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• HiChIP data and analysis in OCI-AML3

  Data and analysis of HiChIP assay of shZNF143 and shControl in OCI-AML3. CTCF was the ChIP antibody. Data files are paired-end reads in FASTQ format from the Illumina NovaSeq 6000 sequencer. Analysis files are paired-end bed files produced by FitHiChIP.

  Dataset EGAD50000001376

• Multiomics characterisation of the response to stimulation in Long Covid patients

  We generated 10X, droplet-based paired snRNAseq+snATACseq (Multiome) of the response to P. Aeruginosa or RPMI in patients suffering from Long Covid. In total, we included 15 patients. Single nuclei libraries are genetically multiplexed across donors, genotype files are available to enable demultiplexing. Phenotype sheets provide information of pools/donors as well as donor phenotype.

  Dataset EGAD50000000203

• BASIS miRNA data

  399 tumors profiled using Agilent miRNA microarrays (Product Number G4872A, design ID 046064). The arrays are based on miRBase release 19.0 and 2006 human miRNAs are represented. 150 ng total RNA was used as input.

  Dataset EGAD00010000917

• Molecular characterization of T-PLL by Next-Generation Sequencing

  Patients with T-cell prolymphocytic leukemia (T-PLL) were profiled with multiple OMICS approaches based on Next-Generation Sequencing (NGS). In total, data from RNA-Seq, Whole-Exome Sequencing, Whole-Genome Sequencing and amplicon panel analyses in 134 samples are available. All samples were processed as paired-end libraries on Illumina sequencing machines. The data are available as paired FastQ files.

  Dataset EGAD00001003825

• ESGI___Whole_Genome_Sequencing_of_samples_from_the_ORCADES_cohort__X10__

  Deep whole genome sequencing of sampels from the Orkney Complex Disease Study (ORCADES), each with data on up to 300 quantitative traits and other risk factors associated with cardiovascular, metabolic and other complex diseases. The samples are sequenced using the Illumina HiSeq X Ten system.

  Study EGAS00001001125

• UCL COVID-19 Single-cell PBMC

  Single-cell multi-omic profiling of COVID19 patients recruited from University College London. Data represent RNA-seq, surface protein measurements (CITE-seq) of 192 antibody targets, along with VDJ-seq profiling of single T cell and B cell receptors. Samples are pooled, with 4 donors per pool. Germ-line genotypes derived from previous single-cell RNA-sequencing are provided (VCF) to aid demultiplexing of single-cell and assignment to specific patient donor samples.

  Dataset EGAD00001007865

• Therapy-related myeloid neoplasms and HSPCs from the International-Berlin-Frankfurt-Münster (I-BFM) Study group

  Dataset contains WGS sequencing data from bulk sorted therapy-related myeloid neoplasms (t-MN) and reference cells (MSCs/B cells/T cells). In addition, from 4 patients, also WGS data from single hematopoietic stem and progenitor cells, obtained from samples of t-MN diagnosis, are included. These are either clonally expanded before WGS, or DNA was directly amplified via the primary template-directed amplification (PTA) protocol (mentioned in the sample name).

  Dataset EGAD00001011256

• Characterizing TP53 and PPM1D Mutations as Resistance Drivers to Radiation Therapy in Diffuse Intrinsic Pontine Gliomas

  Pediatric high-grade gliomas (pHGGs), encompassing diffuse midline gliomas (DMGs) and hemispheric tumors, represent the most common cause of cancer-related deaths in children age 0-14 years. Over the last decade, several landmark papers have revealed recurrent single nucleotide variants (SNVs) in the core histones H3.3 and H3.1, co-occurring with alterations in the TP53 signaling pathway and receptor tyrosine kinases (RTKs). However, the contribution of structural variants (SVs) to gliomagenesis has not been systematically explored. We performed a comprehensive analysis of whole genome sequencing (WGS) data on pediatric high-grade gliomas (pHGGs) from 179 children, including 61 hemispheric tumors and 118 diffuse midline gliomas, or DMGs, of which 61 are novel to this study. Among the DMGs, 84 (71%) were from pre-treatment biopsies including 33 obtained from the first multi-institutional North American clinical trial to incorporate diagnostic biopsies. This represents the largest cohort of pretreatment DMGs with whole genome sequencing to date. This large cohort of whole genome sequences provides an unparalleled opportunity to assess significantly recurrent structural variants in pHGG and their associations with driver SNVs and SCNAs. 

  Study phs002380

• Bacterial Artificial Chromosomes Establish Replication Timing and Sub-Nuclear Compartment De Novo as Extra-Chromosomal Vectors

  The role of DNA sequence in determining replication timing (RT) and chromatin higher order organization remains elusive. To address this question, we have developed an extra-chromosomal replication system consisting of ~200kb human bacteria artificial chromosomes (BACs) modified with Epstein-Barr virus (EBV) replication origin elements (E-BACs). E-BACs were stably maintained as autonomous mini-chromosomes in both HeLa and human induced pluripotent stem cells (hiPSCs) and established distinct RT patterns. An E-BAC harboring an early replicating chromosomal region replicated early during S phase, while E-BACs derived from RT transition regions (TTRs) and late replicating regions replicated in mid to late S phase. Analysis of E-BAC interactions with cellular chromatin (4C-seq) revealed that the early replicating E-BAC interacted broadly throughout the genome and preferentially with the early replicating compartment of the nucleus. In contrast, mid- to late-replicating E-BACs interacted with more specific late replicating chromosomal segments, some of which were shared between different E-BACs. Together, we describe a versatile system in which to study the structure and function of chromosomal segments that are stably maintained separately from the influence of cellular chromosome context.

  Study phs001520

• Single-cell proteo-genomic reference maps of the human hematopoietic system

  We have generated high content single-cell proteo-genomic reference maps of human blood and bone marrow that quantitatively link the expression of up to 197 surface markers to cellular identities and biological processes across all major hematopoietic cell types in healthy aging and leukemia. Please note raw and integrated gene expression data, cell type annotation, metadata and dimensionality reduction are available as Seurat v3 objects through figshare. Access links are https://figshare.com/s/0fda29b169c719223ee3 (97 surface marker, 9 individuals dataset), https://figshare.com/s/313b5739ff469dac8c01 (197 surface marker, bone marrow and blood dataset), https://figshare.com/s/901bcddb9ee18e226031 (97 surface markers and whole transcriptome dataset) and https://figshare.com/s/24e10bf129fae1918316 (97 surface marker, 15 AML datasets).

  Study EGAS00001005593