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• Mixture of 2 (closer mtDNA)

  Mixture of 2 unrelated individuals (of close mtDNA haplogroup) sequenced by 10x as a scRNA-seq. The dataset was then processed by Cell Ranger and deconvoluted to yield each individuals genetic profile. The clustering of SNPs is submitted as the processed file. The Sequencing fastqs are submitted as unprocessed files.

  Dataset EGAD00001008727

• HiC (chromosomal conformation capture) data for Oncogenic 3D genome conformations identify novel therapeutic targets in ependymoma

  This dataset contains chromosomal conformation capture data from fourteen samples (eleven tumor samples and three tumor derived cell lines). Libraries were prepared using the Illumina TruSeq LT sequencing adaptors. Sequencing was performed on the HiSeq X or NovaSeq platforms resulting in 28 FASTQ files.

  Dataset EGAD00001008801

• Paired healthy & tumor organoid Biobank _B16PON

  Organoid cultures derived from colorectal adenomas. RNA and DNA was isolated from these cultures for genome wide profiling.

  Dataset EGAD00001008949

• 2 10X multiomics (RNA+DNA) gray matter brain controls donors

  Single cell multiomics from 2 donor controls, expression and chromatin accessibility. Samples belong to gray matter tissue from the brain.

  Dataset EGAD00001008457

• Metastatic Pediatric Sclerosing Epithelioid Fibrosarcoma

  This dataset contains different samples from a single patient with SEF. The dataset contains whole genome, whole exome and RNAseq information. Two of the DNA sequencing samples also contain matched normals.

  Dataset EGAD00001007516

• single-cell RNA-Seq samples of CRC patients

  The dataset contains samples of 11 CRC patients (2 samples for each patient, tumor and normal adjacent tissue site, 22 samples in total). Dataset is composed by fastq file (paired end) type from 10x single-cell RNA-Seq.

  Dataset EGAD00001009634

• Bulk BCR NGS data from metastatic breast tumours from donors with therapy-resistant lethal metastatic breast cancer.

  Bulk B Cell Receptor high-throughput sequencing data across 27 metastatic breast tumours obtained from 8 donors with therapy-resistant lethal metastatic breast cancer at the time of a warm autopsy. The 35 samples were sequenced on an Illumina MiSeq instrument and their raw FastQ files deposited here.

  Dataset EGAD00001010023

• CHROMATIN ACTIVATION PROFILING OF STEREOTYPED CHRONIC LYMPHOCYTIC LEUKEMIAS

  We used chromatin-immunoprecipitation followed by sequencing (ChIP-Seq) with an antibody for the H3K27ac (a bona fide histone mark for regulatory element activation) in sorted CLL cells from 15 CLL, including cases from stereotyped subsets #1, #2, #4, and #8. The samples were sequenced by Illumina HiSeq 2500.

  Dataset EGAD00001009082

• DNA methylation-based classification of sinonasal tumors [DNA sequencing]

  This dataset contains raw exome sequencing data from nine sinonasal undifferentiated carcinoma FFPE samples and matched normal tissue that were assigned to a shared epigenetic class using DNA methylation-based classification. They were analyzed using the Twist Human Core Exome Plus Kit (Twist Bioscience) on a NovaSeq 6000 sequencer.

  Dataset EGAD00001009668

• GELATO clinical trial whole exome sequencing data (metastatic lesions)

  Paired-end whole exome sequencing of 19 lobular breast cancer metastatic tumors and matched normal samples obtained from 19 unique patients from the GELATO clinical trial. The included raw sequencing data in fastq format was generated using Illumina NovaSeq 6000 from fresh frozen material.

  Dataset EGAD00001009837

• RNA-Seq files for St. Jude Clinical Pilot

  This dataset contains whole genome sequencing BAM files for 78 tumor-normal pairs (a total of 156 samples) used in the St. Jude Clinical Pilot. Mapping was performed using BWA. This dataset accompanies the paper "Clinical Cancer Genomic Profiling by Three-Platform Sequencing of Whole Genome, Whole Exome and Transcriptome"

  Dataset EGAD00001004280

• DDD resource files

  DDD resource files (e.g. link between sample and individual ids)

  Dataset EGAD00001010136

• Metastatic Pediatric Sclerosing Epithelioid Fibrosarcoma

  This dataset contains different samples from a single patient with SEF. The dataset contains whole genome, whole exome and RNAseq information. Two of the DNA sequencing samples also contain matched normals.

