|
| Status |
Public on Nov 13, 2017 |
| Title |
NYJ2_5 |
| Sample type |
SRA |
| |
|
| Source name |
psyllid with Liberibacter solanacearum
|
| Organism |
Solanum tuberosum |
| Characteristics |
tissue: Leaf
age: 49 day old
cultivar: NY138
treatment: psyllid with Liberibacter solanacearum
|
| Treatment protocol |
plant were treated either with J1: Lso minus potato psyllid or infected with Liberibacter solanacearum via insect (psyllid treatment) for a week
|
| Growth protocol |
Tubers were planted in one gallon pots each and grown in growth chmaber/controled condition at 24Celcius 16:8 day night light cycle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Plant Sample were collected and flash frozen in liquid nitrogen / extraction were made with Rneasy kit from qiagen
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 |
analyses was performed on CyVerse.org
The pre-filtered reads were quality-filtered using FASTQC tools.
The RNA-seq reads that passed the quality filters were mapped to the potato reference genome (PGSC_DM_v3.4 gene models ensemblv19-preinstalled in iplantcollaborative.org) using the Tuxedo RNA-seq pipeline (Trapnell et al., 2013, Trapnell et al., 2009, Trapnell et al., 2010).
The Tuxedo pipeline comprised TopHat2 (mapping), Cufflinks2 (transcript assembly), and Cuffmerge2 (transcript merging).
Identification of differential gene expression was conducted using Cuffdiff2, following the defaults parameters in CyVerse.
Supplementary_files_format_and_content: .gtf file
|
| |
|
| Submission date |
Dec 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Cecilia Tamborindeguy |
| E-mail(s) |
[email protected]
|
| Phone |
979 845 2619
|
| Organization name |
Texas A&M University
|
| Street address |
Heep Center
|
| City |
College Station |
| ZIP/Postal code |
77843 |
| Country |
USA |
| |
|
| Platform ID |
GPL16436 |
| Series (1) |
| GSE92312 |
Global gene expression analysis of two potato cultivars in response to “Candidatus Liberibacter solanacearum” infection |
|
| Relations |
| BioSample |
SAMN06134733 |
| SRA |
SRX2417176 |
