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• RNAseq of samples from CLL patients treated with idelalisib in vivo

  The dataset contains RNA sequencing data from 18 paired samples of 9 CLL patients treated with idelalisib in vivo (median time on therapy 4 weeks; range 2-5 weeks).

  Dataset EGAD50000000878

• Transcriptome - Uveal Melanomas

  Total RNA sequencing on 9 uveal melanomas. Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold (Illumina, 20020599). Paired-end libraries (2 x 100 bp) were sequenced on a NovaSeq 6000 instrument (Illumina).

  Dataset EGAD50000000763

• scRNAseq data of primary and metastatic melanoma samples

  Paired-end 10x single-cell RNA sequencing data from 13 melanoma samples. Sequencing was performed on the Illumina NovaSeq 6000 using 10xGenomics Chromium Next GEM Single-Cell 5 Reagent Kits v2.

  Dataset EGAD50000000665

• Whole transcriptome profiling of liquid biopsies from tumour xenografted mouse models: validation cohort

  Total RNA sequencing (SMARTer Stranded Total RNA-Seq Kit v2) data of extracellular RNA (exRNA) from liquid biopsies of the validation PDX/CDX cohort

  Dataset EGAD00001009413

• Human tumor bulk RNA-seq

  We profiled 7 patient neuroblastoma-FOXR2 tumor samples by bulk RNA-seq. The raw fastqs are provided.

  Dataset EGAD00001010901

• WGS of a Li-Fraumeni patient's HSPCs

  WGS data of clonally expanded HSPCs from a Li-Fraumeni patient at the time of second cancer (Burkitt lymphoma and <5% t-MN) after primary osteosarcoma diagnosis and a reference MSC bulk.

  Dataset EGAD00001011257

• Extensive and differential platinum chemotherapy mutagenesis in livers of children - Whole genome NanoSeq

  Whole genome NanoSeq of a cohort predominantly consisting of paired blood, normal liver and liver tumour from children with liver cancer. The cohort includes platinum-exposed and platinum naïve samples.

  Dataset EGAD00001016142

• 200PT : CNA vcf files

  200PT : CNA vcf files. Copy Number Abberation calls generated using TITAN and PhyloWGS, from the CPCGene 200PT Subclonality study

  Dataset EGAD00001004073

• MP-WGS and WES from CCND1-negative MCL

  BAM files from 5 CCND1-negative MCL cases. 4 BAM files corresponded to long insert size Mate Pair-WGS and 3 to WES. In 2 of the cases both technologies were performed.

  Dataset EGAD00001004161

• To determine the transcriptional profiles of Ovarian carcinomas (UW cohort)

  Specific BRCA and immune configurations determine optimal response to platinum-based chemotherapy in triple negative breast and ovarian carcinomas (UW_OvCa_RNAseq)

  Study EGAS00001006012

• COLORS in IBD: Whole exome sequencing of early onset IBD patients

  Exome sequence analysis of individuals with severe early onset inflammatory bowel disease, and their families. Individuals are ascertained through the COLORS in IBD study, which includes centres throughout UK and Europe.

  Dataset EGAD00001001316

• Her2 BC WGS dataset

  We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Dataset EGAD00001001334

• BAM files

  DNA sequencing reads of human adult stem cell cultures from liver, colon and small intestine. Including biopsy or blood samples of the donors.

  Dataset EGAD00001001900

• Triple Negative Breast Cancer RNA Sequencing

  We propose to definitively characterise the somatic genetics of triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Dataset EGAD00001000390

• Next Generation Sequencing in an IBD Pedigree Exome Data

  We perform whole exome sequencing on samples from a large IBD pedigree. The selected samples are from more distantly related family members (healthy and with IBD) and a set of matched population (Ashkenazy Jewish ancestry) samples.

  Dataset EGAD00001000422

• An Interim Report on the Investigator-initiated Phase 2 Study of Pembrolizumab Immunological Response Evaluation (INSPIRE)

  Whole exome sequencing BAM files of 50 metastatic solid tumour and matched blood germline DNA prior to pembrolizumab treatment.

  Dataset EGAD00001004873

• The Pathogenesis and Genetics of Disseminated Coccidioidomycosis

  Whole exome sequencing on patients > 2 years of age with confirmed disseminated coccidioidomycosis, not undergoing active immunosuppressive therapy, negative HIV status. 

  Study phs002881

• NHLBI TOPMed: Characterizing the Response to a Leukotriene Receptor Antagonist and an Inhaled Corticosteroid (CLIC)

  Within-subject clinical responses to either inhaled corticosteroids or Montelukast were compared in 126 children with mild to moderate asthma.

