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| 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
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| 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
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| Overall design |
H3K4me3, H3K9ac, H3K27me3, H3K36me3, DNA methylation and mRNA, small RNA profiled from shoots and roots of 14 day-old maize B73 seedlings
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| Contributor(s) |
Wang X, Deng X |
| Citation(s) |
19376930 |
| Submission date |
Mar 18, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiangfeng Wang |
| E-mail(s) |
bryan4587@hotmail.com
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| Phone |
2035084833
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| Organization name |
Yale University
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| Department |
MCDB
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| Lab |
Xing Wang Deng
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| Street address |
352 OML, 165 Prospect st
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06520-8104 |
| Country |
USA |
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| Platforms (1) |
| GPL9141 |
Illumina Genome Analyzer (Zea mays) |
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| Samples (14)
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| Relations |
| BioProject |
PRJNA116517 |
| SRA |
SRP001359 |
| 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 Selector |
| 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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