Antigen

Antigen Class

RNA polymerase

Antigen

RNA polymerase II

Cell type

Cell type Class

Embryonic fibroblast

Cell type

NIH/3T3

Primary Tissue

Embryo

Tissue Diagnosis

Normal

Sample

source_name

NIH3T3 fibroblasts

culture condition

continuous culture

chemicals

DMSO

chip antibody

Pol II (Santa Cruz Biotechnology, N20, sc-899)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

ChIP-seq: Cells were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody. ChIP-seq: Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase 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 cycles and library fragments of ~250 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 HiSeq 2000 or 2500 following the manufacturer's protocols.

Sequencing Platform

instrument_model

Illumina HiSeq 2000

mm10

Number of total reads

57391256

Reads aligned (%)

96.3

Duplicates removed (%)

40.7

Number of peaks

21573 (qval < 1E-05)

mm9

Number of total reads

57391256

Reads aligned (%)

96.2

Duplicates removed (%)

40.7

Number of peaks

21635 (qval < 1E-05)