Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Embryonic fibroblast
Cell type
NIH/3T3
Primary Tissue
Embryo
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
NIH/3T3 Tet-On® 3G cells
cell line
NIH/3T3 fibroblast cell line
treatment
aphidicolin
chip antibody
NA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with formaldehyde treatment and chromatin fragmented to 200 to 300 bp by sonication. Chromatin from 2 × 107 cells was used for each ChIP experiment, which yielded approximately 200 ng of DNA. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. The ChIP DNA ends were repaired using PNK and Klenow enzyme, followed by treatment with Taq polymerase to generate a protruding 3′ A base used for adaptor ligation. Following ligation of a pair of Solexa adaptors to the repaired ends, the ChIP DNA was amplified using the adaptor primers for 17 cycles and the fragments around 220 bp (mononucleosome + adaptors) isolated from agarose gel. Libraries were sequenced on the Hi-seq following the manufacturer's protocols. As described in Barski et al., 2007 (A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
30423916
Reads aligned (%)
87.8
Duplicates removed (%)
15.0
Number of peaks
438 (qval < 1E-05)

mm9

Number of total reads
30423916
Reads aligned (%)
87.5
Duplicates removed (%)
14.9
Number of peaks
505 (qval < 1E-05)

Base call quality data from DBCLS SRA