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• Exome sequencing data for 40 cases of alopecia areata and vitiligo

  Sequencing of independent unrelated cases of alopecia areata (total/ universal) and vitiligo (>10%, affected family member). DNA obtained from blood

  Study EGAS00001003831

• MGHBoston_Molpheno_Closed

  This dataset contains Whole Genome Sequencing and, if available, RNA-sequencing and/or ATAC-sequencing data of 17 lymphoblastoid cell lines derived from patients with complex genomic rearrangements. Patients have phenotypes in category of intellectual disability and/or multiple congenital anomalies. Data access is closed.

  Dataset EGAD00001004866

• SNP array data for 140 individuals from 5 populations in Pakistan

  We have genotyped 140 individuals from 5 populations in Pakistan, using the OmniExpressExome-8 array, which includes approximately one million autosomal SNP markers.

  Study EGAS00001002965

• cfDNA sWGS BAM — NSCLC stage I–III

  Plasma cfDNA sWGS for NSCLC patients (stage I–III), blood drawn pre-operatively, CHU Montpellier/LUNGDOC study. Libraries: DSP as recorded. Sequencing provider IntegraGen (2022–2024). Alignment to GRCh38 (hg38 canonical), BWA-MEM; BAMs sorted/indexed; only primary mapped reads retained (analysis pages list -F/MAPQ). Controlled access.

  Dataset EGAD50000001878

• 10X snMultiome (ATAC+GEX) sequencing of 5 human reactive tonsil samples

  10X snMultiome (ATAC+GEX) sequencing of 5 human reactive tonsil samples for the study of Non-canonical NF-κB signaling skews B cells away from germinal center to low-affinity effector fate.

  Dataset EGAD50000002366

• WGS from 9 MPNSTs from 2 individuals, including relapses and metastasis. Data from Ortega-Bertran et. al.

  WGS from 2 individuals with MPNSTs. Multiple MPNSTs (independent tumor, relapses and metastasis) from each individual. Data from "Personalized Medicine Strategy for MPNSTs: Using Precision Oncology on PDOX Models to Inform Tumor Boards" by Ortega-Bertran et.al.

  Dataset EGAD50000002171

• circulating cell-free RNAs, CF-miRNAs, Sequencing with Qiaseq and NextSeq 550

  This dataset includes small RNA sequencing data from circulating cell-free RNAs (CF-miRNAs). miRNA libraries were prepared using the Qiaseq miRNA Library Kit with adaptations for low RNA input and sequenced on the Illumina NextSeq 550 platform

  Dataset EGAD50000001503

• snRNA splicing signature RNA-Seq

  This dataset has RNA-Seq fastq files which were generated as part of the snRNA splicing signature study. Analysis can be performed to regenerate splicing signatures found for RNU4-2, RNU5B-1 and RNU5A-1 by comparing cases versus controls.

  Dataset EGAD50000001299

• Shallow Whole Genome Sequencing (sWGS) of pancreatic ductal adenocarcinoma

  Associated with CNA differences between RNA-based subtypes of PDAC. Shallow Whole Genome Sequencing (sWGS) generated 47 .bam files from 37 patients. sWGS was used for Copy number aberrations (CNA) determination.

  Dataset EGAD50000001732

• Strand-seq data of six CK-AML patient samples and three matching PDXs

  We performed strand-specific single-cell sequencing of six primary leukemia samples from four CK-AML patients. We also performed strand-specific single-cell sequencing of three matching patient-derived xenografts (PDXs). The dataset contains BAM files for each cell.

  Dataset EGAD50000000634

• Dataset for desmoplastic small round cell tumor - WGS

  This dataset contains 25 WGS sequencing samples of patients with desmoplastic small round cell tumor. Sequencing was performed on Illumina HiSeq X and NovaSeq 6000 using Illumina TruSeq Nano DNA Kit. The sequencing was always paired.

