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Status |
Public on Nov 10, 2010 |
Title |
Starting material |
Sample type |
SRA |
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Source name |
Liver
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Organism |
Mus musculus |
Characteristics |
fraction: bulk nucleosomes gender: Female age: 8 to 10 weeks
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Treatment protocol |
none
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Growth protocol |
Frozen livers were obtained from Pel Freez Biologicals
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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)).
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Library strategy |
MNase-Seq |
Library source |
genomic |
Library selection |
MNase |
Instrument model |
Illumina Genome Analyzer |
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Description |
mononucleosomal DNA
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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.
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Submission date |
Nov 10, 2009 |
Last update date |
May 15, 2019 |
Contact name |
John Pehrson |
E-mail(s) |
pehrson@vet.upenn.edu
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Organization name |
University of Pennsylvania
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Street address |
3800 Spruce Street
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City |
Philadelphia |
State/province |
PA |
ZIP/Postal code |
19104 |
Country |
USA |
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Platform ID |
GPL9185 |
Series (1) |
GSE18963 |
Distribution of macroH2A1 nucleosomes in mouse liver chromatin |
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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 Selector |
Raw data are available in SRA |
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