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• Tumor Profiler Project - OV bulk transcriptomics data

  The dataset contains bulk transcriptomics data from 39 samples from 36 different patients with ovarian cancer. 34 samples were collected from the tumor, 5 samples from ascites. Sequencing was performed in paired-end mode and sequencing data is provided in fastq format.

  Dataset EGAD50000001413

• Targeted DNA sequence

  Targeted DNA sequencing files that were used in our study. The cohort was composed of 36 cases of tumor-only targeted DNA sequencing data. All files are UMI processed. The panel is designed with Agilent Sure Select and the sequence was performed using DNBSEQ sequencer.

  Dataset EGAD50000000972

• RNA sequencing of 120 AML samples

  This dataset contains fastq-files from bulk RNA sequencing of 120 AML samples. RNA was extracted from either bone marow or peripheral blood from primary AML samples. The libraries were prepared using Illumina Truseq RNA library preparation kit v2 and sequenced on an Illumina NextSeq 500 using 2x151bp paired end chemistry.

  Dataset EGAD50000001576

• RNA bulk sequencing on organoids from different organs with or without TS2/16 antibody

  RNA bulk sequencing on organoids from colon, ileum, jejunum, duodenum and pancreas duct with or without TS2/16 antibody. Also there is difference in extracellular matrix used, BME vs Colagen.

  Dataset EGAD50000001606

• CosMX spatial transcriptomics

  This study consists of the spatial transcriptomics analyis data generated by : CosMxTM Human Universal Cell Characterization RNA Panel (1000-plex); NanoString, USA for n=4 SLD-HCC and n=4 non-SLD-HCC. The goal of this data is to compare SLD-HCC vs non-SLD-HCC as well as response to immunotherapy

  Dataset EGAD50000001507

• 909 bulk mRNA sequencing samples from the UPTIDER program

  Raw sequencing data for 909 bulk mRNA samples that correspond to 749 metastases, 64 primary tumours and 96 normal tissue. These samples were sequenced using NovaSeq6000. Library was prepared with Lexogen QuantSeq 3' FWD. Raw single-end fastq samples have been deposited as gzipped files.

  Dataset EGAD50000001910

• Dataset for desmoplastic small round cell tumor - WES

  This dataset contains 45 WES sequencing samples of patients with desmoplastic small round cell tumor. Sequencing was performed on Illumina HiSeq 2500, Illumina HiSeq 4000 and NovaSeq 6000 using Agilent SureSelect Human All Exon V5 Kit. The sequencing was always paired.

  Dataset EGAD50000000910

• Liquid biopsy-based minimal residual disease monitoring for early risk stratification and decision-making in advanced non-small cell lung cancer - DEDICATION co-hort

  Liquid biopsies generated for minimal residual disease monitoring of non-small cell lung cancer. Ultra deep targeted sequencing of lung cancer related genes with UMIs. This dataset contains the dedication cohort

  Dataset EGAD50000002230

• Liquid biopsy-based minimal residual disease monitoring for early risk stratification and decision-making in advanced non-small cell lung cancer - Biobank co-hort

  Liquid biopsies generated for minimal residual disease monitoring of advanced non-small cell lung cancer. Ultra deep targeted sequencing of lung cancer specific genes, with UMIs. This dataset consists of the biobank cohort

  Dataset EGAD50000002231

• RNA-Seq data for paper titled 'Genomic Landscape of Pediatric Myelodysplastic Syndromes'

  When available (25 primary MDS, 12 MDS/MPN, and 6 AML-MRC cases), high quality RNA (stranded-total) was submitted for RNA-seq. RNA was extracted from bulk myeloid cells which was used as the tumor population. Files uploaded are mapped BAM files.

  Dataset EGAD00001003782

• Sequencing data for oesophageal and related samples - Mourikis et al (RNA)

  Data supporting: "Patient-specific detection of cancer genes reveals recurrently perturbed processes in esophageal adenocarcinoma." Mourikis et al. RNAseq (BAM files) 137 samples

  Dataset EGAD00001004776

• Single cell mRNA sequencing of primary GBM - SF 10345

  We collected fresh tissue from an untreated GBM (SF10345) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

  Dataset EGAD00001002271

• A comprehensive characterisation and analysis of human breast cancers through whole-genome sequencing

  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.

