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• 3D chromatin analysis of clear cell renal cell carcinoma using micro-C

  To investigate the 3D structure of chromatin in ccRCC, we performed micro-C on 3 ccRCC cell lines (786-O, A498, UMRC-2), and 1 normal kidney epithelium cell line (HK-2), cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions

  Study EGAS50000001323

• Genomic profiling of Rare Tumors Release 2

  Utilizing the rare and unique patient samples provided by Pattern Medicine, LLC, MD Anderson will molecularly characterize rare cancer samples, and potentially generate a collection of preclinical models to enable identification of novel therapeutic targets and concepts, as well as evaluation of innovative treatment strategies.

  Study EGAS50000000615

• Determinants of DNA methylation patterning in human placental development and trophoblast stem cell models.

  To assess whether the DNA methylation landscape of human trophoblast stem cells resembles an in vivo cell type, we used post-bisulfite adaptor-tag sequencing to measure genome-wide DNA methylation of preimplantation human trophectoderm and sorted first trimester cytotrophoblast.

  Study EGAS50000000661

• ST dataset of subcortical MS

  Spatial transcriptomics from subcortical white matter controls and MS lesions, specifically chronic active (CA) and chronic inactive (CI), that paired with single-nuclei RNA-sequencing from the same samples , was used to identify spatial niches and key cell interactions driving inflammation and disease progression

  Study EGAS50000000353

• CRISPRi/a of GATA2/NR4A2/SOX17 upon spontaneous iPSC differentiation

  Arrayed CRISPR screens, modulating the expression of key lineage TFs GATA2 (mesoderm), SOX17 (endoderm), and NR4A2 (neuroectoderm) in hiPSCs via CRISPR interference or activation over a time-course of spontaneous differentiation (days cultured in vitro: 0, 4, 12, and 18).

  Study EGAS50000000819

• PASCAL-MID Targeted amplicon sequencing of CD34+ HSPCs (CGD)

  High-throughput amplicon sequencing were performed on CD34+ hematopoietic stem and progenitor cells (HSPCs) derived from 4 healthy donors and one unaffected heterozygous carrier of a CYBB c.252G>A variant causing X-linked granulomatous disease. Targeted genome editing were performed in the HSPCs of CYBA and CYBB genes using CRISPR-Cas9 and recombinant AAV6. To assess gene editing outcomes in CD34+ HSPCs, the targeted loci were amplified from genomic DNA and sequenced on an Illumina iSeq100.

  Dataset EGAD50000001651

• 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

• Human glioblastoma single cell RNA-seq from two patient, sampled at different positions within as well as outside tumor

  We performed deep single-cell RNA sequencing of two rare glioblastoma cases where tissue could be sampled from tumor core to macroscopically normal cortex. We processed two to three replicates per sample with the 10X Genomics V3.1 kits. Deep sequencing was performed to about 100,000 reads per cell on the Illumina NovaSeq 6000 platform, resulting in a total of 37 BAM files.

  Dataset EGAD50000001500

• RNA-seq libraries from FFPE samples using Illumina Ribo-Zero Plus kit

  RNA was extracted from FFPE human tissue samples and used to prepare RNA-seq libraries with the Illumina Stranded Total RNA Prep Ligation kit with Ribo-Zero Plus. cDNA synthesis was performed starting from 100 ng of DNA-free RNA. Libraries were amplified with 16 PCR cycles and sequenced in paired-end mode (2×150 bp) on the Illumina NextSeq 550 platform. Library quality was assessed with Bioanalyzer and Qubit.

  Dataset EGAD50000001553

• 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

• The effects of bioinformatics preprocessing on cell-free DNA analysis

  The dataset contain 20 lung cancer and 20 healthy control cfDNA samples from plasma sequenced using 150bp PE sequencing.

  Dataset EGAD50000000213

• Single-cell multi-omic analysis of control and glioblastoma samples from the brain and border regions.

  Single-cell RNA-sequencing. Some samples were analyzed using CITE-Seq and samples were multiplexed and run on the same 10X reaction

  Dataset EGAD50000000045

• Mutant_clone_mapping_in_normal_oesophagus

  We will use targeted exome sequencing to examine normal appearing epithelium and whole exome and whole genome sequencing of microdissected clones identified by immunostaining Some of the samples will be of low DNA concentration and therefore may require extra rounds of amplification during library prep.

