq of 42 cell-surface proteins to provide a simultaneous landscape of the genetic setting and immunophenotype using the Tapestri platform (MissionBio). We sequenced thousands of cells from 14 MDS patients, where paired bone marrow samples were obtained at the timepoint of diagnosis and after AZA treatment.

  Study EGAS00001007427

• Sensitivity to the Subjective Effects of Amphetamine

  The goal of this study was to identify SNPs associated with subjective, physiological, and behavioral responses to d-amphetamine. The study was double-blind and placebo-controlled. 381 healthy volunteers aged 18-35 years old received oral doses of d-amphetamine (10 and 20 mg) and placebo over the course of three different phenotyping sessions. A subset of subjects received a fourth dose of d-amphetamine (5 mg). Measures of subjective, cardiovascular and behavioral responses were obtained at regular intervals (pre-drug administration and 30, 60, 90, 150, and 180 minutes post-drug administration). The subjective measures included in the study were the Profile of Mood States (POMS), Drug Effects Questionnaire (DEQ) and Addiction Research Center Inventory (ARCI). Tasks included were the Digit Symbol Substitution (DSST) and Stop Task.

  Study phs000832

• Human omentum cell atlas

  This dataset contains single-cell RNA sequencing data derived from freshly dissociated human omental tissue. The study investigates the transcriptomic landscape of the omentum by comparing samples from patients with benign conditions against those with ovarian cancer metastasis. To capture the heterogeneity of the metastatic niche, sampling was performed across distinct anatomical sites, including non-metastasized tissue, distant omental regions, peritumoral zones, and the tumor core. This comprehensive profiling aims to define the cellular remodeling associated with malignant transformation

  Dataset EGAD50000002110

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from the Netherlands (Ophoff)

  This research project was a collaboration between UCLA and the Stanley Center at the Broad Institute. In this project we sequenced and analyzed the whole exomes of 1,965 Bipolar case/control samples from collaborators in the Netherlands and UCLA. Genomic DNA from each sample was sequenced to a mean depth of 20x. The exome used Twist capture and samples were sequenced on Illumina HiSeqX machines producing CRAM files.

  Dataset EGAD50000000983

• Data Access Committee for Deciphering Developmental Disorders (DDD) Project

  Dac EGAC00001000282

• Low coverage whole genome sequencing form CSF-derived cell free DNA

  Low coverage whole genome sequencing form CSF-derived cell free DNA for matching samples with EM-seq cohort

  Dataset EGAD50000002148

• Picuris Pueblo Genomic Project – Ancient Dataset

  Ancient individual from Picuris Pueblo. Please refer to paper for more information.

  Dataset EGAD50000001246

• WES PTCL Data

  Whole Exome Sequencing (WES) of 153 FFPE DNA samples of Peripheral T-Cell Lymphoma. Associated with "Molecular biomarkers for stratification periheral T cell lymphoma" study.

  Dataset EGAD50000001250

• APOBEC Breast Cancer Whole Genome

  Five tumor-normal human breast cancer cases driven by APOBEC mutagenesis, including normal tissue, primary, and metastatic samples for each patient.

  Dataset EGAD50000001275

• SMPaeds PanelSeq of cfDNA at relapse with UMIs

  Deep sequencing of a targeted panel of 67 paediatric cancer related genes for cfDNA with UMIs at approximately 1500xUMI coverage.

  Dataset EGAD50000000781

• RNA-seq of murine osteosarcoma cell line genetically modified for CYR61

  Transcriptomic analysis of K7M2 murine osteosarcoma cells stably modified to overexpress or repress CYR61

  Dataset EGAD50000000747

• Single Cell RNA-Seq

  Examination of Sample Multiplexing Reagents for Single Cell RNA-Seq. Nine techniques applied to samples from four PDX models: #105, #177, #233, #264

  Dataset EGAD50000000216

• SAFIR02_Cytoscan

  Genomics to select patients with metastatic breast cancer for targeted therapy (microarray_cytoscan)

  Dataset EGAD00010002239

• Dataset for desmoplastic small round cell tumor array data

  This dataset contains 24 methylation array samples of patients with desmoplastic small round cell tumor measured on Illumina 850k.

  Dataset EGAD00010002689

• SNParray_PGT_samples_scGBS

  PGT samples for haplotyping and copy-number profiling via SNP array

  Dataset EGAD00010002169

• SNParray_HapMap_samples_scGBS

  HapMap samples for haplotyping and copy-number profiling via SNP array

  Dataset EGAD00010002168

• Batch2_Genotypes_Raw

  Genotypes generated for Puno cohort Batch 2. Case (PRE) and control (PUN) families were recruited in hospital. Raw genotypes no QC. Includes unrelated genotyping controls (HG).

  Dataset EGAD00010002124

• GR@ACE_StageI.v02

  Binary Plink files for post-GWAS quality control in 7409 samples genotyped using Axiom 815K Spanish Biobank array (Thermo Fisher)

  Dataset EGAD00010001653

• Copy Number Arrays for study EGAS00001004165

  Copy Number Alterations arrays from 153 samples performed by Affymetrix 6.0 and Oncoscan CNV platforms

  Dataset EGAD00010001841

• Hi-C of cohesin-mutated and wildtype adult AMLs

  High-throughput chromosome conformation capture (Hi-C) data generated for cohesin-mutated (STAG2 or RAD21) and cohesin-wildtype AMLs.

  Dataset EGAD00001011198

• 7 samples RNA-seq raw data

  Dataset comprising raw paired RNA-seq data in fastq.gz format for 7 samples of rosette forming brain tumors

  Dataset EGAD00001009265

• Biomarker data

  Biomarker data for KATHERINE: Biomarker data include RNA-seq time point, Percent of tumor content, PAM50 subtypes, normalized gene expression of ERBB2, CD8 and CD274, normalized immune signature expression.

  Dataset EGAD00001008786

• liCHi-C Samples of B-ALL

  Libraries of liCHi-C for 2 B-ALL (B Acute Lymphocytic Leukaemia) from human patients. Fastq file format.

  Dataset EGAD00001008829

• KCL PRECSION lpWGS

  KCL lpWGS samples for copy number analysis

  Dataset EGAD00001008380

• Single-nucleus RNA-sequencing of meningiomas

  Single-nucleus RNA-sequencing of meningiomas for integrative molecular classification

  Dataset EGAD00001007677

• Glioblastoma stem cell lines RNA-seq

  RNA-seq data for three Glioblastoma stem cell (GSC) lines exposed to PRMT5 inhibitor and control samples.

  Dataset EGAD00001006095

• Hyperpolarized 13C MRI in breast cancer

  Transcriptomics for samples obtained from six patients (MBR01, MBR03, MBR05, MBR07, MBR10, MBR11)

  Dataset EGAD00001005760

• Neoantigen study samples for prostate cancer

  Whole exome sequencing and RNA sequencing data from 30 patients with prostate cancer.

  Dataset EGAD00001005713

• Reference epigenome ADMSC01_smRNA-Seq data generated from KEP study

  A ADMSC01_smRNA-Seq single end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003867

• Reference epigenome ADMSC02_smRNA-Seq data generated from KEP study

  A ADMSC02_smRNA-Seq single end data for adipose-derived mesenchymal stroaml cells

  Dataset EGAD00001003868