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| Status |
Public on Apr 07, 2017 |
| Title |
Transcriptome-wide RNA 5-methylcytosine methylation in siliques of Arabidopsis thaliana |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Methylation profiling by high throughput sequencing
Other
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| Summary |
Here we use bisulfite conversion of rRNA depleted RNA combined with high-throughput Illumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites transcriptome-wide in Arabidopsis thaliana siliques. m5C sites were also analyzed in an Arabidopsis T-DNA knockout for the RNA methyltransferase TRM4B.
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| Overall design |
RNA bisulfite sequencing was used to identify candidate m5C sites transcriptome-wide in Arabidopsis thaliana siliques, using rRNA depleted RNA. Illumina sequencing was performed on a HiSeq platform. The two genotypes used are wild type and trm4b-1. For wild type (WT) there are two biological replicates. The first biological replicate for wild type siliques has only one technical replicate, while there are two technical replicates for the second wild type biological replicate. There are three biological replicates for trm4b-1
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| Contributor(s) |
David R, Burgess AL, Searle IR |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Apr 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Alice Louise Burgess |
| E-mail(s) |
alice.burgess@adelaide.edu.au
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| Organization name |
University of Adelaide
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| Department |
Genetics and Evolution
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| Lab |
Iain Searle Laboratory
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| Street address |
Frome road
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| City |
Adelaide |
| State/province |
SA |
| ZIP/Postal code |
5005 |
| Country |
Australia |
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| Platforms (1) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
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| Samples (5)
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| This SubSeries is part of SuperSeries: |
| GSE80054 |
Transcriptome-wide RNA 5-methylcytosine methylation in siliques, shoots and roots and root gene expression profiling of Arabidopsis thaliana |
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| Relations |
| BioProject |
PRJNA317689 |
| SRA |
SRP073006 |
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