GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1059025 Query DataSets for GSM1059025
Status Public on Dec 01, 2013
Title Jmjd2c_KD_Ctr9
Sample type SRA
Source name Jmjd2c KD mESCs
Organism Mus musculus
Characteristics strain: 129S4/Svjae
phenotype: agouti
gender: male
cell type: ESC
genotype/variation: Jmjd2c shRNA KD
chip antibody: Ctr9 (A301-395A), Bethyl Laboratories
Treatment protocol mESCs were crosslinked with 1% formaldehyde, reaction was quenched by 0.125M glycine, trypsinized, sonicated in SDS Chip buffer, followed by incubation with 5µg of antibodies overnight. Protein A or G beads were added to ChIP reactions to immunoprecipitate chromatin. Beads were washed several times, de-crosslinked at 65ºC overnight, followed by RNase and Proteinase K treatment to collect ChIP-ed DNA, which was ready for library preparation. For bioChIP reactions, streptavidin beads (Dynabeads MyOne Streptavidin T1- Invitrogen) were used for the precipitation of chromatin, and 2% SDS was applied for first washing step. All other steps were same as conventional ChIP protocol.
Growth protocol mESCs were grown in standard mouse ES cells media with LIF
Extracted molecule genomic DNA
Extraction protocol [Illumina] Purified ChIP DNA was measured in Qubit (Invitrogen). 2-10ng of purified ChIP DNA was used to prepare sequencing libraries, using NEB next generation ChIP sequencing Kit and Illumina ChIP seq kit according to the manufacturer's instructions.
[Helicos] ChIP DNA was processed for 3' polyA tailing, followed by 3'ddATP-blocking. Processing samples by ligation, amplification and size selection are not required by Helicos sequencing.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description Jmjd2c shRNA KD in mESCs
Data processing Basecalls performed using Solexa pipeline for data generated by HiSeq 2000 or Helicos pipeline for data generated by Helicos Heliscope.
Sequencing reads were aligned to mouse genome assembly mm9 using Illumina software pipeline (data generated by HiSeq 2000) or Helisphere (data generated by Helicos).
Only ChIP-seq reads that aligned to exactly one location in the reference mouse genome (mm9) were retained for downstream data analysis.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (
The wig files were generated by a moving window of size 200bp. The tag count in the window was further normalized in unit RPKM (# read per kb per million total reads) for ChIP-seq data generated by HiSeq 2000.
Genome_build: mm9
Supplementary_files_format_and_content: Mapped read bed file (reporting the coordinates of aligned reads) which were converted from BAM files by using BAMtools; wig file which contain the read densities normalized by sequencing depth; and peak bed file which were outputed by MACs (reporting the coordinates of peaks called by MACS).
Submission date Jan 02, 2013
Last update date May 15, 2019
Contact name Zhen Shao
Organization name Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences
Lab Zhen Shao
Street address 320 Yueyang Road
City Shanghai
ZIP/Postal code 230031
Country China
Platform ID GPL13112
Series (2)
GSE43229 Combinatorial role of Jmjd2b and Jmjd2c in mESCs identity
GSE43231 Combinatorial role of Jmjd2b and Jmjd2c in mESC identity
SRA SRX213822
BioSample SAMN01881897

Supplementary file Size Download File type/resource
GSM1059025_Ctr9_2cKD.bed.gz 209.7 Mb (ftp)(http) BED
GSM1059025_Ctr9_2cKD_binsize_200_stepsize_50_fixedstep_rpkm.wig.gz 16.3 Mb (ftp)(http) WIG
GSM1059025_Ctr9_2cKD_pd4_peaks.bed.gz 620.8 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap