|
| Status |
Public on Oct 01, 2015 |
| Title |
trm4a total RNA RBS-seq rep 1 plate |
| Sample type |
SRA |
| |
|
| Source name |
10 days after germination seedlings grown on 1/2 MS media plates
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedling
genotype: trm4a
|
| 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 2
|
| 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 |
SAMN03576707 |
| SRA |
SRX1014754 |
