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Sample GSM469460 Query DataSets for GSM469460
Status Public on Nov 10, 2010
Title Starting material
Sample type SRA
 
Source name Liver
Organism Mus musculus
Characteristics fraction: bulk nucleosomes
gender: Female
age: 8 to 10 weeks
Treatment protocol none
Growth protocol Frozen livers were obtained from Pel Freez Biologicals
Extracted molecule genomic DNA
Extraction protocol The preparation of solubilized chromatin and purification of macroH2A1 nucleosomes is described in Changolkar and Pehrson Mol. Cell Biol. 26, 4410 (2006). Briefly, mono- and oligonucleosomes were prepared by micrococcal nuclease digestion with solubilization facilitated by removing H1 with CM Sepharose. MacroH2A1 nucleosomes were purified by differential thio-affinity chromatography using Activated Thiol Sepharose (GE Healthcare), which does not bind macroH2A1, and Thiopropyl Sepharose (GE Healthcare), which binds macroH2A1 nucleosomes. The specificity of this approach was demonstrated by the absence of purified nucleosomes when macroH2A1 knockout livers were used. Mononucleosomal DNA from macroH2A1 and starting material nucleosomes was gel purified and sequenced using the Solexa 1G Genome Analyzer following manufacturer protocols (Barski et al. Cell 129, 823-837 (2007)).
 
Library strategy MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina Genome Analyzer
 
Description mononucleosomal DNA
Data processing The .bed files and .graph files were prepared as described in Barski et al. Cell 129, 823-837 (2007). Sequence tags are mapped in 200 bp windows in the .graph files.
The sorted.txt file represents sequences mapped to mm8 using ELAND software.
For the relative macroH2A1 content file (see GSE18963 supplementary file), we used tools in the rna-seq workflow of Partek Genomics Suite (version 6.5b, 6.09.0806, Partek Inc.) to calculate the relative macroH2A1 content of individual genes. This program counts and normalizes hits in predefined regions specified in a refFlat file. The gene list was the Mouse build 8 version of refFlat.txt obtained from the UCSC Genome site. All exon information was stripped from the refFlat.txt file, which left only the start and stop sites for the genes. Normalized RPKM (reads per kilobase per million reads) values were compared to calculate fold change and FDR-adjusted p-values for each transcript.
 
Submission date Nov 10, 2009
Last update date May 15, 2019
Contact name John Pehrson
E-mail(s) pehrson@vet.upenn.edu
Organization name University of Pennsylvania
Street address 3800 Spruce Street
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL9185
Series (1)
GSE18963 Distribution of macroH2A1 nucleosomes in mouse liver chromatin
Relations
SRA SRX018617
BioSample SAMN00010742

Supplementary file Size Download File type/resource
GSM469460_StartingMaterial.bed.gz 32.5 Mb (ftp)(http) BED
GSM469460_StartingMaterial.graph.gz 34.3 Mb (ftp)(http) GRAPH
GSM469460_StartingMaterial_sorted.txt.gz 298.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA

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