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• ChIP-seq in colorectal cancer and paired adjacent normal mucosa

  Chip-seq samples for 20 colorectal patients with paired adjacent normal mucosa to characterize H3K27ac and H3K4me1.

  Study EGAS00001005303

• small RNA sequencing for 6 patients

  small RNA sequencing data for 3 patients with type 2D diabetes, and 3 patients with non diabetes. Single end sequencing was performed with read length of 100.

  Dataset EGAD50000001259

• WES data for Heterogeneity of IKZF1 genomic alterations and risk of relapse in childhood BALL

  Whole exome sequencing data for 425 samples with B-cell acute lymphoblastic leukemia

  Dataset EGAD50000000150

• Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

  Sequence reads for pediatric GBM samples for manuscript: Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

  Dataset EGAD00001000134

• Sequencing data for Australian Ovarian Cancer study submitted 20121116

  Sequencing data for Australian Ovarian Cancer study submitted 20121116

  Dataset EGAD00001000293

• WES files for Newman MAP3K8 melanoma

  WES files for Newman MAP3K8 melanoma paper titled "Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas"

  Dataset EGAD00001004566

• WGS files for Newman MAP3K8 melanoma

  WGS files for Newman MAP3K8 melanoma paper titled "Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas"

  Dataset EGAD00001004579

• Whole genome data for study EGAS00001000824 (Diverse modes of genomic alterations in hepatocellular carcinoma)

  Whole genome data (Complete genomics platform) for the study EGAS00001000824

  Dataset EGAD00001001034

• DATA FILES FOR SJOS-WGS-2ndBatch

  DATA FILES FOR SJOS-WGS-2ndBatch

  Dataset EGAD00001001053

• McGill EMC Release 4 in tissue "venous blood" for cell type "CD4-positive helper T cell"

  McGill EMC Release 4 in tissue "venous blood" for cell type "CD4-positive helper T cell"

  Dataset EGAD00001001279

• Whole exome sequencing for ZNF384-rearranged ALL cases

  Whole exome sequencing for the matched germline and tumor DNA from 10 ALL cases with ZNF384 rearrangements.

  Dataset EGAD00001002152

• DATA FILES FOR PCGP SJCBF RNASEQ

  Additional files for "The Genomic Landscape of Core-Binding Factor Acute Myeloid Leukemias" (EGAS00001000349). This dataset includes the processed RNASeq data referenced in this paper.

  Dataset EGAD00001002530

• Exome and RNA seq data for female patient

  Exome and RNA sequencing data for EGAS00001003776 - one female patient with neurofibroma/schwannoma hybrid nerve sheath tumor (N/S HNST)

  Dataset EGAD00001005249

• RNA-SEQ for the Caldas Lab breast cancer PDTX collection

  RNA-SEQ for the Caldas Lab breast cancer PDTX collection. This includes both single and paired end runs

  Dataset EGAD00001006307

• Phenotype data for samples with serum metabolomics

  Phenotypic data for 475 human samples, including: Demographics Anthropometrics Diet data Clinical data Time of day Season in which serum sample was taken

  Dataset EGAD00001006354

• WGBS data for Glioblastoma (EGAS00001003953, H016)

  Whole Genome Bisulfite data for human glioblastoma patients, EGAS00001003953. 68 human samples

  Dataset EGAD00001006546

• Additional WGS files for Genomic Landscape ALL paper

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

  Dataset EGAD00001010270

• Blood Gene Signatures Associated with Stiffness After TKA

  In this study, we used PAXgene Blood RNA tubes collected from patients undergoing total knee arthroplasty (TKA) for osteoarthritis. Samples were collected with IRB approval and patient consent. We identified 8 patients with knee stiffness after TKA (cases) and 10 patients without post-TKA stiffness (controls). We isolated RNA from cases and controls for RNA-seq analyses, comparing samples collected the day of surgery and samples collected at 24 hours after surgery.

  Study phs002927

• EASI-Genomics GM21886 Cell Line High Molecular Weight DNA Sequencing

  An interlaboratory study was performed with GM21886 cells to evaluate methods for high molecular weight (HMW) genomic DNA extraction and compare sample and sequencing QC metrics, and pipelines for structural variant (SV) calling. Four laboratories prepared HMW genomic DNA using four alternative extraction methods FireMonkey (Revolugen), Genomic Tip (QIAGEN), Nanobind (Circulomics), and Puregene (QIAGEN), followed by Short Read Elimination (Circulomics) and long-read sequencing with MinION and PromethION flowcells (Oxford Nanopore Technologies).

