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

Dac ID Contact Person Email Access Information
EGAC00001000649 Janne Ravantti dac-tumorgenomics [at] helsinki [dot] fi No additional information is available

This DAC controls 6 datasets:

Dataset ID Description Technology Samples
EGAD00001003297 NA 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