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• DESIGN-NKI RNA-seq

  RNA-Seq data of 36 HPV-negative HNSCC specimens from patients treated at The Netherlands Cancer Institute, Amsterdam. HNSCC biopsy samples obtained prior to treatment (chemo-radiotherapy) were used for polyA mRNA sequencing.

  Dataset EGAD00001005715

• NKI-MET HNSCC RNA-Seq

  RNA-Seq data of 8 HNSCC specimens from patients diagnosed with metastatic disease at The Netherlands Cancer Institute, Amsterdam. Primary HNSCC biopsy samples obtained prior to treatment were used for polyA mRNA sequencing.

  Dataset EGAD00001005720

• 16S data from IBD patients

  Bacterial 16S V4 rDNA was amplified using two differently barcoded V4 fusion primers. Pooled PCR samples were purified and paired-end sequenced on MiSeq instrument for 250 cycles. The steps from DNA quantification to sequencing were conducted at Second Genome Inc.

  Dataset EGAD00001005482

• 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

• Raw data (FASTQ) and processed data (VCF) of 7 patient-derived Sézary Syndrome (SS) cells

  We profile the whole-transcriptome (bulk RNAseq) of 7 patient-derived Sézary Syndrome (SS) cells to identify expression patterns, functional programs and expressed gene mutations that may provide clues on new therapeutic options for SS patients. The libraries were sequenced on NextSeq500 (Illumina) with a paired-end read length of 2x75bp. Raw data (FASTQ) and obtained processed data (VCF) including all called raw variants are available.

  Dataset EGAD50000001646

• Evolution of four ER+ breast cancers

  The evolution of four breast cancers was analyzed using longitudinal samples collected over 2-15 years. Whole-genome sequencing and single-cell RNA-Seq were used to analyze evolution. We have deposited VCF files for SNV, indel, and structural variant calls from WGS data, and a text file showing transcripts per million (TPM) expression for the single-cell RNA-Seq data.

  Dataset EGAD00001003303

• RNA sequencing of multiple tumor biopsies and patient-derived spheroids from five colorectal cancer patients (BAM files)

  Whole transcriptome, strand-specific RNA-seq libraries were prepared from total RNA purified using RNeasy mini kit (Qiagen) using Ribo-Zero technology (Epicentre, an Illumina company) for depletion of rRNA followed by library preparation using ScriptSeq ScriptSeq RNA-Seq Library preparation Kit from Illumina. The paired raw sequence reads were processed using TopHat2 and mapped to the humane reference genome HG19.

  Dataset EGAD00001003820

• RNA-seq of hepatocellular carcinoma xenografts established from needle biopsies

  RNA-sequencing of human hepatocellular carcinoma biopsies (n=14), 44 HCC xenografts derived from 11 HCC biopsies and 3 lymphoma xenografts derived from 3 HCC biopsies. RNA-sequencing was performed using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (lllumina). SR126 sequencing was performed on an Illumina HiSeq 2500 using v4 SBS chemistry according to the manufacturer’s guidelines.

  Dataset EGAD00001004541

• Single cell RNA sequencing of colorectal cancer

  To understand intrinsic cancer cell signatures and the surrounding microenvironemt and their interactions, we performed single-cell RNA sequencing on 63,689 cells from 23 patients with 23 primary colorectal cancer and 10 matched normal mucosa samples. Analyzing of primary colorectal cancer and normal mucosa samples show a comprehensive cellular landscape of colon cancer, which is a valuable resource for the development of therapeutic strategies.

  Dataset EGAD00001005198

• sWGS of OV cell lines for ACN rascal study

  This dataset contains 60 .bam files of shallow WGS data (~0.1X) from ovarian cancer cell lines. Sequencing reads were aligned to the 1000 Genomes Project GRCh37-derived reference genome using the BWA aligner (v.0.07.17; CRUK-CI alignment pipeline).

  Dataset EGAD00001008118

• Whole genome bisulfite sequencing on 10 multiple myeloma cases

  Whole genome bisulfite sequencing on 10 multiple myeloma cases. Data quality control and adaptor-trimmed were performed with the Trimomatic tool. Paired-reads were mapped to the hg19 human reference with methylCtools aligner.

