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Sample GSM1924749 Query DataSets for GSM1924749
Status Public on May 01, 2017
Title EpiSCA_ZIC2_ChIPseq
Sample type SRA
 
Source name Epiblast stem cells_freed from Activin
Organism Mus musculus
Characteristics strain: 129/Sv
chip target: ZIC2
chip reagent: Streptavidine
tag: biotin
Treatment protocol A suspension of EpiSCs following Accutase treatment was plated on a 10 cm diameter dish and immediately transfected with 5 mg of pCAGGS-BLRP-BirA plasmid to express BLRP-tagged plasmid and Lipofectamine 2000 (Thermo Fisher). After 8 h, the culture medium was refreshed and 5 mM biotin was added.
Growth protocol Feeder-free epiblast stem cell culture in N2/B27-supplemented DMEM/F12 with 20 ng/ml activin and 10 ng/ml Fgf2. EpiSCA cultures were freed from activin for 18 hr before harvest, without significant changes in microarray data and called ChIP-seq peaks.
Extracted molecule genomic DNA
Extraction protocol After 24 h, the cultures were fixed with 1% formalin for 10 min at room temperature, and then the cells were scraped from dishes, washed, collected in a tube and lysed using the lysis buffer containing 1% SDS. Cell lysates were sonicated in a 1–ml vial using COVARIS M220, which produced an average DNA fragment size of approximately 150 bp. The lysate was mixed with streptavidin beads overnight and washed with a series of solutions described in Matsuda K et al. (submitted).
The DNA fragments were ligated with adapters and amplified by PCR using TruSeq ChIP Sample Prep Kit (Illumina), according to the manufacturer’s directions, except that we terminated the PCR reaction at 10 cycles.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Data processing ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2.
ChIP-seq peaks were called using MACS1.4, input DNA without ChIP as reference, and the default settings except for band width, which was adjusted to 150 bases.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated using SraTailor
 
Submission date Nov 03, 2015
Last update date Aug 27, 2019
Contact name Hisato Kondoh
E-mail(s) kondohh@cc.kyoto-su.ac.jp
Phone 81-72-681-9762
Organization name Biohistory Research Hall
Street address Murasakicho 1-1
City Takatsuki
State/province Osaka
ZIP/Postal code 569-1125
Country Japan
 
Platform ID GPL17021
Series (1)
GSE74636 Genome-wide maps of five major transcription factors in epiblast stem cells
Relations
BioSample SAMN04231641
SRA SRX1410924

Supplementary file Size Download File type/resource
GSM1924749_A_ZIC2peaks.bed.gz 1.5 Mb (ftp)(http) BED
GSM1924749_A_ZIC2peaks.bw 122.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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