EGAC00001001864 - Data Access Commitee Princess Maxima Center

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Marion Persoon
biobank-2@prinsesmaximacentrum.nl

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This DAC controls 78 datasets

Dataset ID	Description	Technology	Samples
EGAD00001005063	Tumor and matching normal tissues were collected from 8 patients and organoids were derived from each tissue. Whole exome libraries were prepared for tumor tissue, normal tissue, tumor organoids and normal organoids, and paired-end sequencing was performed using Illumina Novaseq 6000 system. Only tumor and matching normal tissues were sequenced for the patients without available organoids.	Illumina NovaSeq 6000	24
EGAD00001005318	None	Illumina HiSeq 4000	51
EGAD00001005319	None	BGISEQ-500 HiSeq X Ten Illumina NovaSeq 6000	59
EGAD00001005416	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.	Illumina NovaSeq 6000	20
EGAD00001005427	Three SpCas9-ABE (R785X/R785X) and three xCas9-ABE-repaired organoid clones (F508del/R553X) and their respective unrepaired control organoids were paired-end whole genome sequenced using Illumina Novaseq 6000 system. The reads were mapped to hg19 genome assembly and data is provided as BAM files.	Illumina NovaSeq 6000	8
EGAD00001005459	Whole genome sequencing of HSPC and SI clones of 2 disomy- and 1 trisomy 21 fetuses samples (HiSeq X Ten samples). 5 disomy clones and 5 trisomy clones were included in this experiment. Three bulk samples were also included.	HiSeq X Ten	13
EGAD00001005461	This dataset contains two experiments. 1) Single cell RNA-seq of diagnostic samples from patients with MLL-rearranged infant ALL that underwent relapse or not (samples ending in R relapsed, samples ending in N did not). For some of the patients, multiple indipendent plates were produced (each plate is a sample). 2) in vitro prednisolone exposure experiment. diagnostic bone marrow samples from patient 4662R were cultured for three days with and without prednisolone. Single cell experiments were conducted according to Muraro et al (cell systems, 2016, doi:10.1016/j.cels.2016.09.002). Cell barcodes and UMI sequences are embedded in the header of each fastq entry. Cell barcodes irrelevant to this experiment were removed before submission.	NextSeq 500	11
EGAD00001006166	Whole exome sequencing (WES) was performed on the matched tumor and organoid pairs from 7 cervical cancer patients. The DNA was sequenced on NovaSeq6000 platform with 8Gb sequencing coverage. WES data was mapped against human reference genome GRCh38 by using BWA (v0.7.5) mapping tool.	Illumina NovaSeq 6000	17
EGAD00001006338	Whole genome sequencing data (Illumina HiSeq and NovaSeq) of clonal cultures derived from pediatric human bone marrow-derived hematopoietic stem and multipotent progenitor cells (in total 44 samples from 10 donors) and bulk pediatric acute myeloid leukemia blasts (in total 6 samples from 6 patients) to study the mutation accumulation.	HiSeq X Ten Illumina NovaSeq 6000	118
EGAD00001006343	Whole genome sequencing of HSPC and SI clones of 3 disomy- and 3 trisomy 21 fetuses samples and 2 TMD samples (Novaseq 6000 samples). 22 disomy clones, 20 trisomy clones were included in this experiment. 11 bulk samples were also included.	Illumina NovaSeq 6000	53
EGAD00001006352	We performed whole genome sequencing to detect possible off-target mutations induced by prime editing. Liver organoids, derived from a healthy control, were transfected with either control (GFP) plasmids or prime editing plasmids (GFP+PE2+pegRNA+nickRNA) to induce a 6-bp deletion in CTNNB1. One control and two prime-edited organoid lines were clonally expanded from single cells. High-throughput sequencing was performed on the complete genomic DNA isolated from these clonal lines, as well as the starting culture (bulk). After correction for germline mutations in the starting culture, new mutations in the control and prime-edited lines were compared. The same approach was followed in small intestinal organoids, derived from a patient with disease-causing 3-bp deletion in DGAT1. In these small intestinal organoids, prime editing was used to insert the 3 missing nucleotides. Two corrected clones were compared to one control clone.	Illumina NovaSeq 6000	8
