|
| Status |
Public on Aug 25, 2019 |
| Title |
trm5-1 mutant Rep 3 (tRNA) |
| Sample type |
SRA |
| |
|
| Source name |
10-day-old whole seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
background ecotype: Columbia
genotype: trm5 -/-
tissue: whole seedlings
age: 10 days
rna fraction: tRNA size selection
|
| Growth protocol |
Arabidopsis thaliana (Columbia accession) wild type and mutant plants were grown in Phoenix Biosystems growth under metal halide lights as previously described in David et al. 2017.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from wild type and trm5 10-day-old Arabidopsis seedlings using the Spectrum Plant total RNA kit (SIGMA-ALDRICH) and contaminating DNA removed using DNase I (SIGMA-ALDRICH). To enrich for tRNAs, 10μg of total RNA was separated on a 10% polyacrylamide gel, the region containing 65-85 nts was removed and RNA was purified as previously described in Burgess et al. 2015.
Libraries were prepared as per manufacturer's instruction with NEB Ultradirectional RNA library kit
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
trm5-1-Rep3_count.txt
|
| Data processing |
Base calling was done using Illumina RTA 1.18.54 for tRNA deep sequencing.
Adapters were trimmed using Trim Galore v0.4.2. RNA-seq reads were aligned to Arabidopsis thaliana TAIR10 genome using STAR v2.5.3 with default parameters;the tRNA reads were aligned to GtRNAdb Arabidopsis thaliana tRNA reference (generated from tRNA-Scan SE based on Arabidopisis thaliana reference genome TAIR10) using segemehl v0.2.0 with default parameters.
SNPs were called using HaplotypeCaller of GATK v.3.7 for tRNA deep sequencing data; differential expression analysis was performed on the RNA-seq data using Deseq2, raw counts were normalised with Sample-wise size factor.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab delimited text files include SNP counts for each sample, raw counts from fetaureCounts and Sample-wide size factor normalised counts with Deseq2.
|
| |
|
| Submission date |
May 24, 2018 |
| Last update date |
Aug 27, 2019 |
| Contact name |
Iain Robert Searle |
| E-mail(s) |
[email protected]
|
| Phone |
83133266
|
| Organization name |
The University of Adelaide
|
| Department |
Molecular and Biomedical Science
|
| Lab |
Searle Laboratory
|
| Street address |
North Terrace
|
| City |
Adelaide |
| State/province |
South Australia |
| ZIP/Postal code |
5005 |
| Country |
Australia |
| |
|
| Platform ID |
GPL17970 |
| Series (1) |
| GSE114898 |
Arabidopsis TRM5 encodes a nuclear-localised tRNA guanine-N1-methyltransferase and is important for plant growth |
|
| Relations |
| BioSample |
SAMN09257866 |
| SRA |
SRX4122945 |
