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• Dataset for WGS and RNA samples of acute myeloid leukemia with MNX1 expression (non-hipo)

  This dataset contains 115 samples of WGS, ATAC, 4C and RNAseq samples of patients with acute myeloid leukemia. The sequencing was performed on Illumina HiSeq 4000, 2000 and HiSeq X using Illumina TruSeq Nano DNA and Agilent Strand Specific RNA Kits. The sequencing was always paired.

  Dataset EGAD50000001097

• WGA_Fulani_Database

  In total, 329 DNA samples were genotyped on the Illumina Infinium H3Africa Consortium array (designed for 2,271,503 SNPs; using BeadChip type: H3Africa_2019_20037295_B1). Genotyping was performed at the SNP&SEQ Technology Platform (NGI/SciLifeLab Genomics, Sweden). WGA Fulani dataset includes individuals from the following populations: 33 BurkinaFaso_FulaniBanfora, 32 BurkinaFaso_FulaniTindangou, 33 Mali_FulaniDiafarabe, 35 Cameroon_FulaniTcheboua, 34 Chad_FulaniBongor, 24 Chad_FulaniLinia, 25 Niger_FulaniAbalak, 32 Niger_FulaniAder, 31 Niger_FulaniDiffa, 20 Niger_FulaniBalatungur, and 30 Niger_FulaniZinder.

  Dataset EGAD50000000654

• scRNAseq of co-culture of human organoids with polarized pro-inflammatory or anti-inflammatory macrophages

  In order to know if the mechanisms we identified in mice – demonstrating that macrophages are able to orchestrate the intestinal regenerative process – are conserved in humans we develop a co-culture system with human intestinal organoids and human polarized macrophages. We co-culture human organoids with pro-inflammatory or anti-inflammatory macrophages for 48h. On day 3 cells were collected to perform single cell RNA sequencing.

  Dataset EGAD50000000675

• Genetic subtyping by Whole Exome Sequencing across Diffuse Large B Cell Lymphoma and Plasmablastic Lymphoma.

  Whole exome sequencing was performed from 108 Diffuse Large B Cell Lymphoma cases. A library containing whole exome regions was used to isolate the DNA for sequencing (SureSelect XT Human All Exon V6 (Agilent technologies)). Sequencing on a NovaSeq 6000 instrument (Illumina, paired end, 2x100, mean 566Gb per FlowCell) was performed.

  Dataset EGAD50000000546

• RNAseq data

  Bulk RNAseq data for IMbrave151 (N = 96), including raw counts, transcript per million (TPM), and voom transformed values.

  Dataset EGAD50000000568

• Ischemia Reperfusion Responses in Human Lung Transplants at the Single Cell Resolution

  Ischemia reperfusion is an unavoidable step of organ transplantation. Development of therapeutics for lung injury during transplantation has proved challenging; understanding lung injury from human data at the single cell resolution is required to accelerate the development of therapeutics. Donor lung biopsies from six human lung transplant cases were collected at the end of cold preservation and 2-hour reperfusion and underwent single cell RNA sequencing.

  Dataset EGAD50000000704

• MCRI-WEHI GRREAT Ataxia Sequencing Cohort

  This study evaluated the effectiveness of long- and short-read sequencing as diagnostic tools for CA. We recruited 110 individuals (48 females, 62 males) with a clinical diagnosis of CA. Short-read genome sequencing (SR-GS) was performed to identify pathogenic RE and also non-RE variants in 356 genes associated with CA. Long-read adaptive sequencing (LR-AS) was performed to identify pathogenic RE in 67 genes.

  Dataset EGAD50000000815

• CITE-seq AdaptNK

  CITEseq was performed as outlined in Biolegend ‘TotalSeqTM-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 3.1 Protocol’ with minor modifications, using Biolegend oligo-conjugated antibodies and streptavidin TotalSeq reagents. Briefly, ADAPT-NK cells were stained with CD56-biotin mAb (Miltenyi, clone REA196), followed by TotalSeq antibodies and streptavidin-PE and Live/Dead Aqua (Invitrogen). Cells were subsequently sorted for viable CD56+ cells by flow cytometry.

  Dataset EGAD50000000329

• BCR sequences and metadata for cultured single B-cell clones from blood

  The dataset contains VDJ sequences in FASTA format, the same sequences run through IMGT/HighV-QUEST (tsv file) and accompanying metadata (csv file) including antigen specificity (transglutaminase 2-specific or other). The data was generated from cultured single B-cell clones from the peripheral blood of four untreated celiac disease patients. Sequences were obtained by a nested RT-PCR approach targeting the immunoglobulin chains followed by Sanger sequencing.