  Dataset EGAD00001007515

• 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

• A next-generation dual guide CRISPR system for genetic interaction library screening

  Raw sgRNA sequencing data from a pilot CRISPR screening library to test the dual guide vector system (8,914 guide pairs), and from a large scale genetic interaction screen (~100,136 guide pairs) in HT-29 cells. This data refers to Burgold et al. Nature Communications 2025.

  Dataset EGAD00001015754

• Human cross-tissue ILC1

  scRNASeq analysis of human Lin neg lymphocytes from control liver, cirrhotic liver, tonsil, duodenum, and colon tissues.

  Dataset EGAD00001009861

• scRNA Seq of MCSP+ melanoma DCC and bulkRNA Seq of MelDCC lines

  Single cell RNA Seq of: 193 MCSP+ DCC isolated from SLNs of melanoma patients, 9 MCSP+ cells isolated from LNs of non-melanoma patients, 14 melanocytes from a healthy donor. Bulk RNA Seq of 10 samples from 4 DCC-PDX-derived cell lines. Sequencing on NovaSeq6000. Fastq files.

  Dataset EGAD00001009662

• The mutation burden of narrowband ultraviolet B phototherapy in human skin - Nanoseq

  Background: Ultraviolet radiation (UV) is used as a treatment for psoriasis, but UV can also induce mutations which may lead to development of skin cancer. Information on the mutagenicity of narrowband UVB (NBUVB) would help inform clinicians and patients who are concerned about the potential risks of this treatment.

  Dataset EGAD00001015249

• The mutation burden of narrowband ultraviolet B phototherapy in human skin - WGS

  Background: Ultraviolet radiation (UV) is used as a treatment for psoriasis, but UV can also induce mutations which may lead to development of skin cancer. Information on the mutagenicity of narrowband UVB (NBUVB) would help inform clinicians and patients who are concerned about the potential risks of this treatment.

  Dataset EGAD00001015250

• Bulk RNA Seq in FAP Adenoma

  Bulk RNASeq data of Duodenal organoids, sorted ILC3 and duodenal tissue

  Dataset EGAD00001015488

• RRBS data of 48 individuals of the Dutch Hunger Winter Families Study

  The dataset entails 48 RRBS libraries of 24 siblings. 24 individuals are conceived during the Dutch Famine, a severe 6 month famine at the end of World War 2. A same sex sibling was added as a control, allowing partial matching for (early) familial environment and genetics.

  Dataset EGAD00001000733

• Whole exome sequencing for HELIC

  The HELIC study has been whole genome sequencing individuals from 2 Greek isolatedpopulations at 1x depth. The genotype calling process crucially involves a VQSR stepfollowed by imputation-based refinement. We have been investigating optimal ways toincrease calling accuracy. To aid us in setting appropriate parameters for VQSR and otherQC steps, we have carried out whole exome sequencing of a small number ofHELIC samples.

  Dataset EGAD00001001638

• NIHR-BioResource Rare Diseases SPEED IRD August 2016

  Whole exome sequencing BAM files and whole genome sequencing CRAM files for 722 individuals from the NIHR-BioResource Rare Diseases Consortium (SPEED project) with inherited retinal disease.

  Dataset EGAD00001002656

• Predictor_ChemoNEAR_TNBC (2019-08-14)

  In this study a collection of core biopsies from breast cancer patients receiving neoadjuvant chemotherapy as part of the ChemoNEAR trial will be investigated. The study is intended to detect early acquired resistance in women with diagnosed breast carcinoma. Samples will undergo whole genome sequencing and analysis, including use of HR Predict. . This dataset contains all the data available for this study on 2019-08-14.

  Dataset EGAD00001005255

• Validation data for the SV analysis package: GRIDSS, PURPLE, LINX

  Validation data containing sequencing data of 13 samples. An hybrid capture approach was used to validate findings of both Manta and GRIDSS for the samples in the validation set. The dataset also contains the reference sequences used.

  Dataset EGAD00001005525