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| Status |
Public on Jan 04, 2019 |
| Title |
Lso-pos_week1_rep1 |
| Sample type |
SRA |
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| Source name |
Lso-pos, week1, Tomato leaf
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| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: Leaf
insect treatment: Lso-positive psyllids
time: Week1
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| Treatment protocol |
Tomato plants were exposed to no insect (control), 5 male and 5 female Lso-negative psyllids (Lso-neg, P), or 5 male and 5 female Lso-positive psyllids (Lso-pos, L). The treatment lasted for 1, 2 or 4 weeks. There were 27 plants belong to 3 treatment groups and 3 exposure times
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| Growth protocol |
Tomato plants, Solanum lycopersicum cv. Moneymaker were grown from seed in Sun Gro® Metro-Mix 900 soil and transplanted into 4-inch square pots four weeks later. Plants were watered and fertilized weekly according to the label rate of the Miracle-Gro® Water Soluble Tomato Plant Food (18-18-21 NPK). At six-week-old each plant was assigned to the insect treatment
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| Extracted molecule |
total RNA |
| Extraction protocol |
Leaf tissues collected and flash frozen by liquid nitrogen. Plant RNA samples were extracted from plant tissues using Qiagen Plant Rneasy Mini Kit. TURBO DNA-free Kits from Life Technologies were to romove potential DNA contaminant.
Illumina TruSeq RNA Sample Prep Kit was used with 2 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Transcriptome of plant exposed to Lso-positive psyllids at week 1
L1
Barcode: TAGCTT
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| Data processing |
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.
Sequencer basecall (.bcl) files were formatted into fastq files using bcl2fastq 1.8.4 script configureBclToFastq.pl. The sequence raw reads were cleaned using cutadapt 1.0 to remove barcode tags and adaptors. Individual samples were processed with FastQC, and the QC reports were checked as final confirmation of sequence quality.
The processed sequences were uploaded to Discovery Environment (DE) web interface and platform at CyVerse (www.iplantcollaborative.org) (Goff et al., 2011). Tuxedo RNA-Seq apps (TopHat2, Cufflinks2, Cuffmerge2, Cuffdiff2) within DE interface were used to map sequences against the S. lycopersicum genome, Ensembl 14 (Sato et al., 2012), to assemble transcripts, to create full transcriptome, and to identify differentially expressed genes (DEGs) according to the published protocol (Trapnell et al., 2012). The analyses were done with the default false discovery rate (FDR = 0.05) and adjusted with Benjamini-Hochberg correction for multiple comparisons.
Transcriptomes of plants from control and Lso-negative psyllids treatments were compared to evaluate plant response to herbivory. Transcriptomes of plants from control and Lso-positive psyllids treatments were compared to evaluate plant response to herbivory and infection. Transcriptomes of plants from Lso-negative psyllid and Lso-positive psyllid treatments were compared to evaluate the difference in plant responses to Lso-negative and Lso-positive Bactericera cockerelli. Each comparison was done with respect to each time point (week1, week2, week4). In total, nine comparisons were performed.
Genome_build: SL2.40 (source: Ensemblplants)
Supplementary_files_format_and_content: Differentially expressed genes (DEGs) found in each comparative trancriptoms including relative gene expression based on fold change, total FPKMs, q-values (adjusted for multiple comparison), and gene identification
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| Submission date |
Mar 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ordom Brian Huot |
| E-mail(s) |
obh6@tamu.edu
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| Phone |
9797399085
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| Organization name |
Texas A&M University
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| Department |
Entomology
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| Lab |
Tamborindeguy
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| Street address |
2475 Texas A&M University
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| City |
College Station |
| State/province |
Texas |
| ZIP/Postal code |
77843 |
| Country |
USA |
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| Platform ID |
GPL19694 |
| Series (1) |
| GSE95710 |
Global gene regulation in tomato plant (Solanum lycopersicum) responding to vector (Bactericera cockerelli) feeding and pathogen (‘Candidatus Liberibacter solanacearum’) infection |
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| Relations |
| BioSample |
SAMN06480793 |
| SRA |
SRX2613856 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2522422_L1_transcripts.gtf.gz |
4.7 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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