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Sample GSM489077 Query DataSets for GSM489077
Status Public on Jan 20, 2010
Title H3K4me3_ChIPSeq_Nipponbare/93-11
Sample type SRA
 
Source name seedling shoot
Organism Oryza sativa
Characteristics tissue: shoots from four-leaf stage
cultivar: Nipponbare/93-11
antibody: H3K4me3
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.
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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Description Chromatin IP against H3K4me3
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/
 
Submission date Dec 22, 2009
Last update date May 15, 2019
Contact name guangming he
E-mail(s) guangming.he@yale.edu
Organization name Yale University
Department MCDB
Street address 165, prospect st.
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Platform ID GPL9147
Series (1)
GSE19602 Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids.
Relations
SRA SRX016124
BioSample SAMN00008243

Supplementary file Size Download File type/resource
GSM489077_H3K4me3.Nipponbare93-11.mapview.txt.tar.gz 157.8 Mb (ftp)(http) TAR
GSM489077_H3K4me3_Nipponbare93-11_peaks.bed.gz 255.0 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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