Division of Biomedical Genetics UMC Utrecht

Dac ID Contact Person Email Access Information
EGAC00001000432 Edwin Cuppen dacdbg [at] umcutrecht [dot] nl No additional information is available

This DAC controls 14 datasets:

Dataset ID Description Technology Samples
EGAD00001001900 DNA sequencing reads of human adult stem cell cultures from liver, colon and small intestine. Including biopsy or blood samples of the donors. HiSeq X Ten,Illumina HiSeq 2500,NextSeq 500 61
EGAD00001002242 This dataset contains RNA-seq and Hi-C data files of induced pluripotent stem (iPS) cells and iPS cell-derived neural progenitors (NPCs) derived from a germline chromothripsis patient and both parents. iPS cells of the patient (cell lines 14 and 15), the father (lines 23 (with two replicates) and 32) and mother (line 30) were differentiated to NPCs and RNA was collected on day 0, day 7 and day 10 of differentiation. In addition, Hi-C data for two iPS cell-derived NPC lines from the patient (14 and 15) and two lines from the father (23 and 32) was generated. AB 5500xl Genetic Analyzer,Illumina HiSeq 2500,NextSeq 500 22
EGAD00001002719 This dataset contains whole-genome sequencing data files from colon organoid cultures, which were mutated using CRISPR-Cas9 for specific genes (APC, KRAS, TP53 and SMAD4) to generate in vitro transformed cancer cells. After introducing each mutation, the resulting cultures were subjected to whole-genome sequencing. In addition, some cultures were xenotransplanted in recipient mice. The resulting primary tumors and corresponding metastases were subjected to whole-genome sequencing. HiSeq X Ten 30
EGAD00001003291 This dataset represents RNA-sequencing data from 278 primary colon cancers obtained from fresh-frozen tumor sections. RNA-sequencing was performed using TruSeq library preparation and samples were sequenced on Illumina NextSeq and HiSeq. The data are available as Illumina NextSeq and HiSeq fastq files (_R1.fastq and _R2.fastq for each tumor sample, 556 files in total). Illumina HiSeq 2500,NextSeq 500 278
EGAD00001003510 BAM files with sequencing reads derived from Illumina whole genome sequencing of two DNA samples from lymphoblastoid cell lines from two patients with congenital disease. Whole genome sequencing was performed using Illumina HiSeq X Ten and samples were prepared using TruSeq library prep. HiSeq X Ten 2
EGAD00001003511 BAM files with sequencing reads derived from Oxford Nanopore MinION whole genome sequencing of two DNA samples from lymphoblastoid cell lines from two patients with congenital disease. Samples were prepared using 1D and 2D library preps. MinION 2
EGAD00001003595 This dataset consists of TLA data in the parents of 9 healthy families and 11 B-thalasemia risk families during pregnancy, cell-free DNA sequencing data and Fetal DNA sequencing where available. TLA data was collected for the CFTR region in all healthy families and the CYP21A2 region in two of the healthy families. TLA data was collected for the HBB region in the risk families. In each pregnant mother, cell-free DNA was collected, enriched for the region of interest using sureselect pulldown and sequenced. Samples are labled Mother_X, Father_X and CVS_X for the healthy families and HBB_Mother_X, HBB_Father_X and HBB_CVS_X. cfDNA files can be found under the maternal sample, and each consist of three indices used to increase the maximum number of unique molecules per SNP. Both raw and processed cfDNA data is provided, raw data is mapped using BWA MEM, sorted using samtools and restricted to the region of interest for the sake of patient privacy. Processed data is mapped using BWA MEM, sorted using samtools, duplicate filtered using samtools rmdup, overlap-clipped using picardtools and restricted to the region of interest. NextSeq 500 55
EGAD00001003751 Whole genome sequencing data for primary tumors, matching control material from blood and their corresponding organoid. Whole transcriptome data for organoids. HiSeq X Ten,NextSeq 500 102
EGAD00001003779 Whole genome sequencing (WGS) data of human small intestinal organoid cultures, which were deleted for the XPC gene using CRISPR-Cas9. Contains WGS data of 1 clone and 1 subclone. HiSeq X Ten 2
EGAD00001003805 A whole genome mutation analysis of cortical kidney tissue, an early passage kidney organoid culture derived from the kidney tissue sample, and a late passage of the same organoid culture. HiSeq X Ten 3
EGAD00001004013 Organoids are self-organizing 3D structures grown from stem cells that recapitulate essential aspects of organ structure and function. Here we describe a method to establish long-term culture conditions of human airway epithelial organoids that contain all major cell populations and allow personalized human disease modelling. We collected macroscopically inconspicuous lung tissue from non-small-cell lung cancer (NSCLC) patients undergoing medically indicated surgery and isolated epithelial cells to engineer 3D organoids. We exploit the potential to derive sub-clones from AOs to demonstrate the feasibility of CRISPR gene editing. Finally, we show that AOs readily allow modelling of viral infections such as RSV and for the first time demonstrate the possibility to study neutrophil-epithelium interaction in an organoid model. Taken together, we anticipate that human AOs will find broad applications in the study of adult human airway epithelium in health and disease. HiSeq X Ten 4
EGAD00001004105 Clonally expanded liver adult stem cell clones of healthy liver and cirrhotic liver (due to alcohol abuse, NASH and PSC), as well as biopsies of liver cancers were subjected to whole genome sequencing to determine the mutational impact of precancerous liver disease HiSeq X Ten,NextSeq 500 44
EGAD00001004387 WGS of ovarian cancer organoids, tumor samples and blood references. Ovarian cancer (OC) is a heterogeneous disease usually diagnosed at a late stage. Experimental in vitro models that faithfully capture the hallmarks and tumor heterogeneity of OC are limited and hard to establish. We present a novel protocol that enables efficient derivation and long-term expansion of OC organoids. Utilizing this protocol, we have established 56 organoid lines from 32 patients, representing the spectrum of ovarian neoplasms, including non-malignant borderline tumors, as well as mucinous, clear-cell, endometrioid, low- and high-grade serous carcinomas. OC organoids recapitulate histological and genomic features of the pertinent lesion from which they were derived, illustrating intra- and inter-patient heterogeneity, and can be genetically modified. We show that OC organoids can be used for drug screening assays and capture different tumor subtype responses to the gold standard platinum-based chemotherapy, including acquisition of chemoresistance in recurrent disease. Finally, OC organoids can be xenografted, enabling in vivo drug sensitivity assays. Taken together, this demonstrates their potential application for research and personalized medicine. HiSeq X Ten 111
EGAD00001004451 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. HiSeq X Ten 30