  Dataset EGAD00001007821

• RNAseq and ATACseq data

  RNAseq and ATACseq data for the FMF patients and healthy control. The RNAseq data was sequenced on a BGI MGI G400 machine, with PE100 reads. ATAC-seq libraries were prepared with Illumina Nextera primers and sequenced on NovaSeq 6000 platform with 50bp paired-end sequencing, where each sample was sequenced to approximate 60 million reads.

  Dataset EGAD00001010304

• Sequencing data for oesophageal and related samples - Black et al (WGS)

  Data supporting: "Understanding the malignant potential of gastric metaplasia of the oesophagus and its relevance to Barrett’s Oesophagus surveillance: individual-level data analysis" Black et al (WGS BOs/normals)

  Dataset EGAD00001011255

• snRNA sequencing of high-grade pancreatic neuroendocrine carcinoma (panNEC)

  High-grade pancreatic neuroendocrine carcinoma (panNEC) is a rare, aggressive cancer with limited tissue availability. Single-nucleus transcriptomics of five large-cell panNECs revealed two interesting neuroendocrine cell states: one highly proliferative with an aberrant brain-specific neuronal differentiation program and another stress-responsive state enriched for heat stress, hypoxia, and glycolysis. Our findings suggest potential therapeutic vulnerabilities, highlighting the need to evaluate the efficacy of combination therapies.

  Dataset EGAD00001016154

• COVID_19_Challenge_Project_Single_Cell_Profiling

  Single-cell profiling of sero-negative and sero-positive humans that were inoculated with SARS-CoV-2. The cellular response during SARS-CoV-2 is profiled using single-cell transcriptomics, CITE-seq and single cell immune profiling, by sampling PBMCs and nasal swabs before and at multiple time points during SARS-CoV-2 infection. This one-of-a-kind cellular map will give unique temporal resolution of how nasal and immune cells respond to SARS-CoV-2 exposure and infection

  Study EGAS00001005696

• Phenotyping and Therapeutic Approaches for Patients with Sellar/Suprasellar Disorders

  The goal of the study is to phenotype and genotype patients with rare hypothalamic and pituitary disorders and identify biomarkers of disease diagnosis, presentation, and progression. We are investigating genetic mechanisms of pituitary tumorigenesis as well as genomic/transcriptomic markers of disease presentation and severity. Patients with suspected or confirmed hypothalamic and/or pituitary disorders and their family members are recruited. Biospecimens including peripheral blood, urine, tumor tissue (as available), and/or stool are collected. Genetic analysis may include a variety of techniques including peripheral blood or tumor tissue targeted Sanger sequencing of one or few genes, peripheral blood or tumor tissue whole exome sequencing, and other as applicable.

  Study phs003245

• Whole Genome sequencing of individuals from Carlantino, Italy

  This study includes whole-genome sequencing data (at 4x depth) of 100 individuals from an Italian genetic isolate population (Carlantino, abbreviated CARL) of the Italian Network of Genetic Isolates (INGI). The INGI-CARL_SEQ project aims to combine available extensive genetic and phenotypic data to the latest high-throughput genome sequencing technology and ad hoc statistical analysis to identify new rare genetic variants underlying complex traits.

  Dataset EGAD00001000774

• Transcriptome sequencing of Gingivo-buccal Cancer : ICGC-India Project_YR03

  Transcriptome Sequencing of Gingivo-buccal Cancer: ICGC-India ProjectAs a part of the ICGC, India has undertaken genomic studies on gingivobuccal cancer of the oral cavity, which is the most prevalent form of cancer among men in India. There are various known environmental (life-style) correlates of this cancer, the most important of which are tobacco chewing and HPV infection. Transcriptome sequencing of paired RNA samples – isolated from the tumor and adjacent normal tissues of 12 patients – have been performed. Detailed clinical characterization of the patients, collection of data on demographic and environmental exposures, and isolation of DNA samples from adjacent normal and tumor tissues collected from each patient are being done at the Advanced Centre for Research, Treatment and Education on Cancer, Mumbai. Sequencing is being performed at the National Institute of Biomedical Genomics, Kalyani.