  Dataset EGAD00001002740

• Whole exome sequencing of 27 Greenlanders

  The data contain whole exome sequencing of 27 Greenlanders in nine trios. Data were produced by Agilent SureSelect capture followed by paired-end Illumina HiSeq 2000 sequencing to a depth of 90.1X. More details on processing and analysis can be found in Moltke et al, Nature 2014 (PMID 25043022).

  Dataset EGAD00001003813

• BLUEPRINT: ChIP-seq for monocytes & neutrophils

  ChIP-seq for monocytes and neutrophils

  Dataset EGAD00001000676

• WES data generated in multifocal ileal NETs study

  This dataset includes whole-exome sequencing data for multifocal ileal tumor samples from two patients. Exonic sequences were enriched using the Agilent V2 capture probe set and sequenced by 76-bp paired-end reads using the Illumina Genome Analyzer IIx system with a mean coverage of 80x for each base

  Dataset EGAD00001006408

• Single cell mRNA sequencing of primary GBM - SF 10282

  We collected fresh tissue from an untreated GBM (SF10282) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

  Dataset EGAD00001002270

• The British Autozygosity Populations BioResource

  This data set contains whole exome sequences of individuals with self-stated parental relatedness from the East London Genes & Health cohort. Rare frequency functional variants in these healthy individuals will be studied with respect to the genetic health of the participants and loss-of-function analysis of human genes.

  Dataset EGAD00001003215

• Single cell mRNA sequencing of primary GBM - SF 10360

  We collected fresh tissue from an untreated GBM (SF10360) directly from the operating room and subjected the biopsy to single-cell RNA-seq with the fluidigm C1 machine, resulting in sequencing libraries from 96 individual cells.

  Dataset EGAD00001002272

• Chromatin 3D interactions mediate genetic effects on gene expression (RNA-seq)

  RNA-seq data for 168 Lymphoblastoid Cell Lines (LCL) and 78 Fibroblasts (FIB) from the Gencord Cohort. This dataset was generated as part of the following study: Delaneau et al (2019). Chromatin 3D interactions mediate genetic effects on gene expression.

  Dataset EGAD00001004872

• GATCI whole genome sequence data

  Sequence data in fastq format was aligned to the GRCh38 reference genome with BWA-MEM. Aligned sequence was preprocessed with GATK for Indel Realignment and Base Quality Score Recalibration. Duplicates were marked with Picard Mark Duplicates. Aligned sequence is in bam format. Details of the alignment can be found in the bam header

  Dataset EGAD00001005914

• Deep multi-region WGS of lung cancer tumours

  Deep WGS (germline and 2-5 tumour regions) was performed on 20 patients: 13 lung adenocarcinoma, 5 squamous cell carcinoma, 2 small-cell lung cancers. A total of 68 BAM files are provided, where tumours were sequenced to 60x or 150x depth.

  Dataset EGAD00001005287

• smRNA-seq of human post-mortem brain data of frontal lobe (Tuebingen part)

  This dataset contains smRNA-seq data from post-mortem human brain tissue of the frontal lobe of patients with FTD and healthy controls. The smRNA-sequencing was done in two parts, this dataset depicts the data generated at the DZNE Tübingen.

  Dataset EGAD00001006846

• WGS of human colorectal cancer organoid exposed to genotoxic pks+ E. coli

  Organoid cultures were exposed to two different E.Coli strains and a dye control with three biological duplicates. Their original culture was harvested as a control. In total 10 organoid cultures were whole-genome sequenced using the Novaseq6000 platforms. The data is deposited as .bam format.

  Dataset EGAD00001005416

• Correction of a Factor VIII genomic inversion with designer recombinases

  PromethION-based whole genome sequencing of endothelial cells differentiated from patient derived induced pluripotent stem cells (iPSCs) of a hemophilic donor, transiently treated with a Cre recombinase, a RecF8 recombinase, and untreated cells. The dataset contains fastq files with all sequencing reads passing the standard quality filtering.

  Dataset EGAD00001007923