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• Whole exome sequencing of 49 tumor-blood pairs and transcriptome sequencing of 44 tumors for adrenocortical tumors

  Adrenal Cushing syndrome, which leads to type 2 diabetes, obesity and hypertension, is caused by ACTH-independent production of glucocorticoid by adrenocortical tumors. To investigate the genetic origins of cortisol-producing adrenocortical tumors, we performed whole exome sequencing of 49 tumor-blood pairs and transcriptome sequencing of 44 tumors

  Study EGAS00001000712

• Methylation analysis for plasma DNA of patients with organ transplantation

  We developed Genetic-Epigenetic Tissue Mapping (GETMap) to determine the tissue composition of plasma DNA carrying genetic variants not present in the constitutional genome through comparing their methylation profiles with relevant tissues. We validated this approach by showing that, in pregnant women, circulating DNA carrying fetal-specific alleles was entirely placenta-derived.

  Study EGAS00001004788

• Genomic Variant Dataset of 5,309 Jeju Residents: Integrated WGS and SNP Array Analysis

  This dataset comprises genomic data from the Jeju Genome Project (JGP). WGS libraries were prepared using TruSeq Nano DNA kits and sequenced on Illumina NovaSeq 6000, with variants called via the DRAGEN Germline pipeline (v4.0.3). Genotyping was performed using the customized Axiom_JPMI v1 Chip on the Affymetrix GeneTitan platform. Raw data were processed using APT (v2.11.4), followed by phasing with Eagle (v2.4.1) and imputation via Minimac3 (v2.0.1) using a JGP-specific reference panel to optimize accuracy for the Jeju population.

  Dataset EGAD50000002451

• Dataset of 2485 CD8 T cells from non-muscle-invasive bladder cancer patients in context of BCG treatment

  FASTQ files from scRNAseq (smartseq2 protocol) from 2485 CD8 T cells from 4 non-muscle-invasive bladder cancer patients who received BCG treatment (induction treatment of 6 weekly instillations). Concerning the 'phenotype' column in metadata : pre-treatment samples include tumor samples ('Tumor') and normal adjacent bladder tissue ('Extratumor'). For post-treatment samples : no residual tumor was found in the bladder of the 4 patients after the BCG treatment . The post-treatment samples with 'Tumor' as phenotype denote samples from macroscopically suspect zones, but with microscopically no tumor detected.

  Dataset EGAD50000002007

• Single-nuclei multiomic analysis of KOLF2.1J human induced pluripotent stem cells-derived differentiated dopaminergic neurons

  Datasets consists of 12 samples of nuclei from hIPSCs differentiated optimized protocols for generating dopaminergic neurons. 6 single nuclei (RNA-ATAC) samples of XMAS protocol with cells collected at days 0,11,16,28,42 and 56 after differentiation. 3 snRNA-seq samples from AMS protocol of cells collected at days 14,16 and 28 after differentiation and 3 snRNA-seq samples with AMS protocol until day 14 grafted and grafts processed after 5 months grafting.

  Dataset EGAD50000002054

• Bulk RNA and ATACseq of 2 XLP patients and 5-6 HD

  The dataset contains five samples from P1, one pre-HSCT and four post-HSCT, one sample from P2 and 5-6 HD. RNAseq reads were processed using the LUMC BIOWDL RNAseq pipeline v5.0.0 (https://github.com/biowdl/RNA-seq). Genes with log2CPM≥1 in at least 10% of all samples were retained for downstream analysis. Differential gene expression analysis was performed using the dgeAnalysis R-Shiny application (https://github.com/LUMC/dgeAnalysis/tree/v1.4.4). ATACseq reads were processed using the LUMC BIOWDL Chipseq pipeline 1.0.0-dev (https://github.com/biowdl/ChIP-seq).

  Dataset EGAD50000002072

• Single Cell RNASeq for ARMS tumors

  6 samples from 3 mice related to Alveolar Rhabdomysarcoma. In this study, we employ scRNA-seq to analyze ARMS tumors from a conditional mouse model of ARMS. The conditional knock-in mouse model of ARMS, in which the Pax3-Foxo1 allele is activated in the skeletal muscle cell lineage via Myf6Cre (Myf6CrePax3P3Fm/P3FmTrp53F2-10/F2-10; referred to hereafter as GEMM-ARMS) has been described previously23,24. These mice also carry Cre-activated reporters, eYFP to label Pax3::Foxo1-expressing cells and dsRED2 to labels Myh2-expressing cells. Some tumors are derived from GEMM-ARMS mice, and some are allografts of GEMM-ARMS tumors into immunodeficient mice

  Dataset EGAD50000002241

• Dataset of the transcriptomic profiling of skin biopsies from 221 psoriasis patients following treatment with Zasocitinib

  This dataset contains the paired fastq files generated from 221 samples collected from patients with moderate-to-severe plaque psoriasis and sequenced on the Illumina NovaSeq 6000 platform. Patients were randomized in a 1:1:1:1:1 ratio to receive oral Zasocitinib at doses of 2 mg, 5 mg, 15 mg, 30 mg, or placebo once daily for 12 weeks. Clinical response was defined as achieving a PASI 75 response at week 12, while histologic response was defined as the absence of KRT16-positive cells in lesional skin after 12 weeks of treatment.

  Dataset EGAD50000002224

• RNA-seq datatset of primary human thymocyte subsets

  FASTQ-files of RNA-seq experiments of 8 primary human thymocyte subsets, isolated by flow-cytometry (FACS) from neonatal thymus biopsies. All samples were sorted to be negative for the expression of the lineage surface markers CD11c, CD19, CD56, CD141 and CD303 and additionally had the following surface phenotypes: DN1 (CD4-CD8-CD7+CD1a-CD161-CD38-); DN2 (CD4-CD8-CD7+CD1a-CD161-CD38+CD3-TCRab-); DN3 (CD4-CD8-CD7+CD1a+); ISP (CD4+CD8-CD3-TCRab-CD1a+); DPE (CD4+CD8+TCRab-CD69-); DPL (CD4+CD8+TCRab+CD69+); SP4 (CD4+CD8-); SP8 (CD4-CD8+). Samples were sorted from 2-4 pediatric patients undergoing heart surgery.

  Dataset EGAD50000001599

• Common origin and somatic mutation patterns of composite lymphomas and leukemias

  The dataset contains six composite lymphomas and leukemias cases (four composite B-cell lymphomas (case 1-4), and two combinations of B-cell and T-cell lymphoma (case 5+6)). Two tumor and one non-tumor (NTC) sample were sequenced from each case after library prep with NEBNext Ultra DNA Library Prep Kit, Exome capturing was done with NimbleGen SeqCap EZ Choice kit, and sequenced on a Illumina HiSeq 2000 HO and given as fastq files. WGA (Qiagen REPLI-g kit) was used for case 2 and 3. Case 1-4 were microdisected, case 5+6 were flow-sorted.

  Dataset EGAD50000001486