  Dataset EGAD50000000343

• CRC cell line RNA-seq

  RNA-Seq data for C32, CACO2, CL11, HT29, SW403, SW948 MSS CRC cell lines and HCEC-1CT normal colon cell line

  Dataset EGAD50000000297

• CRC cell line ATAC-seq

  ATAC-Seq data for C32, CACO2, CL11, HT29, SW403, SW480, SW948 MSS CRC cell lines, and HCEC-1CT normal colon cell line

  Dataset EGAD50000000296

• Papua New Guinean Lowlanders dataset

  The Papua New Guinean Lowlanders dataset includes 41 whole genome sequences for Papua New Guinean individuals sampled in Daru. DNA was extracted from saliva samples (Oragen kit). Sequencing libraries were prepared using the TruSeq DNA PCR-Free HT kit. 150 bp paired-end sequencing was performed on the Illumina HiSeq X5 sequencer. The PGAP dataset provides Fastq, mapped cram files (GRCh38) and phenotype measurements.

  Dataset EGAD50000000050

• genotyped_bacterial_meningitis

  This study includes 1146 samples of host genotyping data (genotyped) from Illumina Omni arrays. Samples were collected from adults (>16 yrs) patients with CSF confirmed bacterial meningitis in the Netherlands between 2006 and 2015. Metadata includes patient outcome, species of bacteria, and for 467 samples a link to an ENA run with the associated bacterial genome (S. pneumoniae only).

  Dataset EGAD00010002328

• DNA Methylation Profiles of T2D and Control Subjects from the GCAT Cohort Using EPIC v2

  This dataset contains DNA methylation data from 400 individuals (200 Type 2 Diabetes cases and 200 controls) from the GCAT (Genomes for Life) cohort. The methylation profiling was performed using the Illumina Infinium MethylationEPIC v2.0 BeadChip, which offers comprehensive coverage of over 850,000 CpG sites. Data are provided in IDAT file format, enabling raw signal-level analysis and downstream processing.

  Dataset EGAD00010002740

• ISA Nutrition 2015

  Comprehensive data on lifestyle-related modifiable factors, sociodemographic, anthropometric, economic, biochemical, and genetic markers related to the occurrence of cardiometabolic diseases as part of the observational cross-sectional survey (2015 Health Survey of Sao Paulo with Focus on Nutrition (2015 ISA-Nutrition), a population-based study. Data of 805218 SNPs for 841 individuals was genotyped using the Axioma 2.0 Precision Medicine Research Array in the Thermo Fisher Scientific laboratory (Affymetrix Inc, Santa Clara, CA).

  Dataset EGAD00010002678

• Epigenome-wide association study of asthma remission in whole blood and nasal epithelium

  Clinical remission (ClinR) was defined as the absence of asthma symptoms and medication for at least 12 months, and complete remission (ComR) was defined as ClinR with normal lung function and absence of airway hyperresponsiveness. We analyzed differential DNA methylation of ClinR and ComR comparing to persistent asthma (PersA) in whole blood samples (n=72) and nasal brushing samples (n=97) in a longitudinal cohort of well characterized asthma patients.

  Dataset EGAD00010002026

• Blastic plasmacytoid dendritic cell neoplasm (BPDCN)_cases

  Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare hematologic malignancy that is most similar in expression profiles to plasmacytoid dendritic cells. However, patients often exhibit features of AML and can progress to AML. In this project, we will determine the differentially and commonly expressed genes between BPDCN and AML specimens. Available BPDCN and TET2-mutated AML specimens were taken for transcriptome microarray analysis.

  Dataset EGAD00010001727

• FFPE cohort with RNA-seq data of tumor samples

  This dataset contains RNA-seq raw data in fastq format from 14 tumor samples. The samples are from primary tumors or metastasis and represent various cancer entities. The samples are formalin-fixed paraffin-embedded (FFPE) treated. For target enrichment SureSelect XT Human All Exon V6 was used. The libraries were sequenced in paired-end mode (2 x 50 nt) on a NovaSeq6000 S2 flow cell.

  Dataset EGAD00001006781

• Sequencing data for oesophageal and related samples - OACs release 5 (RNA)

  Dataset EGAD00001005383

• Sequencing data for oesophageal and related samples - BOs release 6 (RNA)

  Dataset EGAD00001005377

• Sequencing data for oesophageal and related samples - Normals release 6 (RNA)

  Dataset EGAD00001005376

• Sequencing data for oesophageal and related samples - Normals release 2 (RNA)

  Dataset EGAD00001003838

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - pilot normal and pre/post-chemo

  Dataset EGAD00001000704

• RNA sequencing data of pediatric B-other acute lymphoblastic leukemia (set 3)

  The dataset includes RNA sequencing FASTQ files from diagnostic tumor samples of two B-other ALL patients (ALLT-369, ALLT-378). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and TruSeq Stranded Total RNA Library Prep (Illumina) kit was utilized for rRNA removal. The diagnostic tumor samples were sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002600

• ERDERA WES reanalysis - DPF2 Batch 8

  This dataset comprises processed genomic data from 1001 samples, corresponding to 1001 whole-exome sequencing experiments from ERDERA Data Processing Freeze 2. Data files include CRAM, gVCF (containing short variants, copy number variants, and structural variants), RoH (BED), B-allele frequencies (BW), and variant IGV visualizations (XML). Associated phenotypic and pedigree information for all samples is also included.

  Dataset EGAD50000002635