  Study EGAS00001002851

• Transcriptome sequencing of Gingivo-buccal Cancer : ICGC-India Project_Batch05

  Transcriptome Sequencing of Gingivo-buccal Cancer: ICGC-India ProjectAs a part of the ICGC, India has undertaken genomic studies on gingivobuccal cancer of the oral cavity, which is the most prevalent form of cancer among men in India. There are various known environmental (life-style) correlates of this cancer, the most important of which are tobacco chewing and HPV infection. Transcriptome sequencing of paired RNA samples – isolated from the tumor and adjacent normal tissues of 28 patients – have been performed. Detailed clinical characterization of the patients, collection of data on demographic and environmental exposures, and isolation of DNA samples from adjacent normal and tumor tissues collected from each patient are being done at the Advanced Centre for Research, Treatment and Education on Cancer, Mumbai. Sequencing is being performed at the National Institute of Biomedical Genomics, Kalyani.

  Study EGAS00001003285

• ITER-FIISC Data Access Committee (Sepsis)

  DAC for Whole-exome variant calling of individuals from the study of sepsis and acute distress respiratory syndrome in Spain.

  Dac EGAC50000000641

• Single cell sequencing in D425

  Single cell sequencing aligned BAM files for the D425 cell line

  Dataset EGAD50000002304

• 15x WGS HELIC MANOLIS

  15x whole genome sequencing in samples from the Cretan Greek isolate collection HELIC MANOLIS

  Dataset EGAD00001001897

• 108 WGS of epileptic patients from the CENet cohort

  Dataset is described in doi: https://doi.org/10.1101/2022.12.13.22283363

  Dataset EGAD00001011301

• Aligned FOS RNA sequencing data

  Total RNA-sequencing Paired-End was performed by GenomeScan (Leiden, the Netherlands) on the NovaSeq6000 platform for full-length FOS (FOS FL), truncated FOS (FOSΔ), a FOS isoform with an L376N mutation (FOS mut), untransduced fMSC (unt) and fMSC with empty pLV (pLV) at week 0, 1, 2, and 3 in triplicate (total of 60 samples). Raw RNA-seq data were processed by the RNA-seq BioWDL pipeline pipeline version 5.0.0 developed by the SASC team at LUMC, LUMC, Leiden, the Netherlands).

  Dataset EGAD50000001839

• Aligned reads in the 2kb region centered on the HTT repeat expansion from Illumina HiSeqX and HiSeq2000 whole genome sequence data

  This dataset includes bam files from 58 samples. These bam files include all read pairs where at least one of the reads aligns within 1kb of the HTT repeat expansion. These samples were sequenced using 2x150bp reads on an Illumina HiSeqX sequencer and aligned using bwa. Twelve of the samples used TruSeq Nano library preparation and 46 samples used TruSeq DNA PCR-free sample preparation.

  Dataset EGAD00001003512

• Genetic screening of GPI-anchor protein synthesis (2018-08-13)

  This study will analyse the guide sequence which were used for making mutations in the Cas9-expressing cells. We used GeCKO v2 library which were released by Feng Zhang, 2014. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2018-08-13.

  Dataset EGAD00001004294

• A single-cell atlas of the early COPD lung - Nanopore long-read

  Single cell atlas of the human airways from 10 patients suffering of early stage Chronic Obstructive Pulmonary Disease and 12 healthy age matched volunteers. This dataset was sequenced by 10X Genomics 3’ RNA-seq profiling. It is composed of more than 400 000 cells coming from 119 samples total. Sampling was performed by brushings and biopsies from the nose to the 6 th division of the airways. 14 samples were also sequenced using Nanopore long-read sequencing.

  Dataset EGAD50000001002

• Lymphocyte Gut WGS H38 (2021-02-02)

  We study lymphocyte somatic evolution through the sequencing of normal healthy lymphocytes. We perform whole-genome sequencing of single-cell derived T and B cell colonies to identify somatic mutations, and perform targeted deep-sequencing of these mutations. The lineages of T and B cells, and the frequencies of these mutations reveals the neutral and non-neutral evolutionary processes underlying lymphocyte growth and function. . This dataset contains all the data available for this study on 2021-02-02.

  Dataset EGAD00001006934

• Lymphocyte PanBody WGS H38 (2021-02-02)

  We study lymphocyte somatic evolution through the sequencing of normal healthy lymphocytes. We perform whole-genome sequencing of single-cell derived T and B cell colonies to identify somatic mutations, and perform targeted deep-sequencing of these mutations. The lineages of T and B cells, and the frequencies of these mutations reveals the neutral and non-neutral evolutionary processes underlying lymphocyte growth and function. . This dataset contains all the data available for this study on 2021-02-02.

