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• Single-cell characterization of human GBM reveals regional differences in tumor-infiltrating leukocyte activation

  Background: Glioblastoma (GBM) harbors a highly immunosuppressive tumor microenvironment (TME) which influences glioma growth. Major efforts have been undertaken to describe the TME on a single-cell level. However, human data on regional differences within the TME remain scarce. Goals: we performed single-cell RNA sequencing (scRNAseq) on paired biopsies from the tumor center, peripheral infiltration zone and blood of five patients with primary GBM Details: This EGA study includes raw data sequencing files for the scRNA-seq samples. The processed data (output from Alevin, UMI count matrix and cell metadata) are available from GEO https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197543

  Study EGAS50000000302

• Bulk RNAseq - Calprotectin in vitro effects on human early hematopoiesis

  To explore the effects of calprotectin (CAL) on early hematopoiesis, we incubated CD34+ cells from four healthy donors for 7 days in the presence of stem cell factor (SCF), FLT3-ligand and thrombopoietin (TPO) without and with CAL, interleukin-6 (IL6) and the IL6_CAL combination before collecting cells. We performed the same experiment with CD34+ cells collected from three patients with JAK2-V617F-mediated myelofibrosis (MF). A total of 135,545 cells from healthy donors and 111,725 cells from myelofibrosis patients were analyzed by single-cell RNA sequencing (scRNA-seq) using the 10X Chromium droplet-based platform. Bulk RNAseq 4 conditons : -Control - Calprotectin - IL-6 - Calprotectin+IL-6

  Study EGAS50000000454

• Single cell epigenomic study of H3-K27M mutant diffuse midline glioma across age and location

  Histone 3 lysine27-to-methionine (H3-K27M) mutations most frequently occur in childhood diffuse midline gliomas (DMGs) of the pons, but are also increasingly recognized in adult DMGs. Their potential heterogeneity at different ages and midline locations are vastly understudied. Here, through dissecting the single-cell epigenomic architectures of a comprehensive cohort of patient H3-K27M DMGs, we delineate how age and anatomical location shape glioma cell-intrinsic and -extrinsic features in light of the shared driver mutation. We analyzed the open chromatin profiles of 8 tumors utilizing the single-cell/nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq)

  Study EGAS00001007035

• SNPArray_Viet

  The compressed file contains plink format file for the Affymetrix Human Origins SNP array data of 260 individuals generated and analyzed in Liu et al 2020 study of 22 ethnolinguistic groups in Vietnam.

  Dataset EGAD00010002287

• Long-read sequencing for cell-free DNA analysis (human pacbio)

  8 pregnant women at the 3rd trimesters, 4 hepatitis B carriers, and 4 patients with hepatocellular carcinoma

  Study EGAS00001006609

• H3Africa H3AChipDesign ACCME

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

  Dataset EGAD00001004505

• H3Africa H3AChipDesign TrypanoGEN2

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

  Dataset EGAD00001004220

• H3Africa H3AChipDesign ELSI

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

  Dataset EGAD00001004316

• H3Africa H3AChipDesign NEEDI

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

  Dataset EGAD00001004334

• H3Africa H3AChipDesign CAfGEN

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

  Dataset EGAD00001004533

• WES data for Family 2 from optic atrophy study

  The dataset includes the BAM files from WES experiments performed on a proband presenting with syndromic optic atrophy and his healthy parents - Family 2 in our study

  Dataset EGAD00001005344

• CCMA

  This dataset has the processed WGS data for the cancer models in CCMA.

  Dataset EGAD00001009633

• Targeting Heterochromatin Eliminates Malignant Stem Cells in Chronic Myelomonocytic Leukemia Through Reactivation of Retroelements and Innate Immune pathways

  Hematopoietic stem cell (HSC) aging involves heterochromatin reorganization. These repressive marks together with DNA methylation are essential for suppressing transposable elements (TEs). In this study we analyze heterochromatin and transcriptomic changes occurring at genes and TEs in HSCs from chronic myelomonocytic leukemia, a severe myeloid malignancy affecting the elderly, compared to age-matched cells, and in the presence or absence of a combination of epidrugs.

  Study EGAS50000000688

• Characteristics and Inflammatory Markers in Children with Eosinophilic Esophagitis (EoE)

  The overall protocol for the samples used in this study collects medical information, blood, and biopsy samples from children with eosinophilic esophagitis (EoE) over time to understand clinical characteristics and disease pathogenesis. Our patient population has confirmed EoE and symptoms of esophageal dysfunction characteristic endoscopic findings of EoE. Fibroblasts isolated from esophageal tissue samples from 2 subjects with active EoE and 2 control subjects were evaluated using single cell RNA-sequencing (scRNA-seq).