  Dataset EGAD50000000911

• Exome Sequencing of Multiple Localised Spiradenoma and Spiradenocarcinoma

  Tumor samples were microdissected from formalin-fixed, paraffin-embedded tissue and genomic DNA was extracted. DNA libraries were generated using xGen ssDNA & Low-Input DNA Library Preparation Kit (IDT). The libraries were enriched for the exome using xGen Exome Hyb Panel (IDT) and sequenced on DNBSEQ G400RS.

  Dataset EGAD50000000788

• BAM files from whole-genome sequencing of 3 agressive B-cell lymphoma tumour and non-tumor samples

  This dataset contains BAM files from whole-genome sequencing (WGS) of 3 agressive B-cell lymphoma tumour samples for cases 1, 6, and 7 as well as the corresponding non-tumor whole-genome sequencing BAM files.

  Dataset EGAD50000000800

• ATAC_TPO3_2023

  Human engineered CRC organoids (APC KO; KRAS G12D; TP53 KO) were grown in glucose, lactate or with DCA . Samples were collected and processed for bulk ATAC-seq.

  Dataset EGAD50000000088

• IMvigor130 heatmap Figure 2A

  Source data for Figure.2A heatmap showing the gene expression across samples.

  Dataset EGAD50000000139

• CITE-seq raw count matrix

  Raw count matrix for CITE-seq data of PBMC collected from 113 patients.

  Dataset EGAD50000000141

• Raw count matrix scRNA-seq

  Raw count matrix for scRNA-seq data of PBMC collected from 113 patients.

  Dataset EGAD50000000142

• scRNA-seq of bronchoalveolar lavage (BAL) samples from patients with severe COVID-19 to assess dexamethasone response in the lungs

  Single-cell RNA-sequencing of bronchoalveolar lavage (BAL) samples from patients with severe COVID-19 with or without Dexamethasone treatment and for responders and non-responders was performed using 10x Genomics technology.

  Dataset EGAD50000000292

• Prognostic whole-genome and transcriptome signatures in colorectal cancers

  This dataset consists of RNA-seq CRAM raw-data files of 1063 primary colorectal cancer and 120 adjacent normal tissue samples. The expression profiles for these samples can be found at the ArrayExpress with accession number E-MTAB-12862.

  Dataset EGAD50000000169

• SARS-CoV2 mRNA-vaccination-induced Immunological Memory in Human Non-Lymphoid and Lymphoid Tissues

  This dataset includes combined single-cell RNA-Seq and T cell receptor profiling data for SARS-CoV-2 spike protein-reactive CD4+ T cells and NK cells from blood, liver, lungs, and bone marrow of human donors.

  Dataset EGAD50000000062

• Bulk RNAseq dataset for "Longitudinal Multi-Omics Study Reveals Molecular Drivers and Tumor Microenvironment in Extramedullary Multiple Myeloma"

  This dataset contains 84 paired fastq files of Bulk RNAseq collected from 14 patients with Extramedullary multiple myeloma, 14 patients with newly diagnosed multiple myeloma and 14 patients with Relapsed/refractory multiple myeloma

  Dataset EGAD50000000051

• Age-dependent association of clonal hematopoiesis with COVID-19 mortality in patients over 60 years

  Targeted sequencing with the Myeloid Solutions™ Panel (MYS) of SOPHiA Genetics for COVID-19 patientds (n=241 deceased, n=239 survivors).

  Dataset EGAD50000000001

• H3K27ac HiChIP Dataset for 19 T-ALL patients and one normal control sample

  19 H3K27ac HICHIP from T-ALL patient samples and one healthy normal control sample. Reads were aligned to HG38 reference.

  Dataset EGAD50000000023

• BBMRI – BIOS – Freeze 2 – RNA-seq Counts

  Read counts determined using HTSeq-count for the BBMRI BIOS Freeze 2 RNAseq data

  Dataset EGAD00010001420

• RFMix

  This dataset contains the per-chromosome RFMix input and output files for the local ancestry inference of 59 Aboriginal Australian genomes as reported in Malaspinas et al., 2016. Local ancestry was inferred assuming four mixing ancestral populations represented by: Europeans (27 individuals), Asians (29 individuals), Papuans (13 individuals) and Native Australians (7 individuals from the WCD region).

  Dataset EGAD00010001575