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_ChIP-seq Cbx7 Input
strain background
CAST/Ei x 129/Sv/Jae
Sex
female
cell type
undifferentiated embryonic stem cells
genotype/variation
stable expression of HA-tagged Cbx7, clone 12D
molecule subtype
Genomic DNA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1.1% formaldeyde for 20 min, then nuclei were isolated and lysed. Chromatin was sheared by sonication to a size of 100-500bp. Cleared lysates were incubated overnight with anti-HA tag antibody, with 10% saved as input, then captured with Dynabeads Protein G. After stringent washes, ChIP DNA was eluted from beads, and together with input chromatin was reverse-crosslinked on 650C and treated with proteinase K. DNA was purified by phenol/chloroform extraction and ethanol precipitation. ChIP-seq libraries were constructed using the NEBNext ChIP-Seq Library Prep Master Mix Set (NEB). Multiplexed library, Ilumina barcode#11, GGCTAC.Paired-end 50bp reads

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
42010835
Reads aligned (%)
97.8
Duplicates removed (%)
15.0
Number of peaks
263 (qval < 1E-05)

mm9

Number of total reads
42010835
Reads aligned (%)
97.7
Duplicates removed (%)
15.6
Number of peaks
293 (qval < 1E-05)

Base call quality data from DBCLS SRA