|
| Status |
Public on Sep 09, 2021 |
| Title |
Guard cells, pro17_3_pro∆19 |
| Sample type |
SRA |
| |
|
| Source name |
Leaves
|
| Organism |
Solanum lycopersicum |
| Characteristics |
strain: M82
tissue: Leaves
cell type: Guard cells
genotype: pro17
|
| Growth protocol |
All plants were grown in a growth room set to a photoperiod of 12/12-h night/days, light intensity )cool-white bulbs) of ~250 μmol m-2 s-1, and 25°C. Tomato Solanum lycopersicum cv M82 (sp-/sp ) plants were used throughout this study.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Guard cells from tomato leaves were isolated according to Araújo et al. (2011) With some modifications. Briefly, four fully expanded leaves without the veins were ground twice in a blender in 100 mL cold distilled water, each time for 60 sec. The blended mixture was poured onto a 100-mm mesh (Sefar) and the remaining epidermal peels were rinsed thoroughly with deionized water.
Inhouse poly A based RNA seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
pro17_3
|
| Data processing |
Reads were trimmed using cutadapt
After trimming the reads were mapped to the Solanum Lycopersicum reference genome using STAR v2.4.2a (using options outFilterMismatchNoverLmax 0.04 and alignEndsType EndToEnd)
Counting proceeded over genes annotated in ITAG release 3.2, using htseq-count
Normalization was performed using DESeq2
Genome_build: Solanum Lycopersicum reference genome, release SL3.00
Supplementary_files_format_and_content: Excel file includes the normalized counts and DESEq2 differential expression analysis
|
| |
|
| Submission date |
Jan 21, 2020 |
| Last update date |
Sep 09, 2021 |
| Contact name |
David Weiss |
| E-mail(s) |
david.weiss@mail.huji.ac.il
|
| Organization name |
The Hebrew University of Jerusalem
|
| Street address |
Hertzel st.
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19694 |
| Series (1) |
| GSE143999 |
The role of DELLA protein in tomato plant response to water-deficit stress |
|
| Relations |
| BioSample |
SAMN13895826 |
| SRA |
SRX7586317 |
