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Sample GSM1035397 Query DataSets for GSM1035397
Status Public on Dec 04, 2012
Title rat_ts_h3k9me3
Sample type SRA
Source name Trophoblast stem cells
Organism Rattus norvegicus
Characteristics strain: HSD
chip antibody: H3K9me3 (Abcam, ab8898, lot GR110001)
cell type: Trophoblast stem cells
Growth protocol Mouse TSCs were obtained from Dr. Janet Rossant, Hospital for Sick Children, (Toronto, Canada) and maintained in DMEM/F12 with 15 mM Hepes, 20% FBS, 2 mM glutamine, 100 ug/ml streptomycin, 1 mM sodium pyruvate, 100 uM BME, supplemented with Activin, FGF4, and Heparin following (Erlebacher et al, Developmental Biology 2004). Rat TSCs were cultured as previously (Asanoma et al, Developmental Biology 2011)
Extracted molecule genomic DNA
Extraction protocol Cells were trypsinized for 4 minutes and prepared using the ChIP kit (Millipore). Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Catalog # FC-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200~400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II or HiSeq following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description ChIP DNA
Data processing Basecalls performed using CASAVA version 1.5
ChIP-seq reads were aligned to mm9 or rn4 using BWA 0.9.6 (-q 10 -I), and filtered using samtools view (-q 1) to remove multiply mapping reads.
Individual alignments were merged using samtools merge, then peaks were called using MACS v2.0.9 with default settings, using --broad setting for histone marks.
Genome_build: rn4
Supplementary_files_format_and_content: ChIP-Seq bed files contain peaks called by MACS v2.0.9
Submission date Nov 09, 2012
Last update date May 15, 2019
Contact name Edward Chuong
Organization name University of Colorado Boulder
Department BioFrontiers
Lab Chuong
Street address 596 UCB
City Boulder
ZIP/Postal code 80304
Country USA
Platform ID GPL14844
Series (1)
GSE42207 Rodent trophoblast epigenome
SRA SRX204151
BioSample SAMN01805504

Supplementary file Size Download File type/resource
GSM1035397_r_ts_h3k9me3_broad_peaks.bed.gz 156.4 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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