Illumina HiSeq 2000 paired end sequencing; DNA methylation is required for the control of stem cell differentiation in the small intestine
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
Bisulfite-Seq
Antigen
Bisulfite-Seq
Cell type
Cell type Class
Digestive tract
Cell type
Intestinal epithelium
NA
NA
Attributes by original data submitter
Sample
ENA first public
2014-03-13
ENA last update
2018-03-08
ENA-CHECKLIST
ERC000011
External Id
SAMEA2397530
INSDC center alias
University of Pennsylvania, School of Medicine, Dept. of Genetics
INSDC center name
University of Pennsylvania, School of Medicine, Dept. of Genetics
INSDC first public
2014-03-13T17:00:40Z
INSDC last update
2018-03-08T17:15:54Z
INSDC status
public
Submitter Id
E-MTAB-2350:B61 Dif
age
3 month
broker name
ArrayExpress
cell type
differentiated intestinal epithelium
common name
house mouse
developmental stage
adult
organism part
small intestine
sample name
E-MTAB-2350:B61 Dif
specimen with known storage state
fresh specimen
strain
C57Bl/6 background Lgr5-EGFP-ires-CreERT2
Sequenced DNA Library
library_name
BIS-Seq Library B61 Dif
library_strategy
Bisulfite-Seq
library_source
GENOMIC
library_selection
RANDOM
library_construction_protocol
All procedures involving mice were conducted in accordance with approved Institutional Animal Care and Use Committee protocols. WGSBS was performed as previously published (Lister, Nature 462: 315-322) with the following changes. Isolated genomic DNA was fragmented into 300bp pieces using the S220 Focused - ultrasonicator (Covaris). Sequencing libraries were generated with 500ng genomic DNA using the NEBNext genomic sequencing kit (NEB) and Illumina adaptors (PE-102-1001. PE-102- 1002). Libraries were bisulfite converted using Imprint DNA Modification Kit (Sigma). Size selection of the libraries to 300-600bp was performed on the Pippin Prep DNA size selection system (Sage Science). Amplification of libraries was performed in 18 rounds of PCR using Pfu Turbo Cx Hotstart DNA Polymerase (Agilent Technologies).