DAC
Data access committee for the pseudomyxoma peritonei exome sequencing vcf-files
| Dac ID | Contact Person | 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 |
