|
| Status |
Public on Jul 09, 2015 |
| Title |
M82_Pac_1 |
| Sample type |
SRA |
| |
|
| Source name |
Seedlings young leaves
|
| Organism |
Solanum lycopersicum |
| Characteristics |
genotype: M82
treatments: Paclobutrazol 10mg/l
|
| Treatment protocol |
M82 and pro∆GRAS seedlings were treated with Paclobutrazol (10mg/l) once a day for three days followed by a single GA3 application (100 µM).
|
| Growth protocol |
Tomato plants were grown in a greenhouse under 24/20 ºC (day/night) at natural day length conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the GHC-Phenol chloroform method. cDNA was generated using the SuperScript® II Reverse Transcriptase (Invitrogene)
500ng of total RNA was processed using the TruSeq RNA Sample Preparation Kit v2 protocol (Illumina) (Part # 15026495). Libraries were evaluated by Qubit and TapeStation. Sequencing libraries were constructed with barcodes to allow multiplexing of 8 samples on one lane of flow cell v4 (run on Illumina HiSeq Rapid 2500).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base call and quality scoring was done using RTA (1.18.64).
Reads were aligned to the tomato genome sequence SL2.50 (downloaded from the sol genomics network http://solgenomics.net/organism/Solanum_lycopersicum/genome) using Tophat (v2.0.10).
Counting reads on ITAG2.4 genes (downloaded from sol genomics network) was done with HTSeq-count (version 0.6.1p1)
Differential analysis was carried out using DESeq2 (1.6.3)
Genome_build: SL2.50
Supplementary_files_format_and_content: Tab delimited file including the raw counts, the normalized counts and ratios and p-values (and corrected p-values).
|
| |
|
| Submission date |
Apr 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Gilgi Friedlander |
| Organization name |
Weizmann Institute of Science
|
| Street address |
Hertzel st
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19694 |
| Series (1) |
| GSE68018 |
Next Generation Sequencing of tomato WT, M82 and pro∆GRAS mutant treated with Gibberellin |
|
| Relations |
| BioSample |
SAMN03491045 |
| SRA |
SRX999385 |
