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• DAC - Liquid biopsy: Reference materials and patient with overgrowth syndrome

  Dac EGAC00001002998

• Longitudinal dynamics in relapsed and refractory Hodgkin lymphoma Data Commitee

  Dac EGAC50000000108

• Department of Pathology and Tumor Biology, Kyoto University Data Access Committee

  Dac EGAC00001002159

• Department of Pathology and Tumor Biology, Kyoto University Data Access Committee

  Dac EGAC00001002781

• Single cell data Multiple Sclerosis and other neurological diseases

  Dac EGAC50000000083

• Total proteome and phosphoproteome profiling of Diffuse Midline Glioma

  Study EGAS00001007341

• Transcriptome and epigenome characterization of BMP signaling effects on H3.3K27M DIPG

  Study EGAS00001005374

• Low-C on Human CB-derived LT-HSC and ST-HSC

  Study EGAS00001004744

• Gene expression in CSF and blood of patients with pneumococcal meningitis

  Study EGAS00001003355

• GBM stem cell lines and PRMT5 inhibitor

  Study EGAS00001004397

• Cell of Origin and Early Evolution of Leukemia in Down Syndrome

  Study EGAS00001004780

• Molecular analysis of inflammatory myofibroblastic tumor (WGS and WES)

  Study EGAS00001005081

• Microbiota, Appetite, and Malnutrition in Dutch Community-dwelling older adults

  Study EGAS00001005319

• Human subsistence and signatures of selection on chemosensory genes

  Study EGAS00001007307

• EGAD00010000468

  Uveal melanoma matched Tumour and blood samples

  Dataset EGAD00010000468

• 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

• 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

• 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

• 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

• 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

• 200PT : WG Aligned Sequence (bam)

  200PT : WG Aligned Sequence (bam)/ Aligned WG sequence data in this dataset are from CPCGene Tumour/Normal Pairs used in the 200PT Study

  Dataset EGAD00001004061

• 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

• 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

• Proteogenomic Landscape of Curable Prostate Cancer

  Aligned RNA-seq sequences in this dataset are from the Proteogenomic Landscape of Curable Prostate Cancer study

  Dataset EGAD00001004875

• MGRB dataset. GATK joint called variants of 2570 phase 2 samples.

  This dataset comprises a 2572 sample joint called vcf from the Medical Genome Reference Bank.

  Dataset EGAD00001005228

• PCa mtDNA data

  50 paired benign/cancer samples from prostate tissue generated in 2 different runs - on 3 plates on the IonTorrent Proton. Total of 200 fastq.gz single end runs. Read length ~300 bp. %GC 44 Sequences per file approx 1 Mio.

  Dataset EGAD00001005945

• Epigenetic subtypes of neuroblastoma - ChIPseq

  In the absence of recurrent gene mutations, evidence accumulates that epigenetic deregulation plays a prominent role in neuroblastoma biology. Here we provide genome wide H3K27ac profiles in 60 primary neuroblastoma samples.

  Dataset EGAD00001006285

• Rucaparib in patients presenting a metastatic breast cancer

  Whole genome sequencing was performed on 24 patients (tumor DNA paired to constitutional DNA). WGS libraries were subjected to paired-end (2 x 100 bp) sequencing on NovaSeq (Illumina). The 96 files are in FASTQ format.

  Dataset EGAD00001006458

• EPC (eccrine porocarcinoma) WES samples

  Whole-exome sequencing (WES) in a well-characterized sample of 14 matched EP tumour/healthy surrounding tissue samples. The sequencing was done with paired EXOME sequencing on Illumina HiSeq 4000 using Agilent SureSelect XT HS + Human All Exon V7.

  Dataset EGAD00001006395

• Smart-seq2 raw reads of human kidney glomerular single cells

  Smart-seq2 single cell RNA sequencing reads from kidney glomerular single cells of healthy human individuals. The dataset contains single-end fastq files of 766 single cells.

  Dataset EGAD00001006861

• 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

• Advanced Genomic Techniques in Sequencing of Colorectal Cancer

  We developed a method that uses allelic imbalance information in combination with phased genomic sequencing to generate mega-haplotypes that can encompass entire chromosome arms. We applied this technique to characterize aneuploidy and chromosomal alterations in colorectal cancers.

  Study phs001400

• A study on personalized medicine in genitourinary cancers using genetic biomarkers

  We present a patient with MSI-high castration-resistant PC who showed a remarkable and durable response to pembrolizumab. Whole exome sequencing revealed approximate tumor mutation burden of 61 mutations/Mb as well as biallelic loss of MSH2.