EGAD00001006574	None	Illumina NovaSeq 6000	30
EGAD00001006777	We generated HPRT-only knockout lines as well as the combination of HPRT with MSH2, UNG and XPC. Whole genome sequencing was performed on generated clones and subclones. By subtracting variants present in the clones from those in the subclones, the somatic mutations, that accumulated in between the clonal steps, were determined.	HiSeq X Ten Illumina NovaSeq 6000	11
EGAD00001006824	Whole genome sequencing data (Illumina NovaSeq 6000) of clonal cultures derived from pediatric human bone marrow-derived hematopoietic stem and progenitor cells (in total 35 samples from 7 donors), bulk pediatric acute myeloid/lymphoid leukemia blasts (in total 2 samples from 1 patient) and bulk control mesenchymal stem cell cultures (4 samples from 4 patients) to study the mutation accumulation.	Illumina NovaSeq 6000	81
EGAD00001007078	Dataset contains WGS sequecing data from clonally expanded hematopoietic stem cells from 7 individual pediatric cancer patients. Samples were taken before (DX - diagnosis) or Follow-up (DX2/REM/FU - Diagnosis 2, remission or follow-up, respectively). In addtion, cord blood clones (Designated CB) treated with X-ray radiation, Cisplatin, Maphosphamide, Vincristine and Doxorubicin and untreated cord blood hematopoietic stem/progenitor cells were have been whole-genome sequenced. (Abbreviations RAD, CISPL, MAPH, VINC, DOX and CTRL, respectively)	Illumina NovaSeq 6000	115
EGAD00001007498	None	NextSeq 500	1
EGAD00001007701	None		-
EGAD00001007744	Five edited and two unedited organoid clones with one clone prior to editing were paired-end whole genome sequenced using Illumina Novaseq 6000 system. The reads were mapped to hg38 genome assembly and data is provided as BAM files.	Illumina NovaSeq 6000	8
EGAD00001007752	This dataset contains two experiments. 1) Single cell RNA-seq of peripheral blood diagnostic samples from patients with MLL-rearranged infant ALL that underwent relapse or not (samples ending in R relapsed, samples ending in N did not), sequenced with SORT-seq (see cell systems, 2016, doi:10.1016/j.cels.2016.09.002). For some of the patients, multiple indipendent plates were produced (each plate is a sample). Barcode-well correspondence can be found here: https://bitbucket.org/princessmaximacenter/sharq/src/master/data/celseq2_bc384-v4.csv . 2) Single cell RNA-seq of peripheral blood diagnostic samples from patients with MLL-rearranged infant ALL that underwent relapse or not (samples ending in R relapsed, samples ending in N did not), sequenced with10x Genomics Version 2.	NextSeq 500	26
EGAD00001007947	None	Illumina HiSeq 4000	3
EGAD00001007948	Transcriptome sequencing of rhabdoid tumor tissue, organoids and SMARCB1-reconstituted organoids	Illumina HiSeq 4000 Illumina NovaSeq 6000	6
EGAD00001008152	RNA-Seq data for systematic gene fusion detection in Pediatric Cancer		-
EGAD00001008272	None		-
EGAD00001008466	None		-
EGAD00001008467	None		-
EGAD00001008473	This dataset includes RNAseq data of the fetal ISCs and iPSCs derived of the fetal ISCs to confirm successful reprogramming	unspecified	6
EGAD00001008474	this data set includes deep targeted re-sequencing of fetal bulk tissues of the 4 foetuses (T21=2, D21=2). The tissues include: fetal skin and intestinal organoid cultures passage 0 of all 4 fetuses, and spleen of fetus N01 (T21)	NextSeq 500	9
EGAD00001008475	This data set includes WGS data of the in vivo acquired mutations in fetal ISCs and HSPCs of 4 foetuses ( T21=2, D21= 2). In addition, this data set includes sub-clonal fetal ISCs to determine the culture-associated mutations of fetal ISCs. Also, it concludes clone +subclone WGS data of iPSCs derived of the fetal ISCs	Illumina NovaSeq 6000	47