  Study phs003958

• Influence of pre-analytical processing on blood protein profiles (AMED-Metabolites)

  The purpose of the present study was to assess the differences between the human serum and plasma proteomes, and the stability of human plasma proteins under different storage conditions following blood collection, by means of SWATH-MS analysis. We compared plasma samples prepared by centrifugation after storage of blood at room temperature for 0, 15 or 30 minutes, or under refrigeration at 0-5?C for 1, 4 or 8 hours.

  Study JGAS000223

• Axes of Biological Variation in Diffuse Large B-Cell Lymphoma

  To explore the DLBCL molecular and genetic environment, we conducted genome-wide NGS sequencing on 103 DLBCL biopsy samples (named as Cornell-NCI cohort) with NGS platforms, including bulk WES, etc. The raw fastq files of the bulk WES were deposited on the EGA for user access. For additional information regarding the genomic data associated with the study, please also see the paper companion website at https://llmpp.ccr.cancer.gov/local/DLBCL_singlecell/

  Study EGAS50000001227

• Bone morphogenetic protein-9 controls pulmonary vascular growth and remodeling

  Human PMECs from 10 donor lungs were isolated, cultured (passages 3 to 4), synchronized by serum starvation (0.3% FCS), and stimulated with 10 ng/mL BMP-9 for 4 h. Single-cell profiling was performed using the 10X Genomics Chromium RNA 3' V3.1 kit. Five experimental groups were analyzed using cell hashing and sequenced on an Illumina NextSeq500. Data were processed with Cell Ranger and Seurat for differential gene expression and functional enrichment analysis.

  Study EGAS50000001026

• Bulk and Single-Nuclei RNA-seq with ATAC-seq of Breast Tumors Pre- and Post-Palbo ciclib/Endocrine Therapy

  This dataset comprises bulk and single-nuclei multiomic profiles from patients with ER+/HER2- early breast cancer enrolled in the NeoRHEA phase 2 trial. The bulk RNA-seq component includes 78 pre-treatment and 49 post-treatment tumor samples from 97 patients. The single-nuclei component includes matched pre- and post-treatment samples from 37 patients, totaling 63 samples analyzed by simultaneous snRNA-seq and snATAC-seq. Combined, the data contains bulk transcriptional profiles and single-nuclei gene expression/chromatin accessibility matrices for over 226,000 high-quality nuclei, encompassing tumor, immune, and stromal cells. Technologies used include Illumina NovaSeq 6000 for sequencing and the 10x Genomics Chromium platform (Multiome kit for single-nuclei, standard RNA library prep for bulk).

  Dataset EGAD50000002038

• 13K T2D-GENES analysis files

  This data set includes the following summary level data files used for the 13k analysis of T2D-GENES data: wes.variants.list: list of variants to keep for any analysis of the exomes data wes.assoc.samples.list: list of samples to keep for association analysis wes.assoc.variants.list: list of variants to keep for association analysis wes.sv.assoc.txt: single variant association analysis results wes.gene.ptv.variants.list.txt: list of protein truncating variants to use in gene-level analysis wes.gene.ptv.assoc.txt: results from gene-level tests of protein truncating variants wes.gene.nsstrict.variants.list.txt: list of NSstrict variants to use in gene-level analysis wes.gene.nsstrict.assoc.txt: results from gene-level tests of NSstrict variants wes.gene.nsbroad.variants.list.txt: list of NSbroad variants to use in gene-level analysis wes.gene.nsbroad.assoc.txt: results from gene-level tests of NSbroad variants wes.gene.ns.variants.list.txt: list of non synonymous variants to use in gene-level analysis wes.gene.ns.assoc.txt: results from gene-level tests of non synonymous variants

  Dataset EGAD00010001188

• smRNA-Seq assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

  smRNA-Seq assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001226

• RCRF release 2

  RNA sequencing of a Chromophobe renal cell carcinoma, Non-clear cell chromophobe renal cell carcinoma, Neuroendocrine PDAC and clear cell sarcoma

  Dataset EGAD50000000872

• RNA-seq and WGS data of MB-0152

  Identification of fusion transcripts by RNA-sequencing and Whole genome sequencing of a breast cancer patient sample (METABRIC ID MB-0152)

  Dataset EGAD00001003342

• ICGC Prostate Cancer Whole Genome Sequencing

  A small subsample of EGAD00001000689. Please do not use.

  Dataset EGAD00001000263

• Philippine Ayta Genomes

  Whole genome sequence of Philippine Ayta Magbukon. A total of 5 individuals.

  Dataset EGAD00001007983

• 4C-seq data of a primary AML with t(3;8)

  The viewpoints used in the 4C-seq data were either the EVI1 promoter or the MYC super-enhancer

  Dataset EGAD00001006818

• WES from tFL with PMBL GE signature

  Exome sequencing data from transformed Follicular Lymphoma samples that express a PMBL-like gene expression signature

  Dataset EGAD00001008498

• Identify disease-related genes

  Raw data (idat file) analyzed by Illumina SNP array for patients in the 1st cohort and the 2nd cohort (51 diseases).

