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• 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 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

• Exome sequencing data for Mesothelioma

  Exome sequencing data for Mesothelioma

  Dataset EGAD00001001913

• RNA-Seq data for Mesothelioma.

  RNA-Seq data for Mesothelioma.

  Dataset EGAD00001001915

• 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

• A98294A

  Whole genome sequencing for single cells for library A98294A 994 samples; filetype=bam

  Dataset EGAD00001008266

• 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

• Nanopore sequencing of AML and control samples

  Three AML samples from patients with mutations in DNMT3A, IDH2, TET2, and a control sample of whole genome amplified DNA.

  Dataset EGAD50000001692

• RNA sequencing of AVANT and CALGB trial patient samples

  Transcriptional profiling via high-throughput sequencing was performed on a set of patients from the AVANT and CALGB trials

  Dataset EGAD50000001752

• Whole-genome and transcriptome sequencing of a patient with extrapancreatic acinar cell carcinoma

  Dataset EGAD00001006023

• 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

• Panel sequencing data of IMPACT2 patients

  Patient samples were sequenced by Foundation Medicine, Inc. (Cambridge, MA), using FoundationOne CDx, a comprehensive NGS-based in vitro diagnostic device designed to capture cancer genes.

  Dataset EGAD00001006887

• 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