EGAD00001008687	The mutagenicity of bacteria was assessed by serially exposing human small intestinal organoids to various bacterial species or isolated toxins. We have used the following abbreviations: EWT: Organoids exposed to E. coli described in PMID: 32106218 EKO: Organoids exposed to isogenic E. coli as EWT, with knockout of the deltaClbQ gene, rendering them unable to produce colibactin DYE: Organoids exposed to FastGreen injection control dye NIS: Organoids exposed to E. coli Nissle ETBF: Organoids exposed to the protease toxin BTF produced by ETBF-bacteria.	Illumina NovaSeq 6000	15
EGAD00001008709	None		-
EGAD00001009002	None	NextSeq 500	2
EGAD00001009297	Whole genome sequencing of paired tumor-normal samples of pediatric Wilms tumors		-
EGAD00001009298	Bulk RNA-seq data of pediatric Wilms tumors		-
EGAD00001009301	RNA sequencing data of a collection of 6 pediatric ependymoma cases		6
EGAD00001009385	Single-cell mRNA-sequencing to generate a transcriptomic atlas of soft tissue sarcoma tumors	NextSeq 500	13
EGAD00001009688	In this study single cell RNA-Seq data was used to train a deconvolution algorithm. The algorithm was validated on paired bulk RNA-Seq profiles.		4
EGAD00001009758	A novel in-house-made pediatric MEF2D-BCL9 fusion positive acute lymphoblastic leukemia cell line was characterized	Illumina NovaSeq 6000	3
EGAD00001009759	A novel in-house-made pediatric MEF2D-BCL9 fusion positive acute lymphoblastic leukemia cell line was characterized	Illumina HiSeq 2000	2
EGAD00001009766	Profiling of childhood neuroblastoma by single-cell RNA sequencing	NextSeq 500	24
EGAD00001009793	We demonstrate that ATRT tumoroids retain subgroup-specific epigenetic and gene expression profiles	Illumina NovaSeq 6000	8
EGAD00001009794	We demonstrate that ATRT tumoroids retain subgroup-specific epigenetic and gene expression profiles	Illumina NovaSeq 6000	4
EGAD00001009827	Seven clonal organoid lines and one bulk wild-type control sample were paired-end whole-genome sequenced using the Illumina Novaseq 6000 system. We sequenced four clonal intestinal organoid lines harbouring engineered TP53 and FBXW7 mutations as well as three lines targeted for oncogenic APC/TP53/PIK3CA/SMAD4 mutations. The reads were mapped to hg38 genome assembly and data is provided as BAM files.	Illumina NovaSeq 6000	8
EGAD00001010042	Molecular analysis of cancer genomes in children with Lynch syndrome: exploring causal associations WGS		1
EGAD00001010043	Molecular analysis of cancer genomes in children with Lynch syndrome: exploring causal associations WXS		1
EGAD00001010178	iTHER is a prospective national precision oncology program aiming to define tumor molecular profiles in children and adolescents with primary very high-risk, relapsed, or refractory pediatric tumors in order to identify relevant aberrations to inform treatment.		1
EGAD00001010179	iTHER is a prospective national precision oncology program aiming to define tumor molecular profiles in children and adolescents with primary very high-risk, relapsed, or refractory pediatric tumors in order to identify relevant aberrations to inform treatment.		1
EGAD00001010281	Ither NB in Organoids WXS dataset - We aimed to launch an online repository integrating genomics and transcriptomics with high-throughput drug screening (HTS) of nineteen commonly used neuroblastoma cell lines and fourteen generated neuroblastoma patient-derived organoids (NBL-PDOs) to improve identification of molecularly matched therapies and support clinical uptake.		17
EGAD00001010282	Ither NB in Organoids WGS dataset - We aimed to launch an online repository integrating genomics and transcriptomics with high-throughput drug screening (HTS) of nineteen commonly used neuroblastoma cell lines and fourteen generated neuroblastoma patient-derived organoids (NBL-PDOs) to improve identification of molecularly matched therapies and support clinical uptake.		17
