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• RNAseq of Sjögren's Syndrome and Healthy Volunteers' Salivary Glands

  Mechanistic genetic and inflammatory endpoints were studied to gain insight into the molecular mechanisms of Sjögren's syndrome. Transcriptomic studies allowed the exploration of molecular alterations that might cause or influence the studied salivary gland pathology and potentially elucidate druggable pathways for intervention.

  Study phs001842

• Gene expression matrix for Smart-seq2 data of peripheral blood B cells

  The dataset contains scRNA-seq gene expression matrix (csv file) and metadata (csv file) after quality control filtering for data generated with the Smart-seq2 protocol. Transcript expression was quantified with Salmon v0.11.3 using cDNA sequences from GRCh38.94 and k-mer length 25, and was aggregated to gene level and transcript-length-corrected using tximport v1.8.0. The dataset comprises IgA+ transglutaminase 2-specific and other IgA+ B cells from the peripheral blood of 355 cells from two untreated celiac disease patients.

  Dataset EGAD50000000338

• Genetic investigation of 12q-amplified osteosarcomas

  Further investigation and characterisation of 12q-amplified low- and high-grade osteosarcomas with MDM2 and/or CDK4 amplification focusing on SV, copy number and gene fusion analyses. In total, 25 cases (33 samples total due to multi-sampling) were included, with some form of sequencing data available for 27 samples. Mate-pair whole genome sequencing (Illumina) is available for 19 samples, longread whole genome sequencing (PacBio HiFi) on 10 samples and RNA-sequencing (Illumina Truseq) on 21 samples. Data is available as BAM files.

  Dataset EGAD50000000707

• Multi-omics analysis of CUD in the VS

  The aim was to molecularly characterize the human ventral striatum in CUD. For this, we generated epigenomic, transcriptomic, and proteomic datasets at the bulk-level, performed integrative multi-omics analyses and further analyzed CUD-associated transcriptomic changes at a cell type-specific level using snRNA-seq.

  Study EGAS50000000623

• Non-invasive prediction of immunotherapy response (NIPIT) project

  This project aims to find transcriptomic biomarkers for immunotherapy response prediction in several cancer types. So far, we have performed poly-A RNA-seq using whloe blood and peripheral blood mononuclear cells from 33 non-small cell lung cancer patients, collected before and after the start of immunotherapy.

  Study EGAS50000000266

• Base modification analysis using single molecule real-time sequencing

  This dataset was generated using single-molecule real-time sequencing for both training and testing purposes. The DNA samples isolated from human buffy coats or placenta of healthy individuals (n=4,) were prepared in a way that four types of base modifications were incorporated, including unmodified controls, 5mC, 5hmC, and 6mA. The sequence data for each sample consists of subreads produced by single-molecule real-time sequencing and stored in a bam format. Details of the specific experiments conducted in this study are outlined in our manuscript.

  Dataset EGAD50000000541

• Genome-wide array data from Eivissan and Menorcan Individuals

  22 and 20 genome-wide array data for Eivissan and Menorcan healthy unrelated volunteers, respectively. The affymetrix Human Origins array was used to genotype these individuals. The variant set was lifted over to the hg38 human genome reference. A single gziped VCF file can be found.

  Study EGAS50000000423

• Cohort A spatial transcriptomics sequencing

  Cohort A includes glioma tumors of varied grading and pathology from male and female individuals. Fresh frozen glioma tissues for each sample in cohort A were analyzed with the 10X Genomics Visium Spatial Gene Expression protocol. Processed data is available on the NCBI Gene Expression Omnibus database with accession GSE242352.

  Study EGAS50000000954

• Cohort B spatial transcriptomics sequencing

  Cohort B includes IDH-wild type, EGFR amplified, surgically derived glioblastoma tissue samples from male and female individuals. FFPE tissues for each sample in cohort B were analyzed with the 10X Genomics Visium CytAssist protocol. Processed data is available on the NCBI Gene Expression Omnibus database with accession GSE242352.

  Study EGAS50000000956

• NHLBI TOPMed: Genetic Causes of Complex Pediatric Disorders - Asthma (GCPD-A)

  The Center for Applied Genomics (CAG) at the Children's Hospital of Philadelphia (CHOP) is focused on addressing the roles of both single nucleotide variants and structural copy number variants, and their functional impact, together with gene-environment interactions and their influence on asthma drug response.

  Study phs001661