Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Adipocyte
Cell type
Brown adipocytes
NA
NA

Attributes by original data submitter

Sample

source_name
Wildtype BAT
strain
Prdm16(fl/fl) C57Bl6
tissue
Brown adipose tissue

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Interscapular BAT was isolated and processed for each sacrificed mouse. The tissues were immediately minced, crosslinked in 1 % formaldehyde/PBS. MED1 ChIPs were performed using EGS as an additional crosslinker. For each fat pad, material from 3-4 mice was used for sequencing. To prepare ChIP extracts, crosslinked tissue was suspended in a ChIP buffer containing 20mM Tris, 0.1% SDS, 1% Triton-100, 150 mM NaCl, 1 mM EDTA, protease inhibitors. Samples were incubated at 4 C for 10 min, and subjected to microtip probe sonication under conditions optimized for IP efficiency. Extracts were cleared of insoluble lipid by microfuge centrifugation at full speed followed by extract transfer to a new tube. The process was repeated until minimal lipid accumulated at the top of the extract after centrifugation. ChIP-Seq libraries were produced and sequenced according to Illumina protocols. Libraries were multiplexed for sequencing.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

mm10

Number of total reads
46569363
Reads aligned (%)
87.7
Duplicates removed (%)
39.8
Number of peaks
520 (qval < 1E-05)

mm9

Number of total reads
46569363
Reads aligned (%)
87.6
Duplicates removed (%)
39.9
Number of peaks
590 (qval < 1E-05)

Base call quality data from DBCLS SRA