Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pluripotent stem cell
Cell type
ES cells
NA
NA

Attributes by original data submitter

Sample

source_name
mouse ES cells_input
cell line background
RASlox/lox
genotype/variation
ERF WT+KO mix; (H-Ras-/-;N-Ras-/-;K-Raslox/lox;RERTert/ert)
treated with
none
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 and ERF-DNA complexes were isolated with antibody. Fragmented immunoprecipitated DNA samples, in the range <0.1 to 5ng, were processed with "NEBNext Ultra II DNA Library Prep Kit for Illumina" from New England BioLabs (catalog # E7645). Briefly, samples went through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters. Adapter-ligated libraries were completed by limited-cycle PCR and extracted with a [single] double-sided SPRI size selection. Median fragment sizes were 600 and 480 bp for samples "rep1" and "rep2", respectively, from which 120 bp correspond to adaptor sequences. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina HiSeq2500 instrument by following manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
60081104
Reads aligned (%)
98.0
Duplicates removed (%)
10.1
Number of peaks
568 (qval < 1E-05)

mm9

Number of total reads
60081104
Reads aligned (%)
97.8
Duplicates removed (%)
10.1
Number of peaks
693 (qval < 1E-05)

Base call quality data from DBCLS SRA