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• Black Representation in Genomic Research Whole Blood eQTL Study

  This dataset contains whole genome sequencing (WGS) results, as well as mRNA-seq of RNA extracted from a venous blood sample, from 23andMe research participants of African ancestry. This dataset facilitates the study of gene expression, genetic variation and the genetic architecture of gene expression in individuals of African ancestry.

  Study phs002969

• Methylome of memory B cells with autoproliferation in MS

  Methylome of resting/hi and autoproliferating/Dim memory B cells in Multiple sclerosis patients. In brief, non-proliferating (CFSEhi) and AP+ (CFSEdim) CD19+ CD27+ B cells from PBMCs of 6 natalizumab-treated female RRMS (NAT) patients were sorted following 7 days of autoproliferation. Methylome libraries for 12 samples were constructed by applying the post-bisulfite adaptor tagging (PBAT) method on lysed cells and sequencing was conducted on Illumina NovaSeq 6000. CpGs with minimum 10X coverage were used for differential methylation position (DMP) analysis.

  Dataset EGAD50000001269

• The Genomic Map of Poland in Open Access

  The main goal is to prepare and share WGS/WES of Polish population In this project NGS (next generation sequencing) was performed using Illumina NOVASEQ 6000 and Illumina DRAGEN aligner was used. Shared BAM and BAM.BAI files Library Construction Protocol: Illumina DNA PCR-Free Prep, Tagmentation. Reference Genome: GRCh37.

  Study EGAS50000000096

• Screening for tryptophan conversion in human stool samples

  The goal of this study was to compare the tryptophan metabolism of different human fecal microbiota. To this end we enriched human stool samples in culture medium and measured growth and metabolite concentrations after 48h of culture. We quantified the consumption of tryptophan and the production of typical tryptophan derivaties.

  Study EGAS50000000548

• Investigation of chromatin accessibility in clear cell renal cell carcinoma using ATAC-seq

  To identify regions of open and accessible chromatin in clear cell renal cell carcinoma (ccRCC), we performed ATAC-seq on the 786-O, A-498, UM-RC-2 ccRCC cell lines, as well as HK-2 normal renal epithelium cell line, cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions. Data are provided in raw fastq and processed narrowPeak fomats. Data were processed using the nf-core atacseq pipeline.

  Dataset EGAD50000001885

• The Celiac Gene Expression Data Access Committee

  This study presents RNA sequenced from several intestinal phenotypes such as from patients with damaged intestinal mucosa as well as from those without a damaged intestine but still an autoantibody response to tissue transglutaminase (“potential celiac disease”) or those with treated celiac disease. By combining phenotypes in a much larger number of tissue samples from both peripheral blood and mucosal biopsies, we found highly differentially expressed genes, but also identify genes involved in controlling and triggering celiac disease associated changes. This study identifies molecular mechanisms involved in celiac disease and new possible targets for treatment and for identification of individuals at risk.

  Dac EGAC50000000630

• Transcriptomic analyisis of 54 samples of AC16 cells exposed to trastuzumab

  Data of 54 samples with their 54 paired fastaq files that were sequenced in a Novaseq 6000 platform. Samples correspond to the three biological replicates of AC16 cells (i.e. AC16, C1, C2). Each biological replicate was edited to carry either of the three different genotypes of the rs1136201 variant (i.e. AA, AG, GG) and each genotype was enriched to express HER2 protein in three levels (i.e. low, medium and high expression) as selected by FACS. Additionally, treatment of each sample was performed and sequenced in duplicates (i.e. 1 and 2)

  Dataset EGAD50000001705

• Transcriptomic analysis of hiPSC-derived vascular cells from CADASIL and isogenic control patient lines

  Bulk-RNA sequencing from hiPSC-derived cells (hiPSC; Endothelial Cells; Neural Crests Cells; Vascular Smooth Muscle Cells) from CADASIL patient lines (n=3) and respective isogenic-controls (n=3). CADASIL is a hereditary brain small vessel disease caused by pathogenic variants in the NOTCH3 gene, which lead to deposits of NOTCH3 protein in the walls of small arteries. This causes pathological vessel wall changes including degeneration of vascular smooth muscle cells. To investigate the impact of pathogenic NOTCH3 variants in hiPSC and differentiated cells we performed a bulk-RNA sequencing.

  Dataset EGAD50000002181

• Transcriptomic data from a SARS-CoV-2 human challenge study (Kelly Research Group, Arkansas Children’s Research Institute)

  This dataset contains paired-end RNA-Seq data generated from mid-turbinate nasal and throat samples collected as part of a first-in-human SARS-CoV-2 experimental challenge study conducted in the United Kingdom in 2021. Total RNA was extracted using QIAamp Viral RNA kits (Qiagen), and libraries were prepared using TruSeq RNA Exome kits (Illumina). Sequencing was performed on a NovaSeq X Plus instrument configured for 100 bp paired-end reads. The dataset includes raw FASTQ files and associated de-identified metadata.

