|
| Status |
Public on Oct 01, 2015 |
| Title |
Stress-treated 7B-1 Mutant |
| Sample type |
SRA |
| |
|
| Source name |
seedling
|
| Organism |
Solanum lycopersicum |
| Characteristics |
developmental stage: stress-tolerant
genotype/variation: 7B-1 Mutant
cultivar: Rutgers
|
| Treatment protocol |
Two-week old seedlings grown on MS medium under BL were transferred to mediums supplemented with 10 µM ABA or 140 mM mannitol or 120 mM NaCl and incubated for 0, 2, 4, 8, 12, and 24 h under BL. Cold treatment was carried out by incubating the seedlings at 4°C for 0-24 h under BL.
|
| Growth protocol |
The 7B-1 mutant and wild type (cv. Rutgers) tomatos were grown under continues blue light (BL) in temperature controlled growth chamber set at 23°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy plant miniRNA extraction kit (Qiagen) from stress-treated 7B-1 and WT seedlings and pooled separately in equimolar ratio
Two small RNA libraries were constructed using the TruSeq Small RNA Sample Preparation Kit from Illumina (Illumina, San Diego, CA, USA). In brief, small RNA fractions of 18–28 nt were isolated from 15% denaturing polyacrylamide gels. The fractionated small RNAs were ligated to 3’ TruSeq adaptors and then converted to DNA by RT-PCR following the kit protocol.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Adapter removal step was conducted using the UEA sRNA workbench [Stocks et al, 2012]. The 3' adapter sequence was identified using the first 6 nt. Adapter guessing strategy was also used to double check the adapter removal procedure.
Quality checks including size class distributions and complexity analyses were done before genome matching.
Reads were mapped full length, no mis-matches or gaps allowed to the tomato genome using PatMan [Prueffer et al, 2008]
Differentially expressed small RNAs were determined and annotated.
The miRNAs were identified using the miRCat and miRprof tool within the UEA workbench.
Genome_build: GCF_000188115.2
Supplementary_files_format_and_content: csv file containing the sRNA expression levels.
|
| |
|
| Submission date |
Feb 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Irina Mohorianu |
| E-mail(s) |
irina.mohorianu@paediatrics.ox.ac.uk
|
| Organization name |
University of Oxford
|
| Department |
Medical Sciences Division
|
| Lab |
Oxford Vaccine Group
|
| Street address |
Headington
|
| City |
Oxford |
| ZIP/Postal code |
OX3 7LE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16345 |
| Series (1) |
| GSE65964 |
sRNA profiling between the 7B-1 male-sterile tomato and its wild type in response to abiotic stress |
|
| Relations |
| BioSample |
SAMN03350243 |
| SRA |
SRX878735 |
