|
| Status |
Public on Mar 01, 2015 |
| Title |
Green tomato |
| Sample type |
SRA |
| |
|
| Source name |
Fruit cuticle and parenchyma
|
| Organism |
Solanum lycopersicum |
| Characteristics |
cultivar/strain: Sl-Motelle
|
| Treatment protocol |
Tomato fruits cv. Mottel were inoculated with 7 µl, 106 conidia/ml at 30 inoculation spots per fruit on 5 different fruits per biological replicate with seven biological replicates per treatment. For necrotrophic stage growth a 10 mm2 of ripe tomato fruit cuticle was removed and inoculated with 70 µl of a conidial suspension (106 conidia/ml). Three inoculation spots on each of 10 different fruits were inoculated per biological replicate with seven biological replicate per treatment.
|
| Growth protocol |
Tomato (Solanum lycopersicum) wild-type cultivars Motelle were grown in pots filled with a peat-vermiculite (4:1, v/v) mixture containing slow-release high-N Multicote 4 with microelements (0.3% w/w; Haifa Chemicals, Haifa Bay, Israel). Average temperatures in the greenhouse during the growth period fluctuated from 18 to 25˚C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from 100mg (dry weight) of C. gloeosporioides colonizing tomato fruit. Samples were ground into fine powder and were extracted using Tri-reagent 100 mg/ml (38% water saturated phenol, 0.8M Guanidine thiocyanate, 0.4M Ammonium thiocyanate, 0.1MSodium acetate pH=5, 5% glycerol). Aqueous phase was subsequently extracted twice with chloroform. Follow by isopropanol precipitation and two 70% ethenol washes, the RNA pellet was resuspended in DDW. The RNA was treated with DNase, Amplification Grade (Sigma, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA 1.8.1 (use only Illumin'a passed filter)
Reads were aligned to the Solanum lycopersicu (tomato) genome and to Colletotrichum gloeosporioides contigs (SUB133583, PRJNA176412) release SL2.40 using TopHat V1.3.0 with the option --segment-mismatches 1
Transcripts were defined using cufflinks 1.1.0
Transcripts were quantified using Partek Genomics Suite V6.6 beta
|
| |
|
| Submission date |
Mar 04, 2014 |
| 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 |
GPL16345 |
| Series (1) |
| GSE55553 |
Simultaneous transcriptome analysis of Colletotrichum gloeosporioides and tomato fruits response reveals novel fungal-fruit arm and defense strategies |
|
| Relations |
| BioSample |
SAMN02673245 |
| SRA |
SRX481132 |