EGAD00001010283	Ither NB in Organoids RNA-Seq dataset - We aimed to launch an online repository integrating genomics and transcriptomics with high-throughput drug screening (HTS) of nineteen commonly used neuroblastoma cell lines and fourteen generated neuroblastoma patient-derived organoids (NBL-PDOs) to improve identification of molecularly matched therapies and support clinical uptake.		9
EGAD00001011126	Whole genome sequencing data of 57 single (PTA), clonally expanded and bulk human cells. Cells were obtained from bone marrow samples of patients with Fanconi Anemia (PMCFANCNN) or pediatric AML (PBNNNNN), from a clonal intestinal organoid line (STE0072/D-ORGWTNISL), from human cord blood (PMCCB15) and from a human lymphoblastoid cell line (PMCAHH1). WGS libraries were sequenced to ~15-30x genomic coverage (paired-end) on an Illumina Novaseq.	Illumina NovaSeq 6000	58
EGAD00001011192	This study aims to investigate the dysregulation of RNA translation and identify functional non-canonical open reading frames (ORFs) as potential targets for medulloblastoma treatment. The study involves ribosome profiling and RNAseq of medulloblastoma tissues and cell lines to observe the translation of non-canonical ORFs. Multiple CRISPR-Cas9 screens will be used to identify functional non-canonical ORFs implicated in medulloblastoma cell survival.		4
EGAD00001011193	This study aims to investigate the dysregulation of RNA translation and identify functional non-canonical open reading frames (ORFs) as potential targets for medulloblastoma treatment. The study involves ribosome profiling and RNAseq of medulloblastoma tissues and cell lines to observe the translation of non-canonical ORFs. Multiple CRISPR-Cas9 screens will be used to identify functional non-canonical ORFs implicated in medulloblastoma cell survival.	NextSeq 2000	4
EGAD00001011256	Dataset contains WGS sequencing data from bulk sorted therapy-related myeloid neoplasms (t-MN) and reference cells (MSCs/B cells/T cells). In addition, from 4 patients, also WGS data from single hematopoietic stem and progenitor cells, obtained from samples of t-MN diagnosis, are included. These are either clonally expanded before WGS, or DNA was directly amplified via the primary template-directed amplification (PTA) protocol (mentioned in the sample name).	Illumina NovaSeq 6000	80
EGAD00001011257	WGS data of clonally expanded HSPCs from a Li-Fraumeni patient at the time of second cancer (Burkitt lymphoma and <5% t-MN) after primary osteosarcoma diagnosis and a reference MSC bulk.	Illumina NovaSeq 6000	10
EGAD00001011303	In this study nanopore sequencing was applied to obtain sparse DNA methylation profiles from pediatric CNS tumor samples. A neural network was used to classify the tumor based on the obtained methylation profile.	MinION PromethION	62
EGAD00001011378	Paired tumor-normal whole genome sequencing data from primary tumors of patients diagnosed with neuroblastoma, Ewing sarcoma, Wilms tumor, hepatoblastoma and rhabdomyosarcoma		1
EGAD00001011819	Study describing the dynamics of chromatin organization within malignant rhabdoid tumors. This study describes how this chromatin organization changes upon SMARCB1 rescue within patient-derived organoid models from malignant rhabdoid tumors. Identification of a novel super-enhancer of MYC and identification of patient-specific enhancer utilization to activate MYC expression in these tumors.	NextSeq 550	8
EGAD00001011820	Study describing the dynamics of chromatin organization within malignant rhabdoid tumors. This study describes how this chromatin organization changes upon SMARCB1 rescue within patient-derived organoid models from malignant rhabdoid tumors. Identification of a novel super-enhancer of MYC and identification of patient-specific enhancer utilization to activate MYC expression in these tumors.	Illumina HiSeq 2500 Illumina NovaSeq 6000 NextSeq 550	8