  Dataset EGAD00001006935

• Targeted Next-Generation Sequencing Data of IDH1 Exon 4 in Intrahepatic Cholangiocarcinoma Samples

  This dataset contains targeted next-generation sequencing data from 76 FFPE tumor tissues focusing on IDH1 exon 4 and codon 132. Genomic DNA was isolated using the QIAamp DNA FFPE Tissue Kit and sequenced on the Illumina MiSeq platform with 200x minimum coverage. The results are provided as encrypted somatic variant call files (VCF) generated through the Nextera XT library preparation protocol. This collection represents the specific somatic mutation profiles of the intrahepatic cholangiocarcinoma cohort for controlled access.

  Dataset EGAD50000002345

• RNA-seq from Glioblastoma treated with Indisulam

  The dataset includes RNA-sequencing results from four patient-derived glioblastoma cell lines treated with DMSO (vehicle control) or the splicing modulating-drug indisulam (at 6 and 16 hours), resulting in 12 RNA-seq samples. Paired-end sequencing produced 24 FASTQ.gz files. The RNA libraries were prepared using PolyA selection and ERCC spike-ins and sequenced on a NovaSeq platform. This dataset supports the analysis of drug-induced transcriptomic changes and the prediction of subsequent non-canonical tumor-specific antigens (ncTSAs) using the NovumRNA pipeline.

  Dataset EGAD50000000957

• Oligodendroglia as functional effectors of Multiple Sclerosis risk variants (iPS derived hOPC scCRISPRi/a-seq)

  Study of the regulatory effect of a selection Multiple Sclerosis (MS) associated SNPs applying high-throughput functional genomics in human induced pluripotent stem cell-derived oligodendroglia (iPS-derived hOPCs). Selected cis-regulatory elements were assesed with lentiviral-based pooled single cell (sc)CRISPR-seq screens. CRISPRi/a (dCas9-KRAB and dCas9-p300 respectively) was performed, in combination with direct-capture Perturb-sequencing single-guide RNA (sgRNA) and droplet-based single-cell RNA-seq, allowing high sgRNA capture efficiency and identification of possible transcriptional regulatory mechanisms at a single cell/sgRNA level.

  Study EGAS50000001417

• TOTHER3

  Patritumab deruxtecan in HER2-negative breast cancer: part B results of the window-of-opportunity SOLTI TOT-HER3 trial and biological determinants of early-response

  Dac EGAC50000000255

• Makrani_SNP_genotyping

  Genome-wide SNP genotyping data for 102 Pakistani individuals by Illumina HumanOmni2.5-8 array, used in the EGAS00001002558 study

  Dataset EGAD00010001452

• A thymic ILC1-like progenitor with differentiation potential towards KIR+NKG2A- NK cells

  The dataset contains bulk RNA sequencing data from 12 pediatric thymus samples collected during cardiac surgeries. These samples represent immunologically healthy donors with a mean age of 6 months. The sequencing was performed using Illumina HiSeq4000, and the processed files are available in standard formats such as FASTQ.

  Dataset EGAD50000001120

• Saliva_Fulani_Database

  In total, 90 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). Saliva Fulani dataset includes individuals from the following populations: 30 individuals from Senegal_FulaniLinguere, 30 individuals from Mauritania_FulaniAssaba, and 30 individuals from Mali_FulaniInnerDelta.

  Dataset EGAD50000000653

• GIST Whole Genome Sequencing

  Whole genome sequencing of tumour and normal samples from familial GIST. Multiple family members were affected with multifocal GIST who underwent whole genome sequencing of the germline and tumor. Affected individuals with GIST harbored a germline variant found within exon 13 of the KIT gene, (c.1965T>G; p.Asn655Lys, p.N655K) and a variant in the MSR1 gene (c.877C>T; p.Arg293*, pR293X).

  Dataset EGAD50000000549

• Malagasy Genomics University of Antananarivo Dataset

  Mid-pass whole genome sequencing was performed for 264 Malagasy individuals across three geographic regions across the island of Madagascar (west coast, central highlands, and southern highlands). This dataset includes the VCF from joint variant calling with reference populations as specified in the associated publication.

  Dataset EGAD50000000708

• Single-cell RNA-sequencing of peripheral blood mononuclear cells from patients with achalasia

  The data published here contains single-cell RNA-sequencing (scRNAseq) data as obtained using the 3' scRNAseq using Chromium Single Cell 3’ Reagent from 10X Genomics on peripheral blood mononuclear cells (PBMC) from patients with achalasia. Sequencing was performed in a paired-ended fashion on the NovaSeq6000.

