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Sample GSM288348 Query DataSets for GSM288348
Status Public on Jun 12, 2008
Title ES_Smad1
Sample type SRA
Source name Embryonic stem cells
Organism Mus musculus
Characteristics E14 ES cells
Chromatin immunoprecipitation for Smad1 transcription factor
Treatment protocol The ES cells were fixed in 1% formaldehyde for 10 minutes at room temperature. The formaldehyde was quenched using 0.1 M glycine before harvest for extract preparation.
Growth protocol E14 mouse ES cells, cultured under feeder-free conditions were maintained in Dulbecco's Modified Eagle-Medium (DMEM, GIBCO), with 15% heat-inactivated ES qualified fetal bovine serum (FBS, GIBCO), 0.055 mM beta-mercaptoethanol (GIBCO), 2mM L-glutamine, 0.1 mM MEM non-essential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Chemicon).
Extracted molecule genomic DNA
Extraction protocol Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. ChIP-enriched DNA from multiple ChIP experiments was pooled and quantified using PicoGreen dsDNA quantitation kit (Invitrogen). The ChIP-enriched DNA was processed for Solexa sequencing using ChIP-Seq Sample Prep Kit (Illumina).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
Description sc-7965 (Santa Cruz) antibody was used for ChIP.
Data processing The raw images have been processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, mm8) using Eland software with maximal 2 mis-matches. The ChIP-seq data were processed in 3 steps: a) A peak-finding algorithm was applied to identify the candidate binding site, where the cut-off threshold of peak intensity was determined by false discovery rate approximated with a random model; b) The candidate binding sites were further filtered based on the criterion of 5-fold change in relative to negative control library (GFP); c) The cut-off threshold of peak intensity were refined by qPCR validation. The software for the ChIP-seq data processing is available at

The final processed peak list is linked as a supplementary file at the foot of this record. The file contains Chromosome number, Peak_location (mm8), and Count (abundance). BED files are also available (mm8).
Submission date May 13, 2008
Last update date May 15, 2019
Contact name Chia-Lin Wei
Phone 65 64788074
Fax 65 64789059
Organization name Genome Institute of Singapore
Department Genome Technology & Biology
Street address 60 Biopolis Street #02-01
City Singapore
ZIP/Postal code 138672
Country Singapore
Platform ID GPL9185
Series (1)
GSE11431 Mapping of transcription factor binding sites in mouse embryonic stem cells
SRA SRX000548
BioSample SAMN02195291

Supplementary file Size Download File type/resource
GSM288348_ES_Smad1.txt.gz 11.6 Kb (ftp)(http) TXT
GSM288348_Smad1.bed.gz 23.1 Mb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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