Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
No description
Cell type
NA
NA
NA

Attributes by original data submitter

Sample

ClinicalInformation: Premortem diagnosis of diabetes
No
ClinicalInformation: Premortem non-fasting glycemia
5.1 millimolar
ENA first public
2012-10-03
ENA last update
2018-03-08
External Id
SAMEA1531969
INSDC center alias
Hospital Clinic de Barcelona, IDIBAPS, CIBERDEM
INSDC center name
Hospital Clinic de Barcelona, IDIBAPS, CIBERDEM
INSDC first public
2012-10-03T17:04:06Z
INSDC last update
2018-03-08T15:57:33Z
INSDC status
public
Submitter Id
E-MTAB-1294:HI 32
age
38 year
bmi
22.9kg_per_m2
broker name
ArrayExpress
clinical history
cause of death: trauma
common name
human
sample name
E-MTAB-1294:HI 32
sex
male

Sequenced DNA Library

library_name
Human Islet 32, H3K4me3
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, around 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)).

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
28347603
Reads aligned (%)
96.4
Duplicates removed (%)
32.8
Number of peaks
35545 (qval < 1E-05)

hg19

Number of total reads
28347603
Reads aligned (%)
96.1
Duplicates removed (%)
33.4
Number of peaks
35541 (qval < 1E-05)

Base call quality data from DBCLS SRA