  Dataset EGAD50000002078

• sWGS on cfDNA and matching tumor DNA in pediatric cancer

  This dataset contains shallow whole genome sequencing data from paired cfDNA - tumor DNA samples of various pediatric cancer entities. Files are provided in fastq format. Samples were sequenced on an Ion Proton sequencer (Thermo Fisher Scientific) or a Hiseq3000 (Illumina). Data analysis is available at https://github.com/rmvpaeme/sWGS_pediatric_cancer.

  Study EGAS00001005198

• Whole exome sequencing in familial Multiple Sclerosis

  The purpose of the study is to determine whether variants of genes are associated with greater risk of Multiple Sclerosis (MS). We used whole-exome sequencing in 138 individuals from 23 families including at least 2 members with MS. We compare patients with MS, patients with other autoimmune diseases (AID), and unaffected individuals.

  Study EGAS00001004204

• Personalised Mapping of Tumour Development in Synchronous Colorectal Cancer Patients

  We performed an in-depth characterisation of 12 tumours from 3 syCRC patients by analysing histopathological, whole genome sequencing and RNA-sequencing data. We assessed the extent of genetic overlap between synchronous tumours and examined associations between clinicopathological information and the molecular, microbial and immune features of each tumour genome.

  Study EGAS00001004413

• Characterization of Leukemic Stem Cells in DNMT3Amut and NPM1mut AMLs

  Trascriptomic profile of FACS-sorted LSCs from diagnostic DNMT3Amut and NPM1mut AML patients using a novel sorting strategy. Briefly, positive selection for GPR56 and a negative selection for NKG2DLigands were used to enrich for LSCs in both CD34+ and CD34- subpopulations. Primary samples were retrospectively collected based on their mutational profile.

  Study EGAS00001006527

• Correction of FFPE artefacts in WGS data

  The ability to precisely characterise mutational signatures from FFPE-derived DNA has tremendous translational potential. However, sequencing of DNA derived from FFPE material is known to be riddled with artefacts. To correct for this, we introduce FFPEsig, a computational algorithm to rectify the formalin-induced artefacts in the mutational profile.

  Study EGAS00001005331

• miRNA-seq data for Molecular Characterization of ETMR

  This dataset contains miRNA-seq data from 10 patients. Small RNAs were isolated as described previously57,58 from fresh-frozen tumour material. In brief, total RNA was extracted using guanidinium isothiocyanate/phenol extraction followed by 3′-adaptor ligation of barcoded adenylated adaptors. Samples were pooled in two sets of five samples. Subsequently, gel electrophoresis was used to isolate small RNAs (19–35 nt) and purified using ethanol precipitation. Fragments were then amplified using standard PCR, isolated using gel electropho- resis and purified using ethanol precipitation. Samples were sequenced on a HiSeq 2000 v.4 machine resulting in 10 Fastq files.

  Dataset EGAD00001006218

• Genomic Landscape of Malignant Peripheral Nerve Sheath Tumor-like Melanoma

  Malignant peripheral nerve sheath tumor (MPNST)-like melanoma is a rare malignancy with overlapping characteristics of both neural sarcoma and melanoma. The genomics of MPNST-like melanoma have not been previously described. In this study, we performed whole exome sequencing analysis in 8 samples from 6 patients diagnosed with MPNST-like melanoma. Our results demonstrate that, although MPNST-like melanoma shares oncogenic alterations common to both cutaneous melanoma and MPNST, it also presents unique genomic alterations not previously described in neither of the malignancies.

  Dataset EGAD00001006999

• Whole genome sequencing of Osteosarcoma clonal evolution

  Multiple large-scale genomic profiling efforts have been undertaken in osteosarcoma to define the genomic drivers of tumorigenesis, therapeutic response, and disease recurrence. The spatial and temporal intratumor heterogeneity could also play a role in promoting tumor growth and treatment resistance. Here, we conducted longitudinal whole-genome sequencing of 37 tumor samples from eight patients with osteosarcoma that relapsed or became refractory to initial therapy. We found that the chemoresistant population in recurrent osteosarcoma is subclonal at diagnosis, emerges at the time of primary resection due to selective pressure from neoadjuvant chemotherapy, and is characterized by unique oncogenic amplifications.