  Study EGAS00001001874

• Genetic landscape of pediatric Low Grade Gliomas & Glioneuronal tumors

  We performed whole-genome sequencing of 42 paired tumor/normal LGG genomes and analyzed somatically acquired single nucleotide variations (SNVs), insertion/deletions, structural variations and copy number variations in the cancer genomes

  Study EGAS00001000255

• Landscape of gene mutations in Down syndrome-related myeloid disorders

  To identify the spectrum of gene mutations in Down syndrome-related myeloid disorders, whole genome sequencing of 4 trio samples from TAM/AMKL/complete remission (CR) phases and whole exome sequencing of 15 TAM and 14 DS-AMKL samples were performed.

  Study EGAS00001000546

• Whole genome sequencing of metastatic melanomas from a patient with primary resistance to BRAF inhibition

  Here, we investigated the underlying cause of treatment failure in a patient with BRAF mutant melanoma who presented primary resistance. We used whole-genome sequencing (WGS) to characterise five metastatic tumours from a BRAF mutant melanoma patient who presented intrinsic resistance.

  Study EGAS00001000580

• Whole genome sequences and variant calls from human cells exposed to UV and CX5461

  Bulk whole genome sequencing data from 38 samples, including patient skin biopsies from 15 patients and RPE-1 cell line data. The targeted sequencing depth was 80X. The dataset also also includes somatic short variants from 15 patients treated with CX5461, and somatic short variants from 3 treatments of 2 genotypes of RPE-1 cells.

  Dataset EGAD50000001640

• Mitochondrial DNA (mtDNA) sequences from subjects with intellectual disability (ID) and austism spectrum disorder (ASD)

  Sequences from 95 subjects presenting intellectual disability (ID) and 98 subjects presenting intellectual disability and a diagnosis of autism spectrum disorder (ASD). The mtDNA was amplified by long-range PCR with 3 pairs of primers producing overlapping fragments. The three fragments were mixed in equimolar ratios and each sample was sequenced in an Ion Torrent Personal Machine according to manufacturer's user guide (reference genome: NC_012920.1 (rCRS)).

  Dataset EGAD00001004213

• Childhood cerebellar tumors mirror conserved fetal transcriptional programs

  We used single-cell transcriptomics to study >60,000 cells from the developing murine cerebellum, and show that different molecular subgroups of childhood cerebellar tumors mirror the transcription of cells from distinct, temporally restricted cerebellar lineages.

  Dataset EGAD00001004318

• RNA sequencing of high hyperdiploid and ETV6/RUNX1-positive pediatric acute lymphoblastic leukemia

  RNA-sequencing data of pediatric B-cell precursor acute lymphoblastic leukemia, including 18 high hyperdiploid cases and 9 ETV6/RUNX1-positive cases. Sequencing libraries were constructed using the Human Ribo-Zero rRNA Removal Kit (Illumina, San Diego, CA) and sequenced on an Illumina NextSeq 500. RNA sequencing data were processed using the TCGA mRNA-seq pipeline (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/#mrna-analysis-pipeline).

  Dataset EGAD00001004176

• Taste Receptor Gene Variants: Body Mass Index (BMI) and Longevity

  We evaluated differences in genotype and allele frequencies at the TAS1R2, TAS1R3, TAS2R38, and CD36 single-nucleotide polymorphisms (SNPs) and their associations with BMI and sex in two genetically and environmentally distinct populations: a cohort of near centenarian participants and a control cohort.

  Study EGAS00001008403

• A living biobank of patient-derived ductal carcinoma in situ Mouse-INtraDuctal xenografts identifies factors associated with risk of invasive progression

  Create a living biobank of patient-derived ductal carcinoma in situ (DCIS) Mouse-INtraDuctal (MIND) xenografts to find factors explaining invasive growth. Samples exist of both primary and pdx samples. Invasive growth was scored in the pdx.

  Study EGAS00001006554

• Genomic profiling of Rare Tumors

  Utilizing the rare and unique patient samples provided by Pattern Medicine, LLC, MD Anderson will molecularly characterize rare cancer samples, and potentially generate a collection of preclinical models to enable identification of novel therapeutic targets and concepts, as well as evaluation of innovative treatment strategies.

  Study EGAS00001007103

• Somatic variants in 344 colorectal cancer samples

  The dataset contains somatic variants in 344 colorectal cancer samples. Variants are called with Mutect2 (GRCh38). Important: VCF-files include also variants, which have been annotated as "str_contraction" and "panel_of_normals". Please, use only "PASS" variants in studies, which are not microsatellite repeat related. Samples are sequenced with Novaseq 6000, HiSeq 2000, and HiSeq X Ten instruments (average coverage depth ~30+). The dataset consists of 257 MSS, 58 MSI, 25 MSS IBD, and 4 POLE mutant CRCs.

