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| Status |
Public on Jan 20, 2010 |
| Title |
H3K4me3_ChIPSeq_Nipponbare |
| Sample type |
SRA |
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| Source name |
seedling shoot
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| Organism |
Oryza sativa |
| Characteristics |
tissue: shoots from four-leaf stage
cultivar: Nipponbare
antibody: H3K4me3
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| Growth protocol |
Rice cultivar Nipponbare, 93-11, and their reciprocal F1 hybrids (Nipponbare/93-11 and 93-11/Nipponbare) were used for all experiments in this study. Seeds were grown in soil under 16 hours light/8 hours dark conditions at 28℃ in a greenhouse. After 4 weeks, seedling shoots at the four-leaf stage were harvested, frozen in liquid nitrogen and stored at -80℃ for DNA and total RNA isolation, or processed directly after harvesting for ChIP assay.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer's instructions, and was treated with RNase-free DNase I (New England Biolabs) to remove any possible contaminating genomic DNA. mRNA was extracted from total RNA using Dynabeads Oligo(dT) (Invitrogen Dynal) following the manufacturer's directions. First-and second strand cDNA was generated using SuperscriptII reverse transcriptase (Invitrogen) and random hexamers primers. Double-stranded cDNA was fragmented by nebulization and used for mRNA library construction following the standard Illumina protocol. Small RNAs were gel isolated from total RNA, and were used to create libraries for Illumina sequencing essentially as described previously (Mi et al., 2008; Wang et al., 2009a). Genomic DNA extraction, methylated genomic DNA enrichment and construction of Illumina sequencing libraries were carried out as described previously (Li et al., 2008b; Wang et al., 2009a). Chromatin from seedling shoots was immunoprecipitated with antibodies against H3K4me3 (Upstate), H3K9ac (Upstate) or H3K27me3 (Upstate) as described previously (Gendrel et al., 2005). The eluted ChIP DNA was used to generate Illumina sequencing libraries following the manufacturer's protocol.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
Chromatin IP against H3K4me3
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| Data processing |
Sequencing reads from all libraries were mapped to the reference rice genome using MAQ software. Genomic regions associated with DNA methylation and histone modifications were identified using MACS software, in which default parameters were set up to call peaks representing enriched epigenetic marks.Further details found at http://www.plantcell.org/
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| Submission date |
Dec 22, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
guangming he |
| E-mail(s) |
guangming.he@yale.edu
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| Organization name |
Yale University
|
| Department |
MCDB
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| Street address |
165, prospect st.
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06520 |
| Country |
USA |
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| Platform ID |
GPL9147 |
| Series (1) |
| GSE19602 |
Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids. |
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| Relations |
| SRA |
SRX016122 |
| BioSample |
SAMN00008241 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM489075_H3K4me3.Nipponbare.mapview.txt.tar.gz |
77.5 Mb |
(ftp)(http) |
TAR |
| GSM489075_H3K4me3_Nipponbare_peaks.bed.gz |
235.7 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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