|
| Status |
Public on Nov 23, 2015 |
| Title |
207N_R1 |
| Sample type |
SRA |
| |
|
| Source name |
2 dpa fruits,replicate 1
|
| Organism |
Solanum pimpinellifolium |
| Characteristics |
strain: LA1589
genotype: wild type
age: two-months old
|
| Treatment protocol |
2 dpa fruits were from hand-pollinated flowers.
|
| Growth protocol |
Tomato plants including the transgenic lines were grown in phytotron under the condition of temperature at 20-25 °C and humidity of 70-80%, illuminated for 16 hours daily by light of 150 mE·m–2·s–1 from metal halide and high pressure sodium lamps. Plants were fertilized weekly with all-purpose fertilizer and watered as needed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by Trizol reagent (InvitroGen) from shoot tips including one small visible leaf were collected from one and half month old plants.
Libraries were constructed with Illumina TruSeq Stranded mRNA LT kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
nontransgenic sibling
|
| Data processing |
Reads were mapped to tomato genome using Tophat program v.1.3.2 (Trapnell et al. 2009). Then the transcripts were assembled using cufflinks based on transcripts predicted in SL2.40 assembly from SGN (Trapnell et al. 2010).The expression values of the transcripts were calculated in fragments per kilobase of transcript per million mapped reads (FPKM) (Mortazavi et al. 2008).
Genome_build: Tomato genome assembly SL2.40 from SGN (Sol Genomics Network: solgenomics.net)
the values of columns B-G in 'cds_exp_diff_2D.txt' are FPKM calculated by Cufflinks.
|
| |
|
| Submission date |
Dec 04, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Han Xiao |
| E-mail(s) |
hanxiao@sibs.ac.cn
|
| Phone |
86-21-54924301
|
| Organization name |
Shanghai Institutes for Biological Sciences
|
| Department |
National Key Laboratory of Plant Molecular Genetics
|
| Lab |
Fruit Development
|
| Street address |
300 Fenglin Rd
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL19491 |
| Series (1) |
| GSE63838 |
The Zinc Finger Transcription Factor SlZFP2 Negatively Regulates Abscisic Acid Biosynthesis and Fruit Ripening in Tomato |
|
| Relations |
| BioSample |
SAMN03252629 |
| SRA |
SRX796061 |
