|
| Status |
Public on May 11, 2017 |
| Title |
Col-0_20ºC |
| Sample type |
SRA |
| |
|
| Source name |
leaves from two-week-old plants, WT, 20ºC
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype/background: Col-0
genotype/variation: WT
tissue: leaves
age: two weeks
treatment: 20C
|
| Treatment protocol |
For cold treatment, plants were exposed to 4ºC for 24h under long-day photoperiods (photon flux of 40 µmol m-2 s-1). For high salt treatments, plants were transferred from 0.5X GM medium to 150 mM NaCl-containing plates for 10h under long-day photoperiods (photon flux of 90 µmol m-2 s-1).
|
| Growth protocol |
Plants were grown under long-day photoperiods (photon flux of 90 µmol m-2 s-1). For cold treatments, plants were grown on soil. For high salt treatments, plants were grown on 0.5X GM medium plates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Leaf tissue was collected, immediately frozen on liquid nitrogen and stored at -80ºC. For total RNA extraction, frozen tissue was homogenized to a fine powder and total RNA was extracted using TRIzol® Reagent (Life Technologies), treated with DNaseI (Roche) and further cleaned with RNeasy Plant Mini Kit (Qiagen).
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 |
| |
|
| Description |
Arabidopsis thaliana L.
|
| Data processing |
The original image data produced by the sequencer (Illumina HiSeq 2000) was transferred into sequences, which were defined as "raw reads" (or "raw data") and saved as ".fastq" files.
Raw data was cleaned removing adaptor sequences, reads with a percentage of unknown Ns greater than 5% and low-quality reads (reads with >50% bases with quality index <5). Clean reads were saved as ".fastq" files.
Reads were mapped to reference Arabidopsis genome TAIR10 release using SOAP2 software (Li et al., 2009). No more than five mismatches per read were allowed.
The gene expression level was calculated using the RPKM method (Mortazavi et al., 2008) using uniquely mapped reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include gene identifiers, the number of uniquely mapped clean reads, length, coverage and the corresponding estimation of expression level (RPKM) for each gene model.
|
| |
|
| Submission date |
Sep 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Julio Salinas |
| E-mail(s) |
[email protected]
|
| Organization name |
Centro de Investigaciones Biologicas
|
| Department |
Departamento de Biologia Medioambiental
|
| Lab |
241
|
| Street address |
Ramiro de Maeztu, 9
|
| City |
Madrid |
| ZIP/Postal code |
28040 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE87415 |
Environment-dependent regulation of spliceosome activity by the LSM2-8 complex in Arabidopsis |
|
| Relations |
| BioSample |
SAMN05831039 |
| SRA |
SRX2193680 |
