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Sample GSM863806 Query DataSets for GSM863806
Status Public on Apr 24, 2013
Title ACH3_MEF3_WT
Sample type SRA
Source name ACH3_ChIPseq
Organism Mus musculus
Characteristics strain: C57BL/6J/N
genotype/variation: homozygously constitutively null for H3f3b
cell type: mouse embryonic fibroblasts (MEF)
passages: passage 7, replicate 1
chip-antibody: H3K4Tm3
Growth protocol Frozen cells thawed at passage 5 and grown to passage 7 on 15 cm tissue culture treated plates in DMEM high glucose with L-glutamine and non-essential amino acids. Harvest at passage 7 yielded approximately 2 x 10^6 cells per line.
Extracted molecule genomic DNA
Extraction protocol ChIP-seq: MEF cells were trypsinized, washed, then crosslinked with 1% formaldehyde for 10 minutes, and quenched with a final volume of 0.125M glycine. Cells were washed 3 times in cold PBS, flash-frozen, and stored at -80C. Yield was approximately 2 x 10^6 cells per MEF line. Chromatin immunoprecipitation was performed exactly as described in O'Geen et al. 2011 (PMID: 21913086) with the following modifications: Nuclear pellet was flash frozen in liquid nitrogen after incubation in 100ul nuclear lysis buffer, and thawed on ice to aid disruption of nuclei before sonication. Chromatin was sonicated on a Diagenode Bioruptor in 1.5 ml Eppendorf tubes in a volume of 100 ul nuclear lysis buffer to a fragment size between 100-200 base pairs. ChIP assays were performed using H3K9Ac (Upstate # 06-942, lot number 31636) and H3K4Tm3 (Millipore # 04-475, lot number NG1680351) antibodies. Antibodies were collected with 20 ul magnetic protein G beads, and washed as described. After reversing the crosslinks, samples were purified and eluted in 2 x 10 ul elution buffer using the Qiagen MinElute PCR purification kit.
Libraries were prepared on the library automation system from IntegenX (Apollo324) using the PrepX™ DNA Library Kit.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Data processing Alignment: Sequence reads were obtained and mapped to the mouse (mm9) genome using the bwa aligner (
Peaks: Peak detection was performed Solesearch ( using the input DNA as a control.
Genome Build:
libTMK4MEF3.bed: mm9
TMK4_MEF3_peaks.gff: mm9
Submission date Jan 19, 2012
Last update date May 15, 2019
Contact name Henriette O'Geen
Organization name UC Davis
Street address 1 Shields Avenue
City Davis
State/province CA
ZIP/Postal code 95616
Country USA
Platform ID GPL11002
Series (1)
GSE34546 Endogenous mammalian histone H3.3 exhibits chromatin-related functions during development
SRA SRX116590
BioSample SAMN00774081

Supplementary file Size Download File type/resource
GSM863806.bed.gz 115.6 Mb (ftp)(http) BED
GSM863806.gff.gz 206.5 Kb (ftp)(http) GFF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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