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Sample GSM1671792 Query DataSets for GSM1671792
Status Public on Oct 01, 2015
Title At total RNA RBS-seq rep 1
Sample type SRA
 
Source name 10 days after germination seedlings gown on soil
Organism Arabidopsis thaliana
Characteristics tissue: seedling
genotype: wild type
Extracted molecule total RNA
Extraction protocol RNA was extracted using the Spectrum Plant total RNA kit (SIGMA-ALDRICH) and contaminating DNA removed using DNAse (SIGMA-ALDRICH) and total RNA was bisulfite converted prior to library preparation
RNA libraries were prepared for sequencing using standard Illumina protocols except RNA fragmentation was not performed.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina MiSeq
 
Description experiment 1
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed to remove adaptor sequences, filtered for low-quality reads, then mapped to in silico bisulfite converted rRNA reference sequences using CLC Genomics Workbench 7 (Qiagen) with parameters: mismatch cost =1, insertion cost =3, deletion cost =1, length fraction = 0.8, similarity fraction = 0.9
Methylation percentages of cytosines were extracted from the alignments using CLC genomics workbench 7 (Qiagen). Methylation percentage = (#C divided by #C+#T) times by 100)
Genome_build: TAIR10 annotated ribosomal RNAs
Supplementary_files_format_and_content: excel file with methylation percentages for cytosine residues in rRNAs from A. thaliana wild type and RMTase mutants from bisulfite treated total RNA.
Supplementary_files_format_and_content: excel file with methylation percentages for cytosine residues in rRNAs from A. thaliana wild type and RMTase mutants from bisulfite treated total RNA.
Supplementary_files_format_and_content: excel file with ribosomal RNA reference sequences and gene identifiers and or accession numbers.
 
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
 
Platform ID GPL17970
Series (1)
GSE68444 rRNA 5-methylcytosine in Arabidopsis thaliana
Relations
BioSample SAMN03576691
SRA SRX1014733

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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