|
| Status |
Public on Jan 21, 2016 |
| Title |
Col-0-PEG |
| Sample type |
SRA |
| |
|
| Source name |
leaves from two-week-old plants_drought
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: Col0
developmental stage: two-week-old
tissue: leaves
|
| Treatment protocol |
For cold treatment, plants were exposed to 4ºC for 24h under long-day photoperiod (photon flux of 40µmol m-2 s-1). For drought and high salt treatments, plants were transferred from GM medium to PEG (55%)- or NaCl (150mM)-containning plates for 10h, respectively
|
| Growth protocol |
Plants were grown under long-day photoperiod (photon flux of 90µmol m-2 s-1). For cold treatments, plants were grown on soil. For drought and high salt treatments, plants were grown on GM medium plates
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Stressed plants were colected, inmediately frozen on liquid nitrogen and homogenized. Total RNA was extracted using TRIzol® Reagent (Life Technologies) and cleaned with RNeasy Plant Mini Kit (Quiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNAseq reads were aligned to the TAIR10 Col-0 reference genome using TopHat2 (Kim et al, 2013) with default parameters
Uniquely mapped reads were counted per representative gene model (excluding introns) according to the TAIR10 annotation using custom R scripts
Differential expression between WT and mutant in each condition was calculated using DEseq2 (Love et al. 2014) following its manual
Genome_build: TAIR10
Supplementary_files_format_and_content: Text files include raw counts for each sample
|
| |
|
| Submission date |
Jul 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Carlos Perea-Resa |
| E-mail(s) |
[email protected]
|
| Organization name |
CIB-CSIC
|
| Street address |
Ramiro de Maeztu,9
|
| City |
Madrid |
| ZIP/Postal code |
28040 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE70491 |
The LSM1-7 Complex Differentially Regulates Arabidopsis Tolerance to Abiotic Stress Conditions by Promoting Selective mRNA Decapping |
|
| Relations |
| BioSample |
SAMN03838772 |
| SRA |
SRX1080260 |
