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
Mouse ES cells
cell line name
J1
background strain
129S4/SvJae
cell type
Mouse ES cells

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For each sample 9x106 cells were harvested by trypsinisation and rinsed well in 1xPBS before being resuspended in 1.5ml of PBS. Each sample was fixed with the addition of 40.5 µl of 37% formaldehyde (Sigma) and incubated for 10minutes at room temperature on rotation. 225 µl of 1M glycine was added to quench the formaldehyde and rotated at room temperature for 5minutes. Samples were then centrifuged at 2000rpm for 4 minutes at 4 oC, supernatant discarded and pellets resuspended in 2ml LB1 (50mM Hepes KOH pH7.9, 140mM NaCl,1mM EDTA, 10% glycerol, 0.5% IPEGAL, 0.25% triton X100, 1xComplete EDTA-free protease inhibitor tablet (Roche)) solution and rotated at 4 oC for 4 minutes. This process was repeated resuspending in 2 ml LB2 (10mM TrisHcl pH8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 1xComplete EDTA-free protease inhibitor tablet (Roche)) solution and then repeated resuspending in 200 µl LB3 (10mM TrisHCl Ph8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na Deoxycholate, 0.5% LaurylSulphate, 1xComplete EDTA-free protease inhibitor tablet (Roche)). Chromatin was then sheared at 4 oC using a Diagenode bioruptor set on high for 45 cycles at 30seconds on/30seconds off. 20 µl of 10% triton X in LB3 was then added to each sample and mixed by inversion. Samples were then centrifuged at 13000rpm at 4 oC for 10 minutes to remove nuclear debris and supernatant transferred to a fresh tube. In order to check the efficiency of the sonication process, 8 µl of sheared chromatin was taken, mixed with 1 µl 5M NaCl and 16 µl dH2O, incubated at 98 oC for 15minutes and treated with RNase cocktail before being purified with Qiagen PCR Clean up kit as per manufacturer's instructions . Sheared chromatin was then resolved on 1.5% agarose gel post-stained with EtBr. The DNA smear should be between 100-500bp with peak at 250-300bp. For immunoprecipitation 25 µl of Protein G Dynabeads (Novex Lifetech) was washed 3 times in block solution and then resuspended in 500 µl of block solution. Beads were then incubated with 5 µl of antibody (H3K27me3(Millipore 07449), IgG (Santa Cruz Biotech sc-2027)) and incubated at 4 oC for 4 hours on a rotator. Beads were then washed 3 times in 500 µl block solution and supernatant removed For ChIP, crosslinked chromatin was prepared using standard conditions or the SimpleChIP® Plus Enzymatic Chromatin IP Kit. For ChIP libraries, the NEBNext ChIPSeq library kit or the SimpleChIP® Plus Enzymatic Chromatin IP Kit was used as per instructions. 75bp PE sequencing

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
85574817
Reads aligned (%)
98.2
Duplicates removed (%)
24.8
Number of peaks
55224 (qval < 1E-05)

mm9

Number of total reads
85574817
Reads aligned (%)
98.0
Duplicates removed (%)
24.8
Number of peaks
55140 (qval < 1E-05)

Base call quality data from DBCLS SRA