Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Embryonic fibroblast
Cell type
MEF
Tissue
Embryonic Fibroblast
Lineage
primaryCells
Description
Mouse Embryonic Fibroblast

Attributes by original data submitter

Sample

source_name
EtOH_Input
strain background
129/sv
cell type
embryonic fibroblast
genotype/variation
per1 -/-, per2 -/-, nr1d1 -/-, nr1d2 -/-
transgene
PER2-ER
treated with
EtOH
chip antibody
none
molecule subtype
BMAL1 ChIPed DNA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For RNA-seq, cells were lysed with Trizol (Thermo Fisher Scientiic). After phase separation, RNA was purified by PureLink RNA Mini Kit (Thermo Fisher Scientific). For ChIP-Seq, protein-DNA complex were crosslinked by formaldehyde, sonicated, immunoprecipitated and extracted after reverse-crosslinking (see details in 2016 PNAS 113, E6072) Fisher Scientific) For RNA-seq, use TruSeq stranded mRNA preparation kit (Illumina). For ChIP-seq, use ThruPLEX DNA-seq Kit (RUBICON GENOMICS).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
13736646
Reads aligned (%)
100.0
Duplicates removed (%)
2.8
Number of peaks
128 (qval < 1E-05)

mm9

Number of total reads
13736646
Reads aligned (%)
99.9
Duplicates removed (%)
2.7
Number of peaks
120 (qval < 1E-05)

Base call quality data from DBCLS SRA