Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

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

Attributes by original data submitter

Sample

source_name
mESCs
cell type
embryonic stem cells
strain
129/Ola
chip antibody
Novocastra #CM5P
growth
2i

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ESCs were fixed using 1% formaldehyde (Millipore #344198) for 10 min at room temperature then quenched by adding 1.25M glycine to a final concentration of 0.125M. Cell pellets were snap frozen and stored in -80℃. Every 10 million cells were lysed by 300μL 1% SDS include freshly made Protease Inhibitor (PI) cocktail (Roche #4693132001), sonicated with Diagenode Bioruptor Pico and diluted with 2.7mL PBA (1x PBS + 0.5% BSA) with fresh added PI cocktail. Dynabeads protein A+G (Invitrogen #10008D, 10009D) were washed and pre-blocked with cold PBA for 30 minutes. Diluted chromatin containing 30μg DNA was incubated with 15μg P53 antibody (Novocastra #CM5P) and 60μL pre-blocked beads and rotated at 4℃ overnight. After incubation, beads were washed subsequently with High-NaCl, Low-NaCl, LiCl, TE and TE washing buffers for 10 minutes and transferred to new eppendorf tube. Beads were eluted with 200µL elution buffer (1%SDS, 0.2M NaCl, 0.1μg/μL Proteinase K) at 65°C thermo shaker 1000rpm for 20 minutes. Supernatants were purified with MinElute PCR Purification Kit (QIAGEN #28006). 1-5ng of DNA was used for library construction with KAPA Hyper Prep Kit (KAPA #KK8504).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
29245723
Reads aligned (%)
97.6
Duplicates removed (%)
12.2
Number of peaks
1765 (qval < 1E-05)

mm9

Number of total reads
29245723
Reads aligned (%)
97.5
Duplicates removed (%)
13.3
Number of peaks
1755 (qval < 1E-05)

Base call quality data from DBCLS SRA