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| Status |
Public on Oct 01, 2015 |
| Title |
rRNA 5-methylcytosine in Arabidopsis thaliana |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
Other
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| Summary |
Here we use bisulfite conversion of RNA combined with high-throughput IIlumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites in ribosomal RNAs of all three sub-cellular transcriptomes in Arabidopsis thaliana. m5C sites in rRNAs were also anlyzed in Arabidopsis T-DNA knockouts for the RNA methyltransferases TRM4A, TRM4B, TRDMT1, NSUN5, NOP2A, NOP2B and NOP2C.
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| Overall design |
RNA Bisulfite sequencing was used to identify candidate m5C sites in rRNAs of Arabidopsis thaliana. Illumina sequencing was performed on a MiSeq platform. Two experiments were performed; experiment 1 and experiment 2. In experiment 1, one to three biological replicates were performed for the genotypes wild type, nop2a-2, nop2b-1, nop2b-2, nop2c-1, nop2c-2, nsun5-1 and nsun5-2. In experiment 2, one biological replicate was performed for each of the genotypes wild type, trm4a, trm4b-1, trdmt1 and trdmt1 trm4b.
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| Contributor(s) |
Burgess AL, David R, Searle IR |
| Citation(s) |
26268215 |
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| Submission date |
Apr 30, 2015 |
| 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) |
| GPL17970 |
Illumina MiSeq (Arabidopsis thaliana) |
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| Samples (25)
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| Relations |
| BioProject |
PRJNA282742 |
| SRA |
SRP057846 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE68444_Arabidopsis_rRNA_methylation_expt_1.xls.gz |
11.9 Kb |
(ftp)(http) |
XLS |
| GSE68444_Arabidopsis_rRNA_methylation_expt_2.xls.gz |
11.6 Kb |
(ftp)(http) |
XLS |
| GSE68444_ribosomalRNA_reference_sequences_and_number_of_m5C_sites.xlsx |
64.0 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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