Illumina HiSeq 2000 sequencing; Pancreatic islet epigenomics reveals enhancer clusters that are enriched in Type 2 diabetes risk variants
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
No description
Antigen
NA
Cell type
Cell type Class
Pancreas
Cell type
Pancreatic islets
NA
NA
Attributes by original data submitter
Sample
ENA first public
2014-01-01
ENA last update
2018-03-08
ENA-CHECKLIST
ERC000011
External Id
SAMEA2201384
INSDC center alias
Institut d'Investigacions Biomediques August Pi i Sunyer
INSDC center name
Institut d'Investigacions Biomediques August Pi i Sunyer
INSDC first public
2014-01-01T17:02:15Z
INSDC last update
2018-03-08T16:46:33Z
INSDC status
public
Submitter Id
E-MTAB-1919:Human islets (HI 32)
broker name
ArrayExpress
common name
human
developmental stage
adult
organism part
islet of Langerhans
sample name
E-MTAB-1919:Human islets (HI 32)
Sequenced DNA Library
library_name
HI 32 FOXA2 ChIP-Seq
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Human islets were fixed and sonicated as described previously (Nammo et al, 2012). Briefly, frozen crosslinked cell pellets of 4,000 islets were thawed on ice in 1 mL lysis buffer and disrupted with five 1-min cycles with 0.5 mm glass beads (BioSpec). Samples were sonicated for 10-20 cycles of 30 pulses each (1s on and 0.5 s off) using a Brandson Sonifier 450D at 15 % amplitude. The size for the bulk of chromatin obtained with this procedure was checked to be in the range from 200-1000 bp. For ChIPs, 300-400 human islet equivalents (IEQs) were pre-cleared with A/G sepharose beads (Ge Healthcare) for 1 h, rotating at 4 degrees C, and then incubated with each antibody. Afterwards, samples were rotated for 2 hr at 4 degrees C with protein A/G sepharose beads and then sequentially washed with low salt, high salt, LiCl and TE buffers. Next, chromatin was eluted with SDS 1% buffer and sequentially treated with RNAse (greater than 5 hr at 65 degrees C) and Proteinase K (overnight at 45 degrees C). Finally, DNA was extracted with phenol-chloroform followed by ethanol precipitation. The immunoprecipitated DNA was modified for sequencing following the Illumina sequencing following the manufacturer protocol (Preparing Sample for ChIP Sequencing of DNA (11257047 Rev A)).