Division of Biomedical Genetics UMC Utrecht

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This DAC controls 68 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 854 single cell sequenced colorectal cancer organoids.		854
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
EGAD00001006321	RNA sequencing during time series	Illumina HiSeq 2000	58
EGAD00001006417	single cell sequencing esophagus, stomach and duodenum of : 4 esophagus samples 9 gastric samples 5 duodenum samples		18
EGAD00001006542	This dataset contains: Targeted proximity-ligation assay, enriched using capture probes (1092 samples) Targeted proximity-ligation assay, enriched using 4C (1230 samples) Genome-wide proximity-ligation assay, enriched using HiC ( 6 samples)	Illumina MiniSeq Illumina NovaSeq 6000	2328
EGAD00001006780	Whole genome sequencing BAMs of DNA obtained from blood/saliva of 8 patients with adult granulosa cell tumors. These patients come from four independent families, with each family having 2 affected family members.	Illumina NovaSeq 6000	8
EGAD00001007305	458 single cell samples of multiple colorectal cancer organoids		458
EGAD00001007521	14 samples were processed for single cell DNA sequencing	NextSeq 500	14
EGAD00001007522	13 samples were processed by whole genome sequencing	Illumina NovaSeq 6000	13
EGAD00001007523	17 samples were processed for single cell RNA sequencing (SORT-seq)	NextSeq 500	17
EGAD00001007775	Intrahepatic cholangiocyte organoid clone from patients with chronic alcohol consumption, NASH (nonalcoholic steatohepatitis), and PSC (primary sclerosing cholangitis)	HiSeq X Ten	19
EGAD00001008576	Contains 14 control samples and 26 case samples.	HiSeq X Ten	26
EGAD00001008643	9 tumor biopsies & 84 blood samples	Illumina MiSeq	93
EGAD00001009485	Contains 4 clonal organoid samples + 1 bulk healthy tissue sample	HiSeq X Ten	5
EGAD00001009742	16 additional samples	HiSeq X Ten	16
EGAD00001009785	Contains control and PXR KD human small intestinal organoids	NextSeq 500	18
EGAD00001009884	WGS data normal and hypomethylation	Illumina NovaSeq 6000	6
EGAD00001009885	Nanopore pericentromere normal methylation	MinION	1
EGAD00001009886	Nanopore pericentromere hypomethylation	MinION	1
EGAD00001009887	RNA seq data normal and hypomethylation	Illumina HiSeq 2000	6
EGAD00001010134	patient-derived head and neck cancer organoids	Illumina NovaSeq 6000	64
EGAD00001010148	Contains IMCISION samples sequenced on Flongle flowcells	MinION	1
EGAD00001010149	Contains Synthetic samples sequenced on R9 flowcells	MinION	3
EGAD00001010150	Contains Healthy samples sequenced on Flongle flowcells	MinION	2
EGAD00001010151	Contains Healthy samples sequenced on R9 flowcells	MinION	7
EGAD00001010152	Contains Synthetic samples sequenced on Flongle flowcells	MinION	6
EGAD00001010153	Contains PREDICT samples sequenced on R10 flowcells	MinION	2
EGAD00001010154	Contains IMCISION samples sequenced on R9 flowcells	MinION	13
EGAD00001010155	Contains PREDICT samples sequenced on R9 flowcells	MinION	28
EGAD00001010181	27 Chip-Seq samples from Human CD4+ T cells	NextSeq 500	27
EGAD00001010182	20 RNAseq samples of Human CD4+ cells	NextSeq 500	20
EGAD00001011176	This dataset represent the RNA-seq, which was done on untreated small intestinal organoids; small intestinal organoids treated with chemotherapeutic, busulfan; untreated small intestinal organoids co-cultured wth mesenchymak stromal/stem cells (MSCs; busulfan treated small intestinal organoids co-cultured with MSCs. The same set of samples was done for 3 different primary bone marrow MSC donors.	NextSeq 500	12
EGAD00001011336	Instestinal organoids treated with either busulfan, fludarabine or clofarabine for 24h	NextSeq 500	12
EGAD00010002041	Contains test sample 1-26	Illumina Iscan	26
EGAD00010002404	Methylation array	iScan	6