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
Mouse embryonic fibroblasts
cell type
ATR+/- MEFs
cell line
Passage-immortalized MEFs
treatment
1 uM ATR-45 inhibitor for 18hrs in TIM KD MEFs
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei (sheared to obtain chromatin size <4 kb) and RPA-DNA complexes were isolated with anti-RPA32 antibody. Libraries were prepared according to the NEBNext kit. Briefly, DNA was sonicated to ~200 bp. DNA was end-repaired using a combination of T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation, DNA fragments of ~200 bp (insert plus adaptor) were band isolated from a 2% agarose gel. The purified DNA was PCR amplified with Illumina primers for 18 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina HiSeq following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
7238044
Reads aligned (%)
98.7
Duplicates removed (%)
21.7
Number of peaks
104 (qval < 1E-05)

mm9

Number of total reads
7238044
Reads aligned (%)
98.6
Duplicates removed (%)
21.9
Number of peaks
79 (qval < 1E-05)

Base call quality data from DBCLS SRA