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• scRNA primaries

  Single cell RNA-seq for primary samples

  Dataset EGAD00001006135

• scWGS chordblood

  Single cell WGS (low pass) for chord blood samples

  Dataset EGAD00001006136

• scWGS PDX

  Single cell WGS (low pass) for PT1-derived PDX samples

  Dataset EGAD00001006137

• scWGS primaries

  Single cell WGS (low pass) for primary samples

  Dataset EGAD00001006138

• ctDNA whole exome genome sequencing dataset

  Dataset contains all available exome sequencing paired-end fastq files from our study "A generalizable machine learning framework for classifying DNA repair defects using ctDNA exomes"

  Dataset EGAD00001010069

• Single-cell RNA-Seq (Chromium Next GEM Single Cell 3' Reagent Kits v3.1 from 10X Genomics )

  Human data for transcriptome (scRNA-Seq) in CD34+ B cell precursors.

  Dataset EGAD00001010907

• Mult-omics Palbociclib Resistance Study in HR+/HER2– Metastatic Breast Cancer

  Resistance to CDK4/6 inhibitors and endocrine therapy (ET) are common and poorly understood since they have been real game changer in patients with HR-positive and HER2-negative MBC. A comprehensive genomic and transcriptomic analysis of pre-treatment and post-treatment tumors from patients treated with palbociclib plus ET identified novel markers associated with poor prognosis such as genomic scar features caused by homologous repair deficiency (HRD), estrogen response signatures, and four unique prognostic clusters with distinct molecular features. Tumors with TP53 mutations co-occurring with a unique HRD-high cluster responded poorly. By comparing genomic and transciptomic profiles of paired samples, tumors were found to be further enriched in HRD genomic scars and many had switched to aggressive molecular subtypes. Furthermore, we identified high frequencies of acquired genomic alterations upon disease progression in RB1, ESR1, PTEN, and KMT2C. Our findings provide new insight into potential predictive biomarkers that could be targeted to overcome resistance. (NCT03401359)

  Study EGAS00001005736

• HumanMethylation450K data from Purified Plasma Cells of Monoclonal gammopathy of unknown significance and Multiple myeloma patients and Healthy donors

  HumanMethylation450K data from Purified Plasma Cells of Monoclonal gammopathy of unknown significance and Multiple myeloma patients and Healthy donors

  Study EGAS00001000841

• Molecular characterization of endothelial cells under conditions associated with hematopoietic niche formation in humans

  Using a combinatory approach of cell purification and transcriptomics, we identify a subset of endoglin-expressing endothelial cells enriched in human bone marrow during fetal ontogeny and regeneration after chemotherapeutic injury. Comprehensive transcriptional characterization by massive parallel RNA sequencing of these cells revealed a remarkable phenotypic and molecular similarity to murine H endothelium as well as activation of pathways and angiocrine factors implicated in hematopoiesis, osteogenesis and angiogenesis.

  Study EGAS00001002736

• Responses to Varicella Zoster Virus Vaccination

  The study sequenced antibody heavy chain gene rearrangements from 4 identical twin pairs undergoing vaccination with Varicella Zoster viral vaccine.

  Study phs000817

• Linked-read data of additional normal blood samples

  Linked-read whole genome sequencing data of 15 normal blood samples from brain tumour patients. The dataset consists of BAM files generated by the Long Ranger pipeline from 10x Genomics.

  Dataset EGAD50000001390

• WES bam files associated with 119 breast cancer patients associated with the Liberate Tracer Study

  This dataset contains WES bam/bai files associated with 119 breast cancer patients as part of with the Liberate Tracer Study

  Dataset EGAD50000001133

• BASIS_Genome_Validation_Study

  Bespoke validation experiments will be performed on ER+ Breast Cancer cases to confirm the presence of mutations found in whole genome sequencing.

  Study EGAS00001000403

• Kuusamo whole exome sequencing

  Whole exome sequencing of samples selected from the Finrisk sample collection. The samples sequenced in this study have all been collected in Kuusamo, Finland.

  Dataset EGAD00001000299

• RNA sequencing data of pretreatment tumor biopsies of patients treated in the OpACIN-neo trial

  The dataset includes RNA sequencing on pre-treatment tumor biopsies of lymph node metastases (n=65)

  Dataset EGAD00001006731

• Molecular pathways and cellular subsets associated with adverse clinical outcomes in overlapping immune-related myocarditis and myositis

  ScRNA-seq FASTQ files from myocarditis and control cardiac muscle samples; and myositis and control skeletal muscle samples.

  Dataset EGAD50000000488

• We performed whole exome sequencing (WES) using Hiseq on 22 paired CMLs. We also performed whole exome sequencing (WES) using CG on 88 paired CMLs. All the data belongs to CML in China - ICGC project.

  We performed whole exome sequencing (WES) using Hiseq on 22 paired CMLs. We also performed whole exome sequencing (WES) using CG on 88 paired CMLs.All the data belongs to CML in China - ICGC project.

  Study EGAS00001001742

• subset of DEEP IHEC release 2016 (EGAS00001001937), as used in EGAS00001001656 (bidirectional promotors paper, Fatemeh et al. 2018)

  part of the DEEP project results resulted in the publication of 'Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters', Epigenetics & Chromatin (2018), Fatemeh et al., DOI: 10.1186/s13072-018-0236-7, PMID: 30414612, PMCID: PMC6230222. This dataset contains the subset of DEEP data related to that study.

  Dataset EGAD00001005953

• ATAC-seq, H3K27ac CUT&Tag, and UMI-4C in LCLs derived from constitutional MLH1 epimutation carriers and non-carrier relatives

  ATAC-seq, H3K27ac CUT&Tag, and UMI-4C in lymphoblastoid cell lines derived from constitutional MLH1 epimutation carriers and non-carrier relatives

  Study EGAS50000000499

• Whole genome and RNAseq analysis of pediatric osteosarcoma

  Integrative analysis whole genome sequencing and RNA-seq in pediatric osteosarcoma primary tumors and patient derived tumor xenografts.

  Study EGAS00001003201

• Single cell analyses of transcriptome and epigenome in neuroblastoma infiltrated bone marrow

  We report transcriptional and genome-wide ATAC-seq analyses at single cell resolution of 16 bone marrow samples with and without neuroblastoma infiltration. Our samples span across several neuroblastoma models, including MYCN amplified, ATRX mutated, and sporadic (lacking either alteration).

  Study EGAS00001006106

• Target Capture Sequencing of 12 patients

  We perfomed target capture DNA sequencing of 12 patients to assess the detailed biological mechanisms of resistance to immune checkpoint inhibitors.

  Study JGAS000589

• Sanger sequencing of MV4-11 cell lines targeting the TP53 R284 locus

  Sanger sequencing data of cell lines derived from bulk MV4-11 cells, targeting the R248 locus of TP53, consisting of either wildtype or homozygous mutant lines.

  Dataset EGAD50000000447

• Identification of fungal species in brain tissue from Alzheimer's disease

  Identification of fungal species present in the central nervous system tissue from Alzheimer's disease patients by next-generation sequencing.

  Study EGAS00001002228

• Multiome

  This dataset contains the raw sequencing data (Runs) from all of the 10x Genomics single-cell Multiome Experiments

  Dataset EGAD00001009824