Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

Cell type Class
Adipocyte
Cell type
Visceral adipose tissue
NA
NA

Attributes by original data submitter

Sample

source_name
visceral adipose tissue
strain
C57BL/6
tissue
visceral (epididymal) white adipose tissue (VWAT)
age
14 weeks old
diet
High fat diet (D12492)
time
8 weeks
replicate
1
chip antibody
H3K4me1 (Abcam, ab8895)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The chromatin samples collected from different mice at the same time point were pooled, frozen in liquid nitrogen and stored at -80˚C. Chromatin was subjected to immunoprecipitation with an anti-POLR2B (Santa Cruz Biotechnology, H-201) antibody as described (Le Martelot et al. 2012). Immuno-precipitated complexes were collected by adsorption to ten µl of protein-A-Sepharose beads that had been pre-blocked with 10 µg/ml of salmon sperm DNA and BSA at 4˚C overnight. The beads were washed with dialysis buffer and ChIP wash buffer, as described. The immuno-precipitated complexes were eluted with 50 mM NaHCO3, 1% SDS, 1mM EDTA and 50 mM of Tris pH8 at 65°C, adjusted to 125 mM NaCl, and incubated at 65°C overnight to reverse the cross-links. After successive treatments with 10 µg/ml of RNase A and 20 µg/ml of proteinase-K, the samples were extracted with a NucleoSpin® Kit (Machery Nagel). The DNA concentration was determined by fluorometry on the Qubit system (Invitrogen). 5-10 ng of DNA was used for the preparation of the library. Libraries for ultra-high throughput sequencing were prepared using Diagenode kit (C05010013) according to the manufacturer's instruction and subjected PE sequencing in a HiSeq 2500. Libraries for ultra-high throughput sequencing were prepared with the using Diagenode kit (C05010013) according to the manufacturer's instruction.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
54596122
Reads aligned (%)
94.6
Duplicates removed (%)
8.3
Number of peaks
16959 (qval < 1E-05)

mm9

Number of total reads
54596122
Reads aligned (%)
94.5
Duplicates removed (%)
8.3
Number of peaks
17168 (qval < 1E-05)

Base call quality data from DBCLS SRA