|
| Status |
Public on Aug 24, 2018 |
| Title |
0h_10C |
| Sample type |
SRA |
| |
|
| Source name |
1st pair of true leaves
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar: Moneymaker
developmental stage: Three-weeks-old plants
exposed to: suboptimal growth temperature (10C) for 0h
tissue: 1st pair of true leaves
|
| Treatment protocol |
Three-weeks-old tomato seedlings were incubated at 10°C with a 12h photoperiod (day/night) and a photosynthetically active radiation of 40 µmol m-2 s-1 for the indicated periods of time.
|
| Growth protocol |
Tomato seeds were germinated in the dark at 25°C for 5 days before planting in universal substrate (COMPO, GmbH). Seedlings were grown for 16 days in a growth chamber set at 25°C with a 12h photoperiod (day/night) and a photosynthetically active radiation of 100 µmol m-2 s-1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Leaf tissue was sampled, inmediately frozen on liquid nitrogen and stored at -80C. 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 purified 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 |
The original image data produced by the sequencer (Illumina HiSeq2000) is transferred into sequences, which are 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 10% and low quality reads (reads with >50% bases with quality index <5). Clean reads were saved as ".fastaq" files
Reads were mapped to reference tomato genome ITAG2.3 release using SOAP2 software (Li et al, 2009). No more than two 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: ITAG2.3
Supplementary_files_format_and_content: Text files includes the number of uniquely mapped clean reads and the corresponding estimation of expression level (RPKM) for each gene model .
|
| |
|
| Submission date |
Feb 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Manuel Pineiro |
| Organization name |
Centro de Biotecnologia y Genomica de Plantas (CBGP)
|
| Lab |
179
|
| Street address |
Autopista M-40, Km 38
|
| City |
Pozuelo de Alarcón |
| State/province |
Madrid |
| ZIP/Postal code |
28223 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16345 |
| Series (1) |
| GSE78154 |
Tomato plants increase their tolerance to low temperatures in a chilling acclimation process entailing comprehensive transcriptional and metabolic adjustments |
|
| Relations |
| BioSample |
SAMN04506043 |
| SRA |
SRX1596158 |