EGAD00001011821	Study describing the dynamics of chromatin organization within malignant rhabdoid tumors. This study describes how this chromatin organization changes upon SMARCB1 rescue within patient-derived organoid models from malignant rhabdoid tumors. Identification of a novel super-enhancer of MYC and identification of patient-specific enhancer utilization to activate MYC expression in these tumors.	Illumina HiSeq 2500 Illumina NovaSeq 6000 NextSeq 2000	5
EGAD00001015157	Molecular characterization of 41 tumors from 17 individuals with CMMRD to gain a better understandig of mutational processes driving subsequent tumor development. The molecular characterization includes the investigation of tumor mutational load and mutational signatures.		1
EGAD00001015158	Molecular characterization of 41 tumors from 17 individuals with CMMRD to gain a better understandig of mutational processes driving subsequent tumor development. The molecular characterization includes the investigation of tumor mutational load and mutational signatures.		1
EGAD00001015255	T-cell lymphoblastic lymphoma (T-LBL) is a common pediatric malignancy accounting for approximately 20% of the non-Hodgkin lymphomas during childhood. Survival rates of T-LBL are ~80%, but outcome after relapse is dismal, with salvage rates reaching only ~15. Considering the extremely poor prognosis after relapse and absence of clinically relevant high-risk genetics, there is an urgent need for the identification of molecular risk factors and new prognostic biomarkers in T-LBL, as well as identification of new therapeutic strategies. In this study we present a novel entity of high-risk pediatric T-LBL patients characterized by previously unknown NOTCH1 gene fusions and highly elevated blood TARC levels		1
EGAD00001015357	Due to the lower incidence of T-LBL and difficulties in obtaining diagnostic T-LBL material, extensive research on T-LBL has been hampered whereas genetic aberrations in T-ALL are thoroughly characterized. Given the similarities and differences between T-LBL and T-ALL, the question has been raised whether T-LBL and T-ALL represent two different diseases or different manifestations of the same disease. This study aims to identify the genomic and transcriptomic landscape of T-LBL and compare the findings to what is found T-ALL. Comparison of the molecular aberrations between T-LBL and T-ALL can provide insights into the overlap and differences in malignant development between the two entities, which could lead to improved risk stratification in T-LBL in order to eventually adapt T-LBL treatment protocols based on molecular-genetic prognostic factors.		1
EGAD00001015391	Patient-matched normal kidney organoid (103H) and MRT tumoroid (103T2) models were treated for 24h with either DMSO (ctrl), 400nM MTX, or 50nM BAY to investigate the direct effects of drug treatment on the expression of key metabolic enzymes in the nucleotide biosynthesis pathways.	Illumina NovaSeq X	1
EGAD00001015401	Pediatric acute lymphoblastic leukemia (ALL) is marked by low mutational load at initial diagnosis, which increases at relapse. The elevated mutational load at relapse can partly be explained by at least two therapy-related effects and a combination of therapy and underlying mismatch repair deficiency. However, our understanding of the type and timing of mutational mechanisms in relapsed ALL is limited, and it is unclear to what extent mutational processes contribute to disease progression. We collected a cohort of 29 Dutch ALL patients across multiple treatment protocols who had multiple relapses. Using whole genome sequencing of the sequential tumor samples of each patient we were able to distinguish the mutational processes active in relapsed ALL and could track the activity of mutational processes over time. This allowed us to investigate whether subtype-specific mutational processes at diagnosis can continue in relapse or emerge at relapse if absent in initial diagnosis. Furthermore, we assessed whether the activity of mutational processes contributed to disease development and relapse.	Illumina NovaSeq 6000	135