  Study phs001729

• RNASeq of PAX4 KO vs WT in 7 stages of differentiation from human iPSCs to BLC

  Transcriptomes were profiled along with the differentiation from human induced pluripotent stem cell (iPSC) to beta-like cell (BLC) with PAX4 knocked out or not.

  Dataset EGAD00001008582

• bulk RNAseq from metastatic uveal melanoma tumour biopsies

  Tumour biopsies were obtained from uveal melanoma patients (n = 35) pre and 16 days post treatment with tebentafusp. Biopsies, which were either snap frozen or put in RNA later, were analysed by bulk RNA sequencing (50 million reads per sample) using the Illumina NovaSeq system.

  Dac EGAC50000000519

• Multi-omics characterisation of the response to stimulation in Long Covid patients

  We stimulated immune cells of 15 patients (5 timepoints) with Long Covid with RPMI or P. Aeruginosa strains (4h stimulations).

  Study EGAS50000000143

• 16S rRNA-Seq of rectal mucus from patients suspected to have colorectal cancer

  Metataxonomic sequencing data targeting the 16S rRNA gene hypervariable regions V3 and V4 on 545 rectal mucus samples from patients suspected to have colorectal cancer and healthy controls.

  Dataset EGAD50000001803

• Two scRNA-seq datasets from control and irradiated organoids.

  Dataset includes two scRNA-seq samples from control and irradiated organoids. Files included in the dataset are Fastq files. Sample libraries produced with Chromium X were sequenced on an Illumina NovaSeq 6000 sequencer.

  Dataset EGAD50000001933

• Locally advanced prostate cancer cohort

  Fastq files from RNA sequencing and BAM files from tNGS of normal and tumor samples from 17 patients from the locally advanced prostate cancer cohort.

  Dataset EGAD50000002380

• WGS data from 20 cholangiocarcinoma cases

  WGS data from biliary tract cancer samples (Holzapfel, et al., J Gastrointest Oncol,14(1):379-389, 2023). The dataset includes tumour and normal BAM files sequenced on Illumina HiSeq/NovaSeq and aligned against GRCh38 (n=20 tumour/normal pairs).

  Dataset EGAD50000002307

• Mutation analysis using AVENIO Expanded in cfDNA

  High resolution mutation analysis using the AVENIO ctDNA Expanded Kit V2, which targets 77 cancer-associated genes, in cfDNA in metastatic breast cancer.

  Dataset EGAD50000001669

• Sutherland Nine Raw Sequencing Data

  These Fastq-files contain the raw sequencing output from our two sequencing experiments (Shotgun and Capture). All libraries with "*SG*" refer to Shotgun genomes, while all files containing "*TF*" refer to 1240K capture data.

  Dataset EGAD50000001417

• Targeted sequencing of intestinal metaplasia

  We perform targeted DNA sequencing of intestinal metaplasia of 463 IM and paired germline samples. An additional 48 IM and paired germline samples were included as validation cohort. The dataset contains cram files from 1022 IM and paired normal samples.

  Dataset EGAD50000001540

• Paired-end RNA-seq FASTQ files from amniotic fluid samples

  Paired-end RNA-seq FASTQ files from amniotic fluid samples of 49 extreme premature births, affected and unaffected by the fetal inflammatory response.

  Dataset EGAD50000001260

• Transcriptome - Uveal Melanomas MPI

  Total RNA sequencing on 4 uveal melanoma samples. Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold. Paired-end libraries (2 x 75 bp) were sequenced on HiSeq 4000 instrument (Illumina).

  Dataset EGAD50000001138

• T Cell Signatures (Cityscape)

  T cell signatures from tumor RNAseq in CITYSCAPE with overall survival data. T cell signatures can be associated with the other clinical CITYSCAPE data .

  Dataset EGAD50000000932

• Long read mRNA sequencing of human neural retinal samples

  Long-read (PacBio) RNA sequencing dataset of three neural retinal samples. Files are raw BAM format files generated by a Sequel II machine. Additionally, the ccs3 BAM format files are included.

  Dataset EGAD50000000101

• The Dynamic Immune Behavior of Primary and Metastatic Ovarian Carcinoma

  Single-cell RNA-seq data of prospectively collected normal ovarian tissue sample from 1 healthy individual and tumor tissue samples with or without chemotherapy from 19 HGSOC patients.