  Study phs003869

• Bulk RNAseq from in vitro generated macrophages and T cells, and mUM tumour biopsies

  Monocyte derived macrophages were polarised into M1 or M2 using IFNg+ ILP or IL-4 respectively (n =4) . Pan T cells were cultured with or without IL-2 for 4 days (n=4 - 6). Pan T cells were co-cultured with THP1 tumour cells for 20 hours in the presence or absence of ImmTAC molecules and in the presence or absence of M2 macrophages. Sorted T cells and macrophage populations prior and post co-culture were analysed by bulk RNA sequencing (60 million reads per sample) using the Illumina NovaSeq system. Tumour biopsies were obtained from uveal melanoma patients (n = 35) pre and 16 days post treatment with tebentafusp. Biopsies, which were either snap frozen or put in RNA later, were analysed by bulk RNA sequencing (50 million reads per sample) using the Illumina NovaSeq system

  Dac EGAC50000000518

• Genome-wide association study in multiple human prion diseases suggests genetic risk factors additional to PRNP

  We conducted GWAS of sporadic CJD, variant CJD, iatrogenic CJD, inherited prion disease, kuru and resistance to kuru despite attendance at mortuary feasts. After quality control we analysed 2000 samples and 6015 control individuals (provided by the Wellcome Trust Case Control Consortium and KORA-gen), for 491032-511862 SNPs in the European study. Association studies were done in each geographical and aetiological group followed by several combined analyses.

  Study EGAS00000000097

• Targeting Heterochromatin Eliminates Malignant Stem Cells in Chronic Myelomonocytic Leukemia Through Reactivation of Retroelements and Innate Immune pathways

  Hematopoietic stem cell (HSC) aging involves heterochromatin reorganization. These repressive marks together with DNA methylation are essential for suppressing transposable elements (TEs). In this study we analyze heterochromatin and transcriptomic changes occurring at genes and TEs in HSCs from chronic myelomonocytic leukemia, a severe myeloid malignancy affecting the elderly, compared to age-matched cells, and in the presence or absence of a combination of epidrugs.

  Study EGAS50000000367

• Targeted Sequencing of 52 Genes for Severe COVID-19

  This dataset comprises targeted sequencing data of 52 genes previously implicated in severe COVID-19 outcomes. The study includes samples from 764 individuals with severe COVID-19 and 3,939 population-based controls from the GCAT cohort (Spain). Molecular Inversion Probes (MIPs) were utilized for cost-effective and precise sequencing of the selected genes. The targeted genes include: Inflammasome/IL-1/TNF Pathway: NLRP3, CASP1, CASP8, IL1B, TNF, RIPK1, RIPK3, MYD88, TNFRSF13B SARS-CoV-2 Entry/Replication: ACE2, TMPRSS2, FURIN, SLC6A20, DDX1, DDX58, TLR4, FYCO1, CTSB, CTSL, ADAM17 Complement System: MBL2, CFH, CFI, CFB, ADAM10, CD46 Interferon Signaling: TLR3, IFIH1, IFITM3, TBK1, TLR7, IL10RB, IFNAR1, IFNAR2, SIGLEC1, MYD88, IFNGR1 Chemokine Receptor Signaling: CCR1, CCR3, CCR2, CCR9, IL8, CXCL3, CXCL10, CXCR6, XCR1, CCL2, CCL20 Immunodeficiency Genes: CASP8, CD46, CFB, CFH, CFI, IFNAR1, IFNAR2, IFNGR1, IFIH1, MYD88, NLRP3, RIPK1, TBK1, TLR3, TLR7

  Dataset EGAD50000001378

• RNAseq Data Cyr61-MAC and HUVEC

  Gene expression of MAC enriched by adhesion to Cyr61 in comparison to HUVEC. This dataset includes RNAseq Data from myeloid angiogenic cells (MAC) enriched from peripheral blood by adhesion to Cyr61 (4 samples prepared from different donors) and of human umbilical vein endothelial cells (HUVEC) (4 samples). Illumina NextSeq500 technology was used. FASTQ data are provided.

  Dataset EGAD50000000758

• Whole genome sequencing of Multiple Myeloma CD138positive bone marrow plasma cells and saliva control samples

  Whole genome paired sequencing of Multiple Myeloma CD138positive bone marrow plasma cells and saliva control samples (6 tripletts, tumor1, tumor2, saliva control) from 6 patients. WGS was done on HiSeq X-Ten or Novaseq 6000 with Illumina TruSeq Nano DNA.

  Dataset EGAD00001008618

• The data access committee for Evolution of neoantigen landscape during immune checkpoint blockade in non-small cell lung cancer.

  Dac EGAC00001000757

• Data Access Committee for the study "Somatic chronology of treatment-resistant prostate cancer via deep whole-genome ctDNA sequencing"

  Dac EGAC00001002479

• eQTL-CHiC DAC

  The Data Access Committee for eQTL-CHiC and related data from Ray-Jones et al., 2024.

  Dac EGAC50000000445

• Whole Genome Sequencing of Two Family Trios with 22q.11.2 Deletion Syndrome

  Two subjects with 22q11.2 deletion syndromes (22q11DS) and their parents were recruited for a whole genome sequencing study to identify candidate genetic modifiers of the various phenotypes seen in 22q11DS. Both probands had a typical 3 megabase deletion on chromosome 22q11.2 but discordant phenotypes.

  Study phs000837

• Clones derived from early passage tumoroids of colorectal cancer

  We obtained different clones from early passage CRC tumoroids to study mutational signatures specific for truncal or private somatic alterations. These whole genome sequences are part of a larger study on the heterogeneity and evolution of DNA mutation rates in microsatellite-stable colorectal cancer.

  Study EGAS50000000107