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VIB Institutional DAC

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Rene Custers
dac@vib.be

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This DAC controls 15 datasets

Dataset ID	Description	Technology	Samples
EGAD00001000150	Targeted re-sequencing of 97 genes in T-ALL	454 GS FLX Titanium	33
EGAD00001000291	Exome sequencing identifies mutation of the ribosome in T-cell acute lymphoblastic leukemia	Illumina HiSeq 2000	128
EGAD00001000849	None	Illumina HiSeq 2000	50
EGAD00001003951	Whole genome sequencing of 4 childhood T-ALL patients, which was further used in single-cell analysis in the paper "Single cell sequencing reveals the origin and the order of mutation acquisition in T-cell acute lymphoblastic leukemia".	Illumina HiSeq 2500	4
EGAD00001006167	This dataset contains the raw fastq-files and the VCF files of single cell targeted DNA sequening with the MissionBio Tapestri platform. This was performed on 8 male pediatric T-ALL cases: X09-XB37-XB47-XD83-XF91-XF97-XF100-XF121. For some patients we have timepoints during treatment: XF100 and XG121. XD83 is a patient that relapsed twice.	Illumina NovaSeq 6000	48
EGAD00001006955	This dataset contains single cell DNA amplicon sequencing of 12 B-ALL patients. For all patients a diagnosis sample was processed, while 4 patients were also followed up during treatment, summing up to a total of 23 samples. Mutations were called in the predefined set of amplicons.	Illumina NovaSeq 6000	23
EGAD00001009686	This dataset contains both snRNA-seq and bulk RNA-seq data from 19 different patients, comprising of 9 healthy controls (4 Spinal Cord, 5 Motor Cortex) as well as 5 C9ALS patients and 5 sporadic ALS patients, each with paired data from the spinal cord and motor cortex. For the snRNA-seq data, fastq files containing the raw reads are provided, many of these samples were pooled for sequencing and subsequently require demultiplexing using SNPs using a tool such as freemuxlet. The paired bulk RNA-seq data (raw fastq files) can be used to acquire the ground truth per patient - a list of pooled samples can be found in map.txt. snRNA-seq data was produced using the 10X Genomics 3' v3 kit and bulk RNA-seq was produced using the Illumina TruSeq v2 kit.	Illumina NovaSeq 6000	64
EGAD50000000328	Single-cell, single-nucleus and CITE-sequencing of neuroblastoma tumors with 10X Genomics	Illumina NovaSeq 6000	22
EGAD50000000378	FFPE tissue and liquid biopsy (blood, pleural and peritoneal effusions) samples, processed with the cfRRBS (cell-free reduced representation bisulfite sequencing) protocol.	unspecified	181
EGAD50000000389	This dataset contains 228 paired fastq files sequenced with Illumina Novaseq 6000, and the file with the sample and clinical data.	Illumina NovaSeq 6000	114
EGAD50000000553	cfRRBS data produced from the cfDNA in plasma isolated from healthy, adult donors.	Illumina NovaSeq 6000	44
EGAD50000000554	In this study, we explore the potential of classifying pediatric brain tumors based on methylation profiling of the cell-free DNA in cerebrospinal fluid (CSF). For this proof-of-concept study, we collected 20 cerebrospinal fluid samples of pediatric brain cancer patients via a ventricular drain placed for reasons of increased intracranial pressure. For 11 patients in this study we collected matched tumor DNA. This cohort contains fastQ files of cfRRBS data of these samples.	Illumina NovaSeq 6000	43
EGAD50000000734	cell-free Reduced Representation Bisulfite Sequencing (cfRRBS) data from blood plasma and FFPE tissue samples from patients with esophageal adenocarcinoma, and blood plasma of healthy donors.	Illumina NovaSeq 6000	224
EGAD50000001129	We report single-nuclei RNA sequencing data (n=18) from human livers in metabolic dysfunction-associated steatotic liver disease (MASLD) patients. there are 5 MASH, 4 MASL, 5 control obese and 4 control lean samples.	Illumina NovaSeq 6000	18
EGAD50000001703	This dataset consists of 12 RNA samples derived from peripheral blood mononuclear cells (PBMCs) collected from three healthy donors. The samples cover four experimental conditions: fresh PBMCs (ID: 517210–517212), PBMCs subjected to a single freeze–thaw cycle (ID: 517213–517215), PBMCs refrozen in freezing mix (ID: 517216–517218), and PBMCs refrozen in TRIzol (ID: 517219–517221). Each sample is provided as a FASTQ file, and RNA sequencing was performed using the Illumina platform. This dataset enables the assessment of cryopreservation effects on PBMC transcriptomic profiles.	Illumina NovaSeq 6000	12