Dataset features

Specifications


Application: BS-seq analysis
Number of samples: 15
Release date: Jun 28 2018
Last update date: Nov 28 2018
Access: Public
Diseases: Breast Neoplasms, Neoplasms
Dataset link DREAM of MDA-MB-231 cells with TET1 knockout

Experimental Protocol


Digital restriction enzyme analysis of methylation (DREAM) was performed to determine the methylation profile of MDA_MB_231 cells with TET1 knockout (single clones), including empty vector control pooled cells and empty vector single clones. Briefly, genomic DNA was sequentially digested by SmaI and XmaI, which both recognize the sequence CCCGGG. SmaI is methylation sensitive, where XmaI is methylation insensitive. Distinct signatures, 5’-GGG at unmethylated sites or 5’-CCGGG at methylated sites were created by enzyme digestion and ultimately high througput sequencing was used to map these sites to the genome. Methylation ratios for each individual CCCGGG site were calculated as a proportion of methylated counts to the sum of unmethylated and methylated counts, and subsequently adjusted for differences in restriction enzyme efficiency using values obtained from spiked in standards.

Repositories


GEO

GSE100640

ENA

SRP110720

BioProject

PRJNA392337

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Contact


Jaroslav Jelinek