  Study JGAS000703

• Sensitive gene analysis of hereditary cardiovascular disease

  This research aims to identify disease sensitive genes and their gene variants by genome analysis for hereditary cardiovascular diseases.

  Study JGAS000295

• SPEN loss drives extra-follicular diffuse large B cell lymphoma with female-specific lethality and TLR pathway therapeutic vulnerabilities

  Multiome (ATAC and GEX) sequencing for one rLN sample and one DLBCL sample

  Study EGAS50000001594

• cell-free Methylated DNA by Immunoprecipitation and Sequencing (cfMeDIP) of human meningioma samples.

  Raw data for cell-free Methylated DNA by Immunoprecipitation and Sequencing (cfMeDIP) of human meningioma samples.

  Study EGAS50000001539

• Neuroblastoma Cell Line Circle-seq

  We generated Circle-seq data for 12 neuroblastoma cell lines to describe the landscape of extrachromosomal circular DNA in neuroblastoma.

  Study EGAS00001004796

• Whole-genome sequencing for 61 early-onset diabetes patients and 174 controls

  This dataset contains 241 paired FASTQ files for 61 early-onset diabetes patient and 174 controls sequenced with MGI Tech DNBSEQ-T10 and DNBSEQ-T7.

  Dataset EGAD50000001450

• PCA Atlas donor genotyping arrays (Axiom UK Biobank v2.0)

  Raw Axiom v2.0 UK Biobank Array CEL files for PCA Atlas donor buffy-coat DNA, used to generate SNP genotypes for demultiplexing single-cell and spatial transcriptomics libraries.

  Dataset EGAD00010002818

• Chip-exo and Chip-nexus for five TFs in three colorectal cancer cell lines

  Chip-exo and Chip-nexus for FOXA1, HNF4A, KLF5, MYC, and TCF7L2 in colorectal cancer cell lines LoVo, GP5D, COLO320DM

  Dataset EGAD00001004099

• WGS files for double minute brain tumor paper.

  Whole Genome Sequencing files accompanying the paper titled "Structure and evolution of double minutes in diagnosis and relapse brain tumors". Please read the paper for more details.

  Dataset EGAD00001004337

• H3Africa H3AChipDesign MalSic

  The dataset includes BAM, FASTQ and decompressed gVCF files for 50 samples from Benin generated for the H3Africa Chip Design Study.

  Dataset EGAD00001004557

• McGill EMC Release 4 in tissue "venous blood" for cell type "CD4-positive, alpha-beta T cell"

  McGill EMC Release 4 in tissue "venous blood" for cell type "CD4-positive, alpha-beta T cell"

  Dataset EGAD00001001280

• Whole genome sequencing of 98 tumour-normal pairs for the pancreatic neuroendocrine cancer project

  Whole genome sequencing of 98 tumour-normal pairs for the PAEN-AU pancreatic neuroendocrine cancer project.

  Dataset EGAD00001002684

• Hospital for Sick Children Infant Glioma RNA Sequencing

  Whole transcriptome (n=4) and targetted RNA sequencing (n=15) .bam files of infantile glioma samples reported on at the Hospital for Sick Children

  Dataset EGAD00001005092

• T-WGBS for Naive B Cell

  Tagged-WGBS for 3 Naive B Cell samples of the CancerEpiSys-PRECiSe project.

  Dataset EGAD00001005966

• ATAC data for Glioblastoma (EGAS00001003953, H016)

  ATAC-seq data for 2 glioblastoma cell lines (LN229, ZH487), NT and SOX10KD.

  Dataset EGAD00001006544

• RNAseq for Patients of NIBIT-M4 clinical trial

  RNAseq for Patients of NIBIT-M4 clinical trial

  Dataset EGAD00001009702

• Human Origins array data for 1510 individuals

  Genotype data typed on the Human Origins array for 1510 individuals published in "Dense sampling of ethnic groups within African countries reveals fine-scale genetic structure and extensive historical admixture."

  Dataset EGAD00001010015

• Dataset for transcriptomic sequencing of Merkel cell carcinoma(MCC) samples

  This dataset contains transcriptome sequencing for 5 samples of MCC tumors . The sequencing was performed on Illumina NextSeq 6000 . The sequencing was always paired.

  Dataset EGAD00001015702

• University of Washington Center for Mendelian Genomics (UW-CMG): Atrioventricular Septal Defects (AVSD) Study

  The Centers for Mendelian Genomics project uses next-generation sequencing and computational approaches to discover the genes and variants that underlie Mendelian conditions. By discovering genes that cause Mendelian conditions, we will expand our understanding of their biology to facilitate diagnosis and new treatments.

  Study phs001774