|
| Status |
Public on Apr 11, 2019 |
| Title |
J1-2_S53_L004 |
| Sample type |
SRA |
| |
|
| Source name |
Psyllid-primed tomato
|
| Organism |
Solanum lycopersicum |
| Characteristics |
treatment: Psyllid-primed
tissue: leaf
age: 21 days after infestation
|
| Treatment protocol |
Psyllid infestation of tomato plants was performed when plants were six weeks old. Leaves branching below the apical meristem were caged with a small mesh bag (amazon.com). The bag either had no psyllids (control plants) or three adult male psyllids (psyllid-primed plants). There were five plants in each treatment.
|
| Growth protocol |
Lso-negative tomato psyllids were maintained on tomato plants under a 16:8 h (Light:Dark) photoperiod at room temperature (24±2°C). The absence of Lso in these psyllid colonies was tested monthly and confirmed using diagnostic PCRs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Seven days after infestation, caged tomato leaves were removed with a sterile razor blade. Three weeks later, the top-most, fully-developed leaf was taken from each plant and immediately flash-frozen in liquid nitrogen. Total RNA extraction was performed using the Plant RNeasy Mini Kit following the manufacturer’s protocol.
For transcriptomic sequencing, libraries were developed using the TruSeq RNA Library Prep Kit v2 following the manufacturer’s protocol.
Sequence cluster identification, quality prefiltering, base calling, and uncertainty assessment were done in real time using Illumina’s HCS 2.2.38 and RTA 1.18.61 software with default parameter settings.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Libraries were multiplexed and sequenced on the Illumina PE HiSeq 2500 v4 platform. Sequence cluster identification, quality prefiltering, base calling, and uncertainty assessment were done in real time using Illumina’s HCS 2.2.38 and RTA 1.18.61 software with default parameter settings.
Reads were mapped with TopHat 2.2.1 to the S. lycopersicum genome (vSL3.0) and the vITAG3.20 annotation. Libraries were normalized by hits to known transcripts in the vITAG3.20 S. lycopersicum annotation.
Expression levels of control and psyllid-primed samples were compared using Cuffdiff2 with a Benjamini–Hochberg false discovery rate correction for calculating adjusted q-values.
Genome_build: S. lycopersicum genome (vSL3.0) and the vITAG3.20
Supplementary_files_format_and_content: Tab-delimited txt file containing gene fpkm and DEG q-values (Jone is J1-2_S53_L004 and J1-3_S54_L004)
|
| |
|
| Submission date |
Apr 10, 2019 |
| Last update date |
Apr 11, 2019 |
| Contact name |
Kyle Harrison |
| E-mail(s) |
kyle.harrison@usda.gov
|
| Organization name |
USDA-ARS
|
| Department |
Entomology
|
| Street address |
1700 E Campus Mall
|
| City |
Lincoln |
| State/province |
Nebraska |
| ZIP/Postal code |
68503 |
| Country |
USA |
| |
|
| Platform ID |
GPL19694 |
| Series (1) |
| GSE129610 |
Lasting expression changes in tomato after tomato psyllid (Bactericera cockerelli) infestation |
|
| Relations |
| BioSample |
SAMN11391753 |
| SRA |
SRX5665762 |
