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
ESCs
strain
129/1
cell line
129/1 XY ES cell line
genotype
wild-type
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP for FS2-tagged AEBP2 was performed as described (Farcas et al., 2012) except that we used rProtein A Sepharose beads (GE Healthcare) that had been blocked for 1 hr at 4 °C with 1 mg/ml Bovine Serum Albumin (BSA) and 1 mg/ml yeast tRNA (Sigma). ChIP for endogenous proteins was performed as described (Stock et al., 2007), except approximate concentration after sonication was measured by measuring absorbance using the Nanodrop ND-1000 (ThermoScientific) and 200 μg of chromatin was used per IP and after the washes DNA was purified using ChIP DNA Clean & concentration™ columns (Zymo 13 Research) and eluted in 10 μl volume. NEB Next® DNA Library Prep Master Mix Set for Illumina

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
56330677
Reads aligned (%)
96.7
Duplicates removed (%)
10.2
Number of peaks
1261 (qval < 1E-05)

mm9

Number of total reads
56330677
Reads aligned (%)
96.6
Duplicates removed (%)
10.8
Number of peaks
1259 (qval < 1E-05)

Base call quality data from DBCLS SRA