  Dataset EGAD00001011285

• LCM-ATACseq on human lung macrophages

  In this study we employed Laser Capture Microdissection (LCM) for the multimodal profiling of lung macrophages cell populations as a function of location within the healthy tissue. In detail, macrophage mini-bulks (~100 cells) were collected from 4 healthy human donors in 5 different locations of the airways (a total of 20 biopsies), including parenchyma (L1 – lower left lobe (LLL); L6 – 80% distance from LLL tip), trachea (L2), bronchi (L3 – 1st/2nd generation; L5 – 3rd/4th generation), and processed for ATAC-seq.

  Dataset EGAD00001008693

• LCM-RNAseq on human lung macrophages

  In the reported study, we employed Laser Capture Microdissection (LCM) for the transcriptome profiling of lung macrophages cells populations as a function of location within the healthy tissue. In detail, macrophage mini-bulks (100 cells each) were collected by LCM from 4 healthy human donors in 5 different locations of the airways (a total of 20 biopsies), including parenchyma (L1 – lower left lobe (LLL); L6 – 80% distance from LLL tip), trachea (L2), bronchi (L3 – 1st/2nd generation; L5 – 3rd/4th generation) and processed for RNA-seq.

  Dataset EGAD00001008694

• WGS data of fetal stem cells (15x) and culture-associated mutations of iPSCs and ISC

  This data set includes WGS data of the in vivo acquired mutations in fetal ISCs and HSPCs of 4 foetuses ( T21=2, D21= 2). In addition, this data set includes sub-clonal fetal ISCs to determine the culture-associated mutations of fetal ISCs. Also, it concludes clone +subclone WGS data of iPSCs derived of the fetal ISCs

  Dataset EGAD00001008475

• VCF file from 16 carriers of the BMPR2 p.Arg491Gln mutation in a family affected by HPAH

  VCF file from 16 carriers of the BMPR2 p.Arg491Gln mutation in a family affected by hereditary pulmonary arterial hypertension (HPAH). Whole genome sequencing of these samples was performed in an Illumina HiSeq 4000 instrument. Libraries were prepared using the Fisher PE Kit (Kapa Biosystems). BAM files were processed at the CNAG (Barcelona) with their pipeline, including GATK v3.6 for genotyping and other tools such as snpEff for annotating variants, to produce this VCF file with a total of 9,643,070 variants, out of which 7,891,370 are SNVs.

  Dataset EGAD00001005758

• Population-based analysis of POT1 variants in a cutaneous melanoma case-control cohort

  Pathogenic germline variants in the protection of telomeres 1 gene (POT1) have been associated with predisposition to a range of tumor types, including melanoma, glioma, leukemia and cardioangiosarcoma. We sequenced all coding exons of the POT1 gene in 2,929 European-descent melanoma cases and 3,298 controls, identifying 43 protein-changing genetic variants. We performed functional studies on each of these variants and explored their possible contribution to disease risk.

  Dataset EGAD00001009848

• TK-EPN862 - Patient-derived xenograft model of Posterior Fossa A Ependymoma - RNAseq

  In Vivo Loss of Tumorigenicity in a Patient-Derived Orthotopic Xenograft Mouse Model of Ependymoma. Whitehouse et al. 2023 Frontiers in Oncology. We describe the establishment of a patient-derived orthotopic xenograft (PDOX) model of posterior fossa A (PFA) EPN, derived from a metastatic cranial lesion. Patient and PDOX tumors were analyzed using RNA sequencing. RNAseq data (paired end) provided here correspond to Primary tumour, two metastatic lesions (one spinal, one cranial), and a patient-derived xenograft derived from the patient.

  Dataset EGAD00001009870

• RNA-seq of cells after injection into immunodeficient mice

  This dataset includes 73 samples profiled by high-throughput Illumina sequencing, in bam format, aligned to GRCh37. Normal human CD34+ cord blood (CB), bone marrow (BM), or post-natal thymus (PNT) cells were transduced with various combinations of T-ALL oncogenes, cultured in vitro on OP9-DL1 feeders for up to 25 days, and then transplanted into immunodeficient NSG or NRG mice. The samples were collected after development of frank leukemia in recipient mice.

  Dataset EGAD00001009751

• Comprehensive copy number aberration analysis using digital Multiplex Ligation-dependent Probe Amplification (digitalMLPA) in pediatric B-cell precursor acute lymphoblastic leukemia

  In this study a next-generation sequencing based method was applied to comprehensively screen for recurrent, disease-relevant copy number aberrations in a cohort of Hungarian patients. Diagnostic bone marrow samples from 260 children with B-cell acute lymphoblastic leukemia as well as 72 control samples and were investigated by digital multiplex ligation-dependent probe amplification using the disease-specific D007 probemix. Whole chromosome gains and losses, as well as subchromosomal copy number aberrations were simultaneously profiled.

  Dataset EGAD00001010878