  Dataset EGAD00001006572

• Whole Genome Sequencing of JK Family

  In collaboration with Dr David Savage, we have identified a patient with a very unusual phenotype, lacking almost all visceral fat, but showing a massive accumulation of white fat tissue behind her neck and significantly elevated liver fat. Whole exome sequencing of the proband and her unaffected parents and brother has been run previously, however no causative variant has been found and the sequencing coverage was generally poor. We propose to conduct whole genome sequencing of all 4 family members at a depth of 30X.

  Dataset EGAD00001002227

• A compendium of mutational signatures due to environmental exposures

  Analysis of mutational signatures caused by exposure to known mutagens in human induced pluripotent stem (iPS) cells. A reference human iPS cell-line will be exposed to 100 chemicals known or proposed to be mutagenic. Following exposure to mutagen, cells will undergo a period of recovery before sub clones are generated and sequenced. The progenitor "parental" IPS cell-line will be used to generate reference sequence data, in order to determine the mutational signatures acquired as a result of exposure to different mutagens.

  Dataset EGAD00001005351

• mRNA-seq of in vitro differentiation from induced pluripotent stem cells to hepatocyte-like cells

  Fastq files of mRNA-seq data of induced pluripotent stem cells (iPSC), definitive endoderm (DE) and hepatocyte-like cells (HLC). The dataset comprises data from the in vitro differentiation protocol Cellartis (Takara Bio, "CEL", n = 4) and several interventions (11x3 replicates).

  Dataset EGAD00001005935

• RNA-seq data from primary AML samples with t(3;8)

  RNA-seq was generated to investigate differences in gene expression between t(3;8) AML and other primary AMLs. Briefly, sample libraries were prepared using 500 ng of input RNA according to the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche) using Unique Dual Index adapters (Integrated DNA Technologies, Inc.). Amplified sample libraries were paired-end sequenced (2x100 bp) on the Novaseq 6000 platform (Illumina

  Dataset EGAD00001006819

• Single circulating tumor cells in hepatocellular carcinoma

  We determined intra- and inter-vascular transcriptional heterogeneity within the circulatory system using single-cell RNA-sequencing of 113 CTCs isolated from four key vascular sites along their dissemination route in ten HCC patients. The dataset consists of 146 paired-end fastq files from 113 sigle CTCs, HuH-7 cell line, Hep3B cellline, white blood cell, tumor and normal bulk tissue.

  Dataset EGAD00001007642

• ATAC-seq data from primary AML samples with t(3;8)

  Open chromatin regions in the MYC super-enhancer region were investigated by ATAC-seq in t(3;8) AML. ATAC-seq was performed as described (Buenrostro et al, 2013) with a modification in the lysis buffer (0.30 M sucrose, 10 mM Tris pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.1% NP40, 0.15 mM Spermine, 0.5 mM Spermidine, 2 mM 6AA) to reduce mitochondrial DNA contamination.

  Dataset EGAD00001007910

• Triple negative breast cancer matched patient and pdx dataset

  PDX aCGH (txt), WES (fastq) and RNASeq (fastq) samples from mice treated with cisplatin. Primary samples and matched pdx samples from multiple passages. Models from the Marie Curie Instute (HBCx1, HBCx4B, HBCx8, HBCx10, HBCx12B, HBCx14, HBCx15, HBCx16, HBCx17, HBCx23, HBCx24, HBCx27, HBCx28, HBCx30, HBCx31, HBCx33, HBCx39, HBCx40, HBCx43, HBCx51, HBCx63, HBCx66, HBCx92, HBCx106) and the NKI (T127, T162, T241, T250, T283, T302, T336).

  Dataset EGAD00001009046

• VRK3 depletion in Pontine Diffuse Midline Glioma DMG-K27 altered cells

  In order to investigate possible mechanisms underlying the phenotype of cell fitness decline observed following decrease of VRK3 in pontine DMG-K27 altered cells 7, we examined differences in global gene expression. RNA-seq was performed 44h and 60h post-transduction with two distinct shRNAs targeting VRK3 to be able to evaluate the early impact of VRK3 knock-down (KD) in four independent in vitro models of DMG

  Dataset EGAD00001010097

• Multiple myeloma follow-up Dataset

  77 samples collected from 35 multiple myeloma patients. Each patient provided one healthy sample and one primary tumor sample and, in some cases, also samples collected after the progression of the disease.

