MOMA Data Access Committee

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This DAC controls 33 datasets

Dataset ID	Description	Technology	Samples
EGAD00001000711	None	Illumina HiSeq 2000	42
EGAD00001000712	None	Illumina HiSeq 2000	72
EGAD00001000713	None	Illumina HiSeq 2000	12
EGAD00001000829	None	Illumina HiSeq 2000	16
EGAD00001000830	None	Illumina HiSeq 2000	14
EGAD00001000831	None	Illumina HiSeq 2000	30
EGAD00001000832	None	Illumina HiSeq 2000	16
EGAD00001000833	None	Illumina HiSeq 2000	10
EGAD00001000834	None	Illumina HiSeq 2000	20
EGAD00001000835	None	Illumina HiSeq 2000	8
EGAD00001001939	Mapped whole transcriptome RNA-Seq data from 476 human samples of early stage urothelial carcinoma.	Illumina HiSeq 2000	476
EGAD00001001940	Un-mapped whole transcriptome RNA-Seq data from 476 human samples of early stage urothelial carcinoma.	Illumina HiSeq 2000	476
EGAD00001001941	Variants derived from mapped whole transcriptome RNA-Seq data from 476 human samples of early stage urothelial carcinoma.		476
EGAD00001002716	In this study we characterized genomic alterations in two to five metachronous bladder tumors from 29 patients initially diagnosed with early stage disease. Fourteen patients (32 tumors) had non progressive disease (NPD) and 15 patients (34 tumors) had progressive disease (PD). Whole exome sequencing (WES, ~50x mean read depth and whole transcriptome RNA-seq was performed (RNA was not advalible for 4 tumors) Data provided here consist of 122 Bam files for WES (83 Tumors and 39 blood)	Illumina HiSeq 2000	122
EGAD00001002717	In this study we characterized genomic alterations in two to five metachronous bladder tumors from 29 patients initially diagnosed with early stage disease. Fourteen patients (32 tumors) had non progressive disease (NPD) and 15 patients (34 tumors) had progressive disease (PD). Whole exome sequencing (WES, ~50x mean read depth and whole transcriptome RNA-seq was performed (RNA was not advalible for 4 tumors). Data provided here consist of 71 unmapped Bam files form whole transcriptome RNA-seq.	Illumina HiSeq 2000	71
EGAD00001002718	In this study we characterized genomic alterations in two to five metachronous bladder tumors from 29 patients initially diagnosed with early stage disease. Fourteen patients (32 tumors) had non progressive disease (NPD) and 15 patients (34 tumors) had progressive disease (PD). Whole exome sequencing (WES, ~50x mean read depth and whole transcriptome RNA-seq was performed (RNA was not advalible for 4 tumors). Data provided here consist of 71 mapped Bam files form whole transcriptome RNA-seq.	Illumina HiSeq 2000	71
EGAD00001002772	In this study we characterized genomic alterations in three bladder cancer patients with metastatic disease courses. Multiple regions were procured by laser microdissection or punctures from primary tumor, lymph node metastases and from distant metastases. Data provided here consist of 35 Bam files for WES (32 Tumors and 2 blood, 1 adjacent normal)	NextSeq 500	35
EGAD00001003428	RNAseq data from the study: "Widespread DNA hypomethylation and differential gene expression in Turner syndrome".	Illumina HiSeq 2000 NextSeq 500	37
EGAD00001003820	Whole transcriptome, strand-specific RNA-seq libraries were prepared from total RNA purified using RNeasy mini kit (Qiagen) using Ribo-Zero technology (Epicentre, an Illumina company) for depletion of rRNA followed by library preparation using ScriptSeq ScriptSeq RNA-Seq Library preparation Kit from Illumina. The paired raw sequence reads were processed using TopHat2 and mapped to the humane reference genome HG19.	NextSeq 500	16
EGAD00001003821	WES was performed using the KAPA-Hyper prep kit from Illumina (Roche, Basel, Switzerland) for library construction, followed by exome capture using Niblegen SeqCap EZ Human Exome Library v3.0 (Roche). Reads were mapped using BWA MEM against the humane reference genome HG19.	NextSeq 500	42
EGAD00001003823	Somatic mutations were called using whole exome Sequencing (WES) data from colorectal cancer samples (dataset EGAD00001003821) using MuTect2, with matched constitutional WES-data obtained from leukocytes samples as reference.		37
EGAD00001006636	RNA sequencing of a total of 41 tumor biopsies taken from a total of 14 patients with colorectal cancer. Ribosomal RNA was removed using the Ribo-Zero Gold rRNA Removal Kit (Illumina, CA, USA) and Paired-end sequencing were performed using ScriptSeq v2 RNA-seq Library preparation Kit (Illumina). Data processing of the paired raw sequence reads was performed using TopHat2, with mapping to the human reference genome HG19. Forty-one BAM files with reads mapping the the human reference genome (HG19) is enclosed.	NextSeq 500	41
EGAD00001008126	Bulk RNAseq of human skeletal muscle RNAseq of FACS sorted human skeletal muscle cells scRNAseq of human skeletal muscle	Illumina HiSeq 2000 Illumina HiSeq 4000 NextSeq 500	41
EGAD00001010052	Samples of blood, muscle and fat were collected from individuals with TS (n = 33) and KS (n = 22) and from male (n = 16) and female (n = 44) controls. The RNA-seq libraries were multiplexed paired-end sequenced on an Illumina Novaseq 6000 (100 bp) and subjected to initial quality control using FastQC (BAbraham Bioinformatics). In addition to trimming of low-quality ends, adaptor removal was conducted using Trim Galore with default settings (BAbraham Bioinformatics).	Illumina NovaSeq 6000	212
EGAD00001010078	RNA-sequencing profiling of leucocytes from peripheral blood samples from 9 KS patients, 9 control males and 13 female controls	Illumina NovaSeq 6000	18
EGAD00010000508	Matched control samples using SNP 6.0 Array	GenomeWideSNP_6-BirdseedV2	12
EGAD00010000510	Matched control samples using HumanOmni1-Quad	GenomeWideSNP_6-BirdseedV2	12
EGAD00010000512	Case samples using HumanOmni1-Quad	GenomeWideSNP_6-BirdseedV2	12
EGAD00010000514	Case samples using SNP 6.0 Array	GenomeWideSNP_6-BirdseedV2	12
EGAD00010001260	DNAm Case samples using Illumina Infinium 450K	Illumina 450K array	33
EGAD00010001261	DNAm Case samples using Illumina Infinium 450K	Illumina 450K array	33
EGAD00010001262	DNAm Case samples using Illumina Infinium 450K	Illumina 450K array	32
EGAD00010001888	Illumina 450K DNA methylation profiles of 314 fresh-frozen colorectal mucosa, adenoma or adenocarcinoma samples.	Illumina 450k	314