EGAD00001015417	Creation of living organoid biobank for ewing and ewing-like sarcomas		1
EGAD00001015418	Creation of living organoid biobank for ewing and ewing-like sarcomas	Illumina NovaSeq 6000	11
EGAD00001015419	Creation of living organoid biobank for ewing and ewing-like sarcomas		1
EGAD00010002400	We demonstrate that ATRT tumoroids retain subgroup-specific epigenetic and gene expression profiles	Illumina Infinium EPIC	8
EGAD00010002599	In this study nanopore sequencing was applied to obtain sparse DNA methylation profiles from pediatric CNS tumor samples. A neural network was used to classify the tumor based on the obtained methylation profile.	Illumina Infinium EPIC	94
EGAD50000000304	Organoid cultures were exposed to different E.Coli strains and a dye control. In total 25 organoid cultures were whole-genome sequenced using the Novaseq6000 platforms. The data is deposited as .bam format.	Illumina NovaSeq 6000	25
EGAD50000000447	Sanger sequencing data of cell lines derived from bulk MV4-11 cells, targeting the R248 locus of TP53, consisting of either wildtype or homozygous mutant lines.	AB 3730xL Genetic Analyzer	4
EGAD50000000533	10x Genomics immune profiling including sequenced libraries of: 5'-end mRNA transcriptomics Beta and alpha chain VDJ transcripts Cell surface expression by 204 DNA barcoded antibodies	Illumina NovaSeq 6000	143
EGAD50000000626	Here, we applied single-cell RNA-sequencing (scRNA-seq) on isolated HRS cells and the immune cells from the same pediatric classical Hodgkin Lymphoma (cHL) tumors. Specifically, 13 cHL patients and 3 reactive lymph node control samples were included in this cohort. This allowed us to identify genes of cell surface proteins that are consistently overexpressed in HRS cells and can potentially be used as targets for antibody-drug conjugates or CAR T cells. Finally, we identify potential interactions by which HRS cells inhibit T cells, among which the Galectin-1/CD69 and HLA-DRA/LAG3 interactions. However, high levels of inter-patient heterogeneity of the interaction strength were observed. In conclusion, this study identifies new potential therapeutic targets for cHL and highlights the importance of studying heterogeneity when identifying therapy targets.	NextSeq 2000 NextSeq 500	15
EGAD50000000794	10X Genomics single-cell transcriptomics of hepatoblastoma tissues using Chromium Next GEM Single-Cell 3’ Reagent Kits v3.1. Single-cell transcriptomics data (bam files) of PT9, post-chemotherapy tumor sample, and PT13, treatment naive tumor sample. Single-cell solutions were obtained from viably frozen tissue samples using enzymatic digestion.	Illumina NovaSeq 6000	2
EGAD50000000795	10X Genomics single-cell multiome profiling of hepatoblastoma tumor organoids using Chromium Next GEM Single-Cell Multiome ATAC + Gene Expression Kit. Single-cell transcriptomics data (bam file) of multiplexed sample of hepatoblastoma tumor organoids: 3E, 8F1, 10F2, 13F2, 13E, 17E and 96F1. Single-cell solutions were obtained from fresh organoid samples using enzymatic digestion.	Illumina NovaSeq 6000	7
EGAD50000000796	10X Genomics single-cell transcriptomic profiling of hepatoblastoma tumor organoids using Chromium Next GEM Single-Cell 3’ Reagent Kits v3.1 or 3’ CellPlex Multiplexing Kit. Single-cell transcriptomics data (bam files) of hepatoblastoma tumor organoids: 3E, 8F1, 10F2, 13F2, 13F2 late, 13E, 17E, 17F1, 22E, 27F1, 28F1, 31E, 96F1, 121E and 135. Single-cell solutions were obtained from fresh organoid samples using enzymatic digestion.	Illumina NovaSeq 6000	15
EGAD50000000797	10X Genomics Visium Spatial transcriptomics analysis of hepatoblastoma and adjacent normal liver. Spatial data of normal liver and PT2 (fastq files), and and PT13, PT14 and PT16 (bam files) using the Visium Spatial Gene Expression Solution. All samples, except PT13, were collected post-chemotherapy.	Illumina NovaSeq 6000	5