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Sample GSM1014546 Query DataSets for GSM1014546
Status Public on Feb 20, 2013
Title Kdm2b_Ctrl
Sample type SRA
Source name Control mouse ES cells
Organism Mus musculus
Characteristics chip antibody: Flag
antibody manufacturer: Sigma
antibody catalog number: F7425
antibody lot number: N/A
strain: inbred 129
cell line: E14
cell type: embryonbic stem cells
genotype: Control
Treatment protocol Around 1x10^5 ES cells/well in 24-well plates are infected with lentiviral vectors at 10 MOI. 48 hours after transduction, puromycin (2ug/ml) is added to the medium for selecting transduced cells.
Growth protocol E14 mESCs are cultured on the 0.1% gelatin coated plates in the DMEM medium (Sigma) supplemented with 100U/ml penicillin/streptomycin, 15% fetal bovine serum (Sigma), 1x nonessential amino acid, 1x sodium pyruvate, 1x GlutaMax, 1x beta-mercaptoethanol (Invitrogen) and 1000 units/ml leukemia inhibitory factor (ESGRO, EMD Millipore).
Extracted molecule genomic DNA
Extraction protocol Libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (NEB) following manufacture's instructions.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description Kdm2b ChIP-seq was done by Flag antibody because we knocked in a Flag tag upstream of Kdm2b gene.
Data processing Basecalls were performed using CASAVA version v.1.8.2
Sequenced reads were de-multiplexed, trimmed and mapped to mm8 whole genome using bowtie v0.12.7
Peak calling were performed using MACS 1.4.1, meanwhile, wiggle files were generated
Genome_build: mm8
Supplementary_files_format_and_content: wiggle files (scores represent tag numbers per 10 million reads)
Submission date Oct 03, 2012
Last update date May 15, 2019
Contact name Li Shen
Organization name HHMI/Boston Children's Hospital/Harvard Medical School
Street address 200 Longwood Ave
City Boston
ZIP/Postal code 02115
Country USA
Platform ID GPL13112
Series (2)
GSE41314 Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of lineage genes [ChIP-Seq]
GSE41316 Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of developmental genes
SRA SRX191070
BioSample SAMN01757980
Named Annotation GSM1014546_Kdm2b_Ctrl.wig.gz

Supplementary file Size Download File type/resource
GSM1014546_Kdm2b_Ctrl.wig.gz 102.6 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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