  Dataset EGAD00001010161

• Whole Exome and Whole Genome Profiling as well Genome-Wide Methylation Profiling from Early to Advanced Chronic Lymphocytic leukemia (CLL), Genome-Wide Methylation Profiling in Monoclonal B Cell Lymphocytosis (MBL)

  Serial whole exome sequencing of samples collected from 21 patients at multiple time points during progression from early to late chronic lymphocytic leukemia (CLL) and one matching non-tumor tissue sample from each patient. Additional whole genome sequencing of samples from 3 selected patients. Genome-wide B cell methylation compared between 5 healthy donors from the same age group as patients, 20 patients with monoclonal B cell lymphocytosis and in serial CLL samples with matching whole exome sequencing. Moreover, genome-wide single-cell RRBS-profiling of B cells from one healthy donor and from one patient with CLL was performed using a protocol newly developed by the A. Meissner group.

  Study phs001431

• Neo-CheckRay

  Patients with oestrogen receptor-positive (ER+), HER2-negative, early breast cancer (BC) have low pathological complete response (pCR) rates following neoadjuvant chemotherapy (NACT). Phase 3 trials showed that adding an anti-PD-1 immune checkpoint inhibitor (ICI) improves pCR, but there was less benefit in the PD-L1 negative tumours, characterised by an immune “cold” tumour microenvironment (TME). We hypothesized that immune-modulating stereotactic body radiation therapy (iSBRT) could enhance treatment response by reprogramming the immune deprived TME in early ER+/HER2- BCA. We conducted a phase 2, randomized, multicentre trial evaluating NACT plus iSBRT, with or without durvalumab (anti-PD-L1) and with or without oleclumab (anti-CD73) in 147 patients with high-risk, early, ER+/HER2- breast cancer patients.

  Study EGAS50000001777

• Hematopoietic differentiation at single-cell resolution in NPM1-mutated AML

  To investigate the relationship between somatic mutations and phenotypic hematologic differentiation at the single-cell level, we used a droplet-based multi-omics single-cell platform on eleven NPM1-mutated AML diagnostic samples. We developed a bioinformatics framework to perform phylogeny-driven genotype correction, that allowed us to study 52 103 single cells. Intra-leukemic genetic heterogeneity was detectable in all patients, including a branched architecture in nine of them, always owing to co-occurring signaling mutations. We identified two groups of NPM1-mutated AML, one characterized by a progenitor immunophenotype and a second one with a predominant monocytic differentiation. We also identified various degrees of intra-leukemic immunophenotype heterogeneity, sometimes associated with strong genetic/phenotype correlations.

  Study EGAS00001006565

• Neuroblastoma tumor heterogeneity and cell plasticity (from patients)

  Two cell identities, noradrenergic and mesenchymal, have been characterized in neuroblastoma cell lines according to their epigenetic landscapes relying on specific core regulatory circuitries of transcription factors. Yet, their relationship and relative contribution in patient tumors remain to be defined. Here, we document a spontaneous plasticity between the noradrenergic and mesenchymal identities in a subset of cell lines. Strikingly, mesenchymal neuroblastoma cells revert to a noradrenergic phenotype in vivo. Consistently, tumor cells with a mesenchymal identity are detected in single-cell transcriptomic analyses of neuroblastoma tumors and PDX models. Our data also highlight neuroblastoma intra-tumor heterogeneity with the co-existence of distinct tumor populations, including sympathoblast-like and chromaffin-like cells suggesting that neuroblastoma cells arise from a common sympatho-adrenal progenitor.

  Study EGAS00001005322

• The University of Hong Kong Colon Cancer Organoids Genomics Study Data Access Committee

  Dac EGAC00001001405

• Data Access Committee of the Department of Molecular Neurology, UKEr

  Dac EGAC00001002455

• The Chinese University of Hong Kong (CUHK) Circulating Nucleic Acids Research Group (CNARG)

  Dac EGAC00001002648

• Tracking the evolution of esophageal squamous cell carcinoma under dynamic immune selection by multi-omics sequencing

  Dac EGAC00001002881

• DAC - Dept. of Pathology LUMC

  DAC of the Department of Pathology of Leiden University Medical Center

  Dac EGAC50000000376

• Single cell sequencing: Capturing the origin and dynamics of chromosomal copy-number heterogeneity

  Study EGAS00001003812

• Human gastrointestinal epithelia of the esophagus, stomach and duodenum resolved at single-cell resolution

  Study EGAS00001004695

• The DNA methylome of cervical cells and risk of ovarian cancer

  Study EGAS00001005045

• JAK/STAT signaling promotes the emergence of regenerative cell states in ulcerative colitis

  Study EGAS00001007098

• Y chromosome alignment

  Variations on the Y chromosome from 44 samples

  Dataset EGAD00010001573

• The storage time FFPE set

  Dataset EGAD00001000829

• EGAD00000000085

  Gabriel samples from the German Gabriel Advanced Survey

  Dataset EGAD00000000085

• EGAD00000000084

  Gabriel samples from the German Gabriel Advanced Survey

  Dataset EGAD00000000084