  Dataset EGAD50000000250

• RNA sequencing data of pediatric ETV6::RUNX1 acute lymphoblastic leukemia (set 4)

  The dataset includes RNA sequencing FASTQ files from a diagnostic tumor sample of one ETV6::RUNX1 ALL patient (ALLK-132). Novogene's internal method was used in directional library preparation including rRNA removal. The diagnostic tumor sample was sequenced using Illumina Novaseq X Plus, and the target sequencing depth was 21 Gb.

  Dataset EGAD50000002590

• RNA-seq data from hypothalamic tissue from individuals with Prader-Willi syndrome and age-matched controls.

  RNA-seq data (bam files) from the hypothalamus of 4 individuals with Prader-Willi syndrome and 4 age-matched control individuals. Detailed information about the study design, case-control matching and RNA-seq data processing is provided in the accompanying publication [Bochukova et al (2018) Cell Reports].

  Dataset EGAD00001004034

• Primary breast cancers and paired brain metastases

  Targeted next-generation-sequencing of 494 cancer-associated genes was done in a series of 14 frozen pairs of matched primary breast cancers and brain metastases (28 samples). DNA libraries of all coding exons were prepared using the Haloplex Target Enrichment System. Sequencing was done using the 2*150bp paired-end technology on the Illumina NextSeq500 platform.

  Dataset EGAD00001004309

• Whole exome profiling of spatial biopsies of high grade serous epithelial ovarian cancer patients

  This data set is comprised of data from seven distinct high grade serous epithelial ovarian cancer (HGS-EOC) partients, from whom multiple biopsies were taken at the time of surgery, from the ovary and from different locations in the peritoneal cavity. This data set contains 28 samples, sequenced with a whole exome sequencing approach.

  Dataset EGAD00001004154

• FFPE CRC sequence data and somatic variants

  We included 3 BAM files of the genome sequencing data: 2 of 3 are from tumour samples, namely 1 repaired-FFPE and 1 unrepaired FFPE; the third BAM file is from normal tissue of FFPE block. There is also a VCF file containing all somatic mutations in the dataset.

  Dataset EGAD00001007723

• Understanding the multicellular dynamics of clear cell renal cell carcinoma - spatial transcriptomics

  The dataset comprises of transcriptomes of tissue sections derived from either the tumour normal interface or tumour core from clear cell renal cell carcinomas. 16 sections are sampled in total using 10x Genomics' Visium technology.

  Dataset EGAD00001008781

• CASCADE germline whole genome sequencing data

  High-coverage whole genome sequencing data (median coverage: 23.5X, range: 14.14X-32.62X)) from white blood cells of the patients from isolated buffy coat of the blood drawn postmortem from patients who participated in the CASCADE rapid autopsy program and died of metastatic castration resistant prostate cancer.

  Dataset EGAD00001009493

• Elucidation of molecular mechanisms of tumorigenesis and development of diagnoses and treatments based on comprehensive genomic analyses in pancreatic tumors, duodenal tumors and biliary tumors

  We performed whole genome and whole exome sequencing analyses of pancreatic tumors, duodenal tumors and biliary tumors and investigated the molecular mechanisms of tumorigenesis based on the comprehensive genome profiling.

  Study JGAS000359

• Processed miRNA Counts for the miRNA Profiling from Indian HFrEF Cohort Dataset

  This dataset contains processed miRNA count data for the 49 Heart Failure samples profiled by miRNAseq for the Indian HFrEF Cohort from the study Integrated Transcriptomic and Regulatory RNA Profiling Reflects Complex Pathophysiology and Uncovers a Conserved Gene Signature in End Stage Heart Failure RNA-Seq data.

  Dataset EGAD50000001195

• Processed Total RNA Counts for the RNA Profiling from Indian HFrEF Cohort Dataset

  This dataset contains processed RNA count data for the 49 Heart Failure samples profiled by RNAseq for the Indian HFrEF Cohort from the study Integrated Transcriptomic and Regulatory RNA Profiling Reflects Complex Pathophysiology and Uncovers a Conserved Gene Signature in End Stage Heart Failure RNA-Seq data.

  Dataset EGAD50000001193

• 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