  Study JGAS000510

• Transcriptome analysis of Familial dysautonomia patient cells treated with splice-regulating compounds

  In order to investigate familial dysautonomia patient fibroblasts in response to splice-regulating compounds, cells were treated with RECTAS or TG003 and transcriptome study was conducted by RNA-seq. Splicing profiles of cells in each condition were then analyzed.

  Study JGAS000170

• Transcriptome analysis of Fabry disease iPSC-derived cardiomyocytes treated with splice-regulating compound; RECTAS

  In order to investigate transcriptome profiles in response to splice-regulating compounds, iPSC-derived cardyomyocytes were treated with RECTAS and transcriptome study was conducted by RNA-seq. Splicing profiles of cells in each condition were then analyzed.

  Study JGAS000225

• Analysis of T cells in follicular lymphoma

  This study aimed to identify new heterogeneities in human T cells of follicular lymphoma. To do so, we performed scRNA-seq of human lymph node and follicular lymphoma samples. We identified minor T cell subsets expanding in follicular lymphoma.

  Study EGAS50000000778

• Single-cell multiome ATAC and gene expression profiling of hepatoblastoma tumor organoids

  10X Genomics single-cell multiome profiling of hepatoblastoma tumor organoids using Chromium Next GEM Single-Cell Multiome ATAC + Gene Expression Kit. Single-cell transcriptomics data (bam file) of multiplexed sample of hepatoblastoma tumor organoids: 3E, 8F1, 10F2, 13F2, 13E, 17E and 96F1. Single-cell solutions were obtained from fresh organoid samples using enzymatic digestion.

  Dataset EGAD50000000795

• Alternative splicing in Shh-MB

  We analyzed alternative splicing with Shh medulloblastoma. This dataset contains bam files of whole genome sequencing from 4 cases. Genomic DNA was isolated from both tumor and matched control specimens. We performed whole genome sequence on Illumina Hiseq.

  Study EGAS00001003220

• Genomics of enteropathy-associated T cell lymphoma (EATL)

  Whole exome sequencing of enteropathy-associated T cell lymphoma (EATL) tumors and paired normals, as well as RNA-sequencing of EATL tumors: including (1) 69 exome capture, paired-end Illumina Hiseq sequencing, BAM files from EATL tumor samples, (2) 36 exome capture, paired-end Illumina Hiseq sequencing, BAM files from EATL paired normal samples, and (3) 32 RNAseq, paired-end Illumina Hiseq sequencing, BAM files from EATL tumor samples.

  Dataset EGAD00001003284

• Exome sequencing data of 15 French Caucasian and 10 African-Caribbean men with prostate Cancer.

  Exome sequencing data of 15 French Caucasian and 10 African-Caribbean men with prostate Cancer.

  Dataset EGAD00001003306

• Methylation profiles in patients with blastic plasmacytoid dendritic cell neoplasm

  We added 7 additional samples to our previous cohort (EGAS00001006166). Each samples comprises RNA-seq and whole exome sequencing data. Methylation EPIC Array data have been deposited in Gene Expression Omnibus (GEO) under accession number GSE230487.

  Study EGAS00001007201

• DDD DATAFREEZE 2017-12-15: 13,462 trios and probands only - exome sequence VCF files

  DDD DATAFREEZE 2017-12-15: 13,462 trios and probands only - exome sequence VCF files

  Dataset EGAD00001004389

• DDD DATAFREEZE 2017-12-15: 13,462 trios and probands only - exome sequence CRAM files

  DDD DATAFREEZE 2017-12-15: 13,462 trios and probands only - exome sequence CRAM files

  Dataset EGAD00001004390

• Human Biofluid RNA Atlas

  This dataset contains small RNA sequencing data and mRNA capture sequencing data from 20 different human biofluids (amniotic fluid, aqueous humor, ascites, bile, bronchial lavage fluid, breast milk, cerebrospinal fluid, colostrum, gastric fluid, pancreatic cyst fluid, plasma, saliva, seminal fluid, serum, sputum, stool, synovial fluid, sweat, tear fluid and urine). In total, 180 samples were sequenced. Files are provided in fastQ format. Samples were sequenced on a NextSeq 500.

  Dataset EGAD00001005439

• MDS primary and xenografted samples treated with LOXL inhibitor

  This dataset contains bam files mapped to hg19 (exome and panel) or hg38 (RNA) that either were primary bone marrow cells or sorted human cells after long term engraftment in NSG mice treated with LOXL inhibitor

  Dataset EGAD00001008695

• Single-cell multi-omics data of human gliomas

  We profiled CD45- enriched, viable cells from GBM (n = 7) and IDH-MUT (n = 7) primary samples with multi-modality single-cell sequencing of scDNAme (by reduced representation bisulfite sequencing [RRBS]) and scRNAseq (Smart-seq2).

  Dataset EGAD00001009694