|
| Status |
Public on Feb 19, 2017 |
| Title |
WT - repeat 1 |
| Sample type |
SRA |
| |
|
| Source name |
WT tomato apex
|
| Organism |
Solanum lycopersicum |
| Characteristics |
genotype/variation: WT
tissue: The sample contains the shoot apical meristem (SAM) and the two youngest leaf primordia.
|
| Treatment protocol |
Seedlings were fixed in acetone and shoot apical meristems were dissected
|
| Growth protocol |
Seedlings were grown in a greenhouse for 14-18 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy kit, QIAGEN, Cat. #74004
Truseq RNA Sample prep-Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
WT1
|
| Data processing |
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: Excel file including the normalized counts, ratios and p-values (and adjusted p-values).
|
| |
|
| Submission date |
Jan 12, 2017 |
| 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) |
| GSE93540 |
Transcriptome analysis of tomato leafless (lfs) mutants and TIBA-induced pins |
|
| Relations |
| BioSample |
SAMN06220050 |
| SRA |
SRX2486274 |
