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Series GSE15286 Query DataSets for GSE15286
Status Public on Apr 28, 2009
Title Epigenetic modifications and their relationships to smRNA and mRNA transcriptomes in maize
Organism Zea mays
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and smRNA transcriptomes in maize
We report an integrated genome-wide analysis of DNA methylation, histone modifications, smRNAs and mRNA transcriptional activity, using maize as a model. We surveyed the epigenomes of the maize inbred line B73 in shoot and root tissue by Illumina/Solexa 1G parallel sequencing after digesting genomic DNA with a methylation-sensitive restriction enzyme and after conducting chromatin immunoprecipitations (ChIP) using antibodies that target specific histone modifications (H3K4me3, H3K9ac, H3K27me3, H3K36me3, respectively). Additionally, we profiled RNA pools (micro RNA (miRNA), siRNA and mRNA) using the same sequencing strategy.

Keywords: Epigenetics, mRNA transcription and small RNAs
Overall design H3K4me3, H3K9ac, H3K27me3, H3K36me3, DNA methylation and mRNA, small RNA profiled from shoots and roots of 14 day-old maize B73 seedlings
Contributor(s) Wang X, Deng X
Citation(s) 19376930
Submission date Mar 18, 2009
Last update date May 15, 2019
Contact name Xiangfeng Wang
Phone 2035084833
Organization name Yale University
Department MCDB
Lab Xing Wang Deng
Street address 352 OML, 165 Prospect st
City New Haven
State/province CT
ZIP/Postal code 06520-8104
Country USA
Platforms (1)
GPL9141 Illumina Genome Analyzer (Zea mays)
Samples (14)
GSM381695 H3K4me3_ChIPSeq_shoot
GSM381697 H3K9ac_ChIPSeq_shoot
GSM381699 H3K27me3_ChIPSeq_shoot
BioProject PRJNA116517
SRA SRP001359

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE15286_B73.ALL_GENES.txt.gz 8.4 Mb (ftp)(http) TXT
GSE15286_RAW.tar 6.0 Mb (http)(custom) TAR (of BED, TXT)
GSE15286_Unmapped_smRNA.root.fa.gz 2.9 Mb (ftp)(http) FA
GSE15286_Unmapped_smRNA.shoot.fa.gz 5.9 Mb (ftp)(http) FA
GSE15286_known_miRNA.root.fa.gz 947 b (ftp)(http) FA
GSE15286_known_miRNA.shoot.fa.gz 987 b (ftp)(http) FA
GSE15286_shRNA.root.fa.gz 327.4 Kb (ftp)(http) FA
GSE15286_shRNA.shoot.fa.gz 115.3 Kb (ftp)(http) FA
GSE15286_siRNA.root.fa.gz 6.8 Mb (ftp)(http) FA
GSE15286_siRNA.shoot.fa.gz 16.6 Mb (ftp)(http) FA
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data included within Sample table
Processed data are available on Series record
Raw data are available in SRA

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