Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Adipocyte
Cell type
Brown preadipocytes
NA
NA

Attributes by original data submitter

Sample

source_name
Brown preadipocyte cell
genotype/variation
LSL-K4M;CreER
treatment
Mock
cell type
BAT isolated brown preadipocytes
stage of adipogenesis
Immature adipocytes (D4)
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-Seq: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. ChIP-Seq: Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA sample prep kit (Cat no. FC-121-2001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15-18 cycles and library fragments of 200-400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. RNA-Seq: Total RNA was harvested using Trizol reagent. mRNA wasfurther purified using Invitrogen Dynabeads® mRNA DIRECT™ Kit (Cat. 610-11). RNA-Seq: RNA libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
27170479
Reads aligned (%)
98.5
Duplicates removed (%)
14.4
Number of peaks
532 (qval < 1E-05)

mm9

Number of total reads
27170479
Reads aligned (%)
98.2
Duplicates removed (%)
14.4
Number of peaks
576 (qval < 1E-05)

Base call quality data from DBCLS SRA