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| Status |
Public on Jun 15, 2009 |
| Title |
Histone-Mnase Lane 1 |
| Sample type |
SRA |
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| Source name |
Sperm Donor D1
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| Organism |
Homo sapiens |
| Characteristics |
cell type: sperm
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| Growth protocol |
Sperm samples were obtained from four known fertile donors attending the University of Utah Andrology laboratory, consented for research.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Sperm samples were collected after 2-5 days abstinence and subjected to an ISolate density gradient (to purify viable, motile, mature sperm) and treated with somatic cell lysis buffer (0.1% SDS, 0.5% Triton X in DEPC H2O) for 20 min on ice to eliminate white blood cell contamination. Samples were centrifuged at 10,000 G for 3 min and the sperm pellet was resuspended in 1X PBS and used immediately for chromatin preparation. Chromatin was prepared as previously described by Zalenskaya et al Biochem Biophys Res Commun 279, 213-8 (2000) in the absence of crosslinking reagent. Sperm was treated with sequential and increasing MNase (10U-160U), and centrifuged to sediment protamine-associated DNA, releasing mononucleosomes. The pooled mononucleosomes were used for chromatin immunopreciptation (below), or the DNA extracted and gel purified (~140-155bp) for array analysis. All Chromatin IPs (ChIPs) were performed as previously described by Gordon et al Mol Cell Biol 27, 4058-69 (2007).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
Histone bound DNA enrichment via Mnase digestions and nucleosome purification
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| Data processing |
Reads were aligned to Hg18/ NCBI 36.1/ H_sapiens_Mar_2006 using the Illumina Pipeline's ELAND extended aligner and enriched regions relative to input identified using the USeq analysis package (http://useq.sourceforge.net, Nix et al BMC Bioinfo Dec 5:9(1):523 (2008)).
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| Submission date |
Apr 15, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Bradley R. Cairns |
| Organization name |
HHMI and Huntsman Cancer Institute
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| Department |
Oncological Sciences
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| Street address |
2000 Circle of Hope
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| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84102 |
| Country |
USA |
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| Platform ID |
GPL9052 |
| Series (2) |
| GSE15594 |
Distinctive Chromatin in Human Sperm Packages Genes that Guide Embryo Development |
| GSE15690 |
Distinctive Chromatin in Human Sperm Packages Genes that Guide Embryo Development: ChIP-seq |
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| Relations |
| SRA |
SRX007049 |
| BioSample |
SAMN02197787 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM392701_HistoneMnase.D1_080313_s_1_sorted.txt.gz |
134.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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