|
| Status |
Public on Oct 01, 2024 |
| Title |
Control, Day 5, Mature, Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Single leaflet of mature leaf
|
| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: Single leaflet of mature leaf
genotype: WT (cv MoneyMaker)
treatment: Control
|
| Treatment protocol |
Well watered plants were watered every other day to soil capacity. Water deficit plants were subjected to complete water withholding
|
| Growth protocol |
Solanum lycopersicum cv Moneymaker plants were germinated on full-strength Murashige-Skoog medium containing 3% sucrose. After three weeks, the most developed seedlings were transferred into 3 L pots containing potting soil, vermiculite and sand in a 25:8:2 ratio, supplemented with 3 tablespoons osmocote fertilizer. Plants were maintained at 70% relative humidity, with a long day (16h/8h) day/night cycle at at 200 µmol/m2/s light intensity.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA has been extracted using TriZol, following the manufacturer's instructions
Library preparation was performed in-house by BGI genomics (P_Standard library & Seq (PE100), library was validated on the Agilent Technologies 2100 bioanalyzer)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
5d-WW-2
|
| Data processing |
Read trimming, and alignment an mapping of reads were performed in CLC Genomics workbench (QIAGEN). Reads were aligned to the Solanum lycopersicum SL4.00 genome release, using ITAG4.1 gene annotation data, using the following parameters: Mismatch cost: 2, insertion cost: 3, deletion cost: 3. Normalization and differential expression analyses were performed using the DESeq2 package in R (4.3.1).
Assembly: Solanum lycopersicum SL4.00
Supplementary files format and content: comma separated values (.csv) file, contains raw readcounts for each sample
|
| |
|
| Submission date |
Jun 19, 2024 |
| Last update date |
Oct 01, 2024 |
| Contact name |
Salma Balazadeh |
| E-mail(s) |
balazadehlabgeo@gmail.com
|
| Phone |
0639661529
|
| Organization name |
Leiden University
|
| Street address |
Slviusweg 72
|
| City |
Leiden |
| ZIP/Postal code |
2333BE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL28981 |
| Series (1) |
| GSE270245 |
Integrating Gene Expression Analysis and Ecophysiological Responses to Water Deficit in Leaves of Tomato Plants |
|
| Relations |
| SRA |
SRX24976652 |
| BioSample |
SAMN41910893 |