  Dataset EGAD50000000057

• Methylation Array of pre- and post-5ZA-treated head and neck cancer patients refractory to anto-PD-1 therapy

  Illumina MethylationEpic Beachip data generated from tissue samples collected from head and neck cancer patients refractory to anti-PD-1 therapy, collected before and after the 5AZA treatment

  Dataset EGAD00010002718

• Pan Prostate Cancer Group Germany BAM files

  German early-onset prostate cancer whole-genome sequencing samples of the Pan-Prostate Cancer Genome (PPCG) project. Whole Genome Sequencing Illumina data from men with prostate cancer. Samples were taken from primary tissue obtained at prostatectomy with matched blood control.

  Dataset EGAD00001005997

• Signatures of mismatch repair deficiency in cancer genomes

  DNA replication errors occurring in mismatch repair (MMR) deficient cells persist as mismatch mutations and predispose to a range of tumors. Here, we sequenced the first whole-genomes from MMR-deficient endometrial tumors.

  Dataset EGAD00001000641

• WXS of IgAN-tGBM, IgAN and TBMN

  The dataset consists of 258 bam files by whole exome sequencing. 122 from IgAN-tGBM patients, 64 from IgAN patients and 72 fromTBMN patients.

  Dataset EGAD00001009287

• bulkRNA seq from fibroblasts stimmulated with bead or CD8 T cell supernatant

  CD8 T cells (5 Samples treated, 5 samples control) form the same donors (5 donors, paired design) was subject to RNA-seq (Illumina stranded mRNA) processing. Single end fastq-files are supplied.

  Dataset EGAD00001010004

• Human tumor single-cell mutiome

  We profiled 1 patient neuroblastoma-FOXR2 tumor sample by single-cell multiome RNA + ATAC. The raw fastqs are provided.

  Dataset EGAD00001010902

• Human tumor single-nuclei RNA-seq

  We profiled 4 patient neuroblastoma-FORX2 tumor samples by single-nuclei RNA-seq using 10X Chromium 3'. The raw fastqs are provided.

  Dataset EGAD00001010903

• Human tumor single-cell RNA-seq

  We profiled 16 patient tumor samples by single-cell or single-nuclei RNA-seq using 10X Chromium 3'. It includes 4 low-grade gliomas and 12 ependymomas. The raw fastqs are provided.

  Dataset EGAD00001011315

• Extensive and differential platinum chemotherapy mutagenesis in livers of children - RNA

  Bulk RNA sequencing of normal liver and liver tumours from children. Five of the children had liver cancer and samples was taken at surgery. Two children had non-liver type of cancer and liver samples were obtained postmortem.

  Dataset EGAD00001016117

• Whole Exome Data of RFWD3 Fanconi anemia patient

  Dataset contains one sample derived from gDNA of human fibroblasts. Files are in FASTQ format and were generated using the Agilent SureSelect Human All Exon 50Mb Kit and followed by Next Generation Sequencing on a HighSeq2000 instrument (Illumina).

  Dataset EGAD00001003311

• In vitro mutational load

  Clonally expanded human pluripotent and adult (liver + intestine) stem cell clones were subjected to whole genome sequencing to determine the mutational impact of in vitro culture

  Dataset EGAD00001004104

• WGS of HSPCs and MSCs

  Whole genome sequencing data of organoid cultures derived from human bone marrow-derived and cord blood-derived hematopoietic stem and multipotent progenitor cells to study the mutation accumulation.

  Dataset EGAD00001004451

• SLC9A3R1 variant associated with age-related hearing loss

  The dataset contains one BAM file that includes a SLC9A3R1 variant identified in two Italian patients affected by age-related hearing loss. Data have been produced by targeted re-sequencing, using Ion Torrent PGM platform.

  Dataset EGAD00001004171

• To determine the genomic profiles of Triple Negative Breast Cancers (COH cohort)

  Specific BRCA and immune configurations determine optimal response to platinum-based chemotherapy in triple negative breast and ovarian carcinomas (COH_TNBC_WGS)

  Study EGAS00001006085

• To determine the genomic profiles of Ovarian carcinomas (UW cohort)

  Specific BRCA and immune configurations determine optimal response to platinum-based chemotherapy in triple negative breast and ovarian carcinomas (UW_OvCa_WGS)

  Study EGAS00001006048

• Use of deep sequencing to detect clonal mutations in sun exposed human epidermis - whole genome

  Deep sequencing of two skin biopsies to study the landscape of somatic mutations in human adult tissues.

  Dataset EGAD00001001123

• Hepatocellular adenomas samples

  Whole exome sequencing data from 30 donors (46 tumors and 30 non-tumoral whole exome sequencing, paired-end, HiSeq 2000, Illumina) collected by the Inserm U674, PI Jessica Zucman-Rossi - Institut National du Cancer (INCa), PI Fabien Calvo, France.

  Dataset EGAD00001000737