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Series GSE68444 Query DataSets for GSE68444
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
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.
 
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.
 
Contributor(s) Burgess AL, David R, Searle IR
Citation(s) 26268215
Submission date Apr 30, 2015
Last update date May 15, 2019
Contact name Alice Louise Burgess
E-mail(s) alice.burgess@adelaide.edu.au
Organization name University of Adelaide
Department Genetics and Evolution
Lab Iain Searle Laboratory
Street address Frome road
City Adelaide
State/province SA
ZIP/Postal code 5005
Country Australia
 
Platforms (1)
GPL17970 Illumina MiSeq (Arabidopsis thaliana)
Samples (25)
GSM1671792 At total RNA RBS-seq rep 1
GSM1671793 At total RNA RBS-seq rep 2
GSM1671794 At total RNA RBS-seq rep 3
Relations
BioProject PRJNA282742
SRA SRP057846

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
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 SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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