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Sample GSM1148111 Query DataSets for GSM1148111
Status Public on Aug 13, 2013
Title QSC_y_H3K27me3_ChIPSeq
Sample type SRA
Source name hindlimb muscles
Organism Mus musculus
Characteristics strain: C57BL/6
gender: male
age: 2-3 months
sorting markers: VCAM+ / CD31- / CD45- / Sca1-
chip antibody: H3K27me3 (Millipore 07-449)
Treatment protocol FACS-purified QSCs from young mice were plated on ECM coated surface in F10 media supplemented with 10% horse serum for 3 days to obtain ASCs.
Growth protocol QSCs were FACS-purified from hindlimb muscle of healthy mice at the indicated ages.
Extracted molecule genomic DNA
Extraction protocol FACS-sorted cells were crosslinked with 1% formaldehyde at room temperature with gentle agitation for 10 minutes. The crosslink was terminated by Glycine at a final concentration of 0.125 M. Cells were then washed three times with ice-cold PBS and stored at -80°C until a sufficient number of cells had been obtained. ChIP was performed following standard ChIP protocols with the following major modifications: 10E6 cells were resuspended in 200 ml lysis buffer and sonicated to obtain DNA fragments from 150 to 500 bp in size. Each ChIP reaction was performed with 10E6 cells and 5 ug of antibody.
The ChIP DNA was size-selected for fragments between 150-400 bp by 2% low-melt agarose gel electrophoresis (NuSieve). A library for deep sequencing was generated with Illumina ChIP-seq Sample Prep Kit (Part# IP-102-1001) with the following modification to the standard protocol: The adaptor solution was diluted 50 times for ligation. 15 cycles of PCR amplification were performed immediately following adaptor ligation. Size-selection of fragments between 200-400 bp was performed after PCR amplification. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Data processing Basecalling was performed using Illumina RTA
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie.
Unique reads mapped to a single genomic location (allowing a maximal of 2 mismatches) were used for peak detection by Model-based Analysis of ChIP-Seq (MACS) with alignment of the ChIP input DNA as control.
Genome_build: mm9
Supplementary_files_format_and_content: .bed files for ChIP-seq analysis containing peak location and −10*log10(p value) are provided.
Submission date May 24, 2013
Last update date May 15, 2019
Contact name Ling Liu
Organization name Stanford University
Street address 300 Pasteur Drive
City Palo Alto
ZIP/Postal code 94306
Country USA
Platform ID GPL11002
Series (1)
GSE47362 Epigenetic determinants of muscle stem cell quiescence and chronological aging (ChIP-seq)
BioSample SAMN02178764
SRA SRX286489

Supplementary file Size Download File type/resource
GSM1148111_yQ_K27m3_peaks_w_input_control_peaks.bed.gz 167.0 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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