DAC

Division of Biomedical Genetics UMC Utrecht

Dac ID Contact Person Email Access Information
EGAC00001000432 DAC DBG dacdbg [at] umcutrecht [dot] nl http://ubec.nl/data-access-committee/

This DAC controls 35 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
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
EGAD00001003997 From 2nd trimester human foetuses we derived liver and intestinal stem cells. These were clonally expanded until enough material was available for whole genome sequencing. For each foetus, reference tissue (skin or bulk liver) was also sequenced to determine all germline variants. These were subtracted from the clones to determine all somatic mutations that had been acquired during embryonic and fetal development. HiSeq X Ten,NextSeq 500 50
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
EGAD00001004104 Clonally expanded human pluripotent and adult (liver + intestine) stem cell clones were subjected to whole genome sequencing to determine the mutational impact of in vitro culture HiSeq X Ten,NextSeq 500 11
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
EGAD00001004500 Mapped data for 10 Colon MSI cancer samples Illumina HiSeq 2500 10
EGAD00001004509 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. NextSeq 500 50
EGAD00001004528 This dataset contains 31 pancreatic organoid samples used in the 'organoid data of pancreatic cancers ' study HiSeq X Ten 31
EGAD00001004529 This dataset contains 53 blood samples used as controls in study EGAXXXXX and EGAXXXXX HiSeq X Ten 53
EGAD00001004863 This dataset contains Whole Genome Sequencing, RNA-sequencing and ATAC-sequencing data obtained from PBMCs derived from blood samples of one patient with complex genomic rearrangements and the biological parents. The patient has multiple congenital anomalies and delayed development. Data access is closed. HiSeq X Ten,NextSeq 500 9
EGAD00001004864 This dataset contains Whole Genome Sequencing and, if available, RNA-sequencing and/or ATAC-sequencing data obtained from PBMCs derived from blood samples of two patients with intellectual disability and/or multiple congenital anomalies and eight parents included in the University Medical Center Utrecht (The Netherlands). Data access is closed. HiSeq X Ten,NextSeq 500 15
EGAD00001004865 This dataset contains Whole Genome Sequencing and, if available, RNA-sequencing and/or ATAC-sequencing data obtained from PBMCs derived from blood samples of 34 patients with intellectual disability and/or multiple congenital anomalies and their biological parents (58) included in the University Medical Center Utrecht (The Netherlands). HiSeq X Ten 15
EGAD00001004866 This dataset contains Whole Genome Sequencing and, if available, RNA-sequencing and/or ATAC-sequencing data of 17 lymphoblastoid cell lines derived from patients with complex genomic rearrangements. Patients have phenotypes in category of intellectual disability and/or multiple congenital anomalies. Data access is closed. HiSeq X Ten 15
EGAD00001004943 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. NextSeq 500 4
EGAD00001004959 This dataset contains all samples used in study 'Whole genome characterisation of 5-FU treated organoids' HiSeq X Ten 3
EGAD00001005217 RNA sequencing of 31 pancreatic cancer organiods NextSeq 500 31
EGAD00001005225 This dataset contains RNA sequencing data for 20 intra/extra hepatic bileduct organiods. Data is in BAM format and was processed by STAR. NextSeq 500 20
EGAD00001005380 Contains RNAseq data for 14 transduced/non-transduced organoids Illumina NovaSeq 6000 14
EGAD00001005422 Dataset contains 371 single cell sequenced colorectal cancer organoids. Illumina NovaSeq 6000,NextSeq 500 371
EGAD00001005472 Low coverage nanopore sequencing of ovarian cancer tumors GridION,MinION 4
EGAD00001005473 Low coverage nanopore sequencing of prostate cancer tumors GridION 5
EGAD00001005476 WGS Nanopore nanopore sequencing of organoid line HGS-3.1 and matching blood reference HGS-3 MinION 2
EGAD00001005707 WGS of more samples in the ovarian cancer organoid biobank dataset. HiSeq X Ten 23
EGAD00001005999 Contains 46 aGCT tumor sample WGS BAMs from 33 patients and corresponding 33 germline reference WGS BAMs from those 33 patients Illumina NovaSeq 6000 79
EGAD00001006111 Targeted long-read nanopore sequencing. Abstract: Fusion genes are hallmarks of various cancer types and important determinants for diagnosis, prognosis and treatment. Fusion gene partner choice and breakpoint-position promiscuity restricts diagnostic detection, even for known and recurrent configurations. To accurately and impartially identify fusions, we developed FUDGE: FUsion Detection from Gene Enrichment. FUDGE couples target-selected and strand-specific CRISPR/Cas9 activity for fusion gene driver enrichment - without prior knowledge of fusion partner or breakpoint-location – to long-read Nanopore sequencing with the bioinformatics pipeline NanoFG. FUDGE has flexible target-loci choices and enables multiplexed enrichment for simultaneous analysis of several genes in multiple samples in one sequencing run. We observe on-average 665 fold breakpoint-site enrichment and identify nucleotide resolution fusion breakpoints - within two days. The assay identifies cancer cell line and tumor sample fusions irrespective of partner gene or breakpoint-position. FUDGE is a rapid and versatile fusion detection assay, providing unparalleled opportunity for diagnostic pan-cancer fusion detection. GridION 17