Data access committee for the pseudomyxoma peritonei exome sequencing vcf-files

Janne Ravantti
dac-tumorgenomics@helsinki.fi

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Dataset ID	Description	Technology	Samples
EGAD00001003297	None		9
EGAD00001003802	106 FFPE tumor samples from small bowel were sequenced with Illumina HiSeq 4000. Exome capture was performed with NimbleGen SeqCap EZ Exome Library v3 Kit. Reads were aligned with BWA–MEM v.0.7.12 to GRCh37 reference genome. Variant calls were produced with GATK HaplotypeCaller. Variant calls were filtered against all data from gnomAD database using allele frequency threshold 0.0001 in order to remove germline variation.		106
EGAD00001004098	siRNA knockdown of 43 Allelic Imbalance target TFs followed by mRNA-seq done in triplicates in three (GP5D, LoVo, COLO320DM) different cell colorectal adenocarcinoma cell lines.	Illumina HiSeq 2000 Illumina HiSeq 4000	426
EGAD00001004099	Chip-exo and Chip-nexus for FOXA1, HNF4A, KLF5, MYC, and TCF7L2 in colorectal cancer cell lines LoVo, GP5D, COLO320DM	Illumina HiSeq 4000	23
EGAD00001004100	Whole genome sequencing of commercial LoVo, GP5D, COLO320DM, CaCo-2 and RPE1 cell lines and three RPE1-TP53 knock-out cell lines separated by 6 months of culture from their most recent common ancestor.	HiSeq X Ten Illumina HiSeq 2500	8
EGAD00010001566	Allelic imbalance data for cell lines derived from RPE1 with TP53 knockout	humanomniexpress-24-v1-1-a	2