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| Status |
Public on Nov 06, 2013 |
| Title |
0.5U Mnase digest anti-CENH3 |
| Sample type |
SRA |
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| Source name |
leaf DNA, 0.5U Mnase digest anti-CENH3
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| Organism |
Oryza sativa |
| Characteristics |
developmental stage: two-week old seedling
tissue: leaf
cultivar: Nipponbare
mnase digestion: 0.5U Mnase
chip antibody: anti-CENH3 (custom Ab; Nagaki, 2004, Nature Genetics)
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| Growth protocol |
Rice cultivar “Nipponbare” seeds were germinated at room temperature for three days. Germinated seeds were then sowed in soil to continue to grow in the greenhouse. Two-week old seedlings were collected for nuclei and DNA isolation.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The collected seedlings were grounded into fine powder in liquid nitrogen. The ChIP procedure, including nuclei isolation, MNase digestion, immunoprecipitation using anti-cenH3 antibodies and recovery of ChIPed DNA for development of ChIP-seq libraries, was carried out by following the published protocols (Zhang et al., 2012)
ChIPed DNA and input DNA corresponding to 0.5 U and 2.5 U MNase digested chromatins were used for customized ChIP-seq library development following the published protocols (Henikoff et al., 2011), which can recover insert sizes down to 20 bp.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sample 1
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| Data processing |
DNA fragments were mapped to rice genome (TIGR7/IRGSP1) (Kawahara et al., 2013; Sakai et al., 2013), with Bowtie (Langmead et al., 2009) reporting non-mismatches and uniquely mapped sites.
The centers of CENH3 nucleosomes were identified by nucleR (Flores and Orozco, 2011).
Genome_build: TIGR7
Supplementary_files_format_and_content: The wig files report nucleR's score. The peak sites are the center of CENH3 nucleosomes.
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| Submission date |
Sep 10, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Tao Zhang |
| Organization name |
University of Wisconsin Madison
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| Department |
Horticulture
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| Lab |
Jiming Jiang Lab
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| Street address |
1575 Linden Dr.
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
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| Platform ID |
GPL13160 |
| Series (1) |
| GSE50755 |
The CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres |
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| Relations |
| BioSample |
SAMN02352875 |
| SRA |
SRX347767 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1228040_CENH3_0.5U.wig.gz |
9.0 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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