|
| Status |
Public on Jun 06, 2020 |
| Title |
BTx623, mock (treated with water), replicate #2 |
| Sample type |
SRA |
| |
|
| Source name |
BTx623, mock (treated with water)
|
| Organism |
Sorghum bicolor |
| Characteristics |
line: BTx623
|
| Treatment protocol |
Leaf discs of the second youngest leaves of fifteen-day old Sorghum bicolor lines were treated with 10 ml of water (mock), 1 µM of flg22 or 100 µg/ml chitin (Sigma-Aldrich, catalog# C3641) for 1 hr. The samples were collected and stored at -80 oC for RNA extraction.
|
| Growth protocol |
Sorghum seeds of BTx623 and SC155-14E were surface sterilized (70% ethanol for 1 min and then 10% bleach for 10 min, rinsed with autoclaved water) and planted in autoclaved Sunshine potting mix and germinated in growth chambers (16hr/8hr light/dark, 28/26 oC, 60-70% humidity). Fifteen-day old plants were used for experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA extraction was performed using the Direct-zol RNA Miniprep Plus kit from Zymoresearch (catalog #R2071) according to the manufacturer’s instructions.
Non-strand-specific RNA-seq libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads for each sample are aligned to the reference genome with TopHat
The alignment files are provided to Cufflinks to assemble transcripts for each sample.
Samples from the same condition are then merged together using Cuffmerge.
The merged assembly are fed to Chuffdiff, which calculates expression levels and tests the statistical significance of observed changes between two conditions.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jun 05, 2020 |
| Last update date |
Jun 06, 2020 |
| Contact name |
Gary Stacey |
| Organization name |
University of Missouri
|
| Department |
Divisions of Plant Science and Biochemistry
|
| Lab |
#202, C. S. Bond Life Sciences Center
|
| Street address |
1201 Rollins st.
|
| City |
Columbia |
| State/province |
Missouri |
| ZIP/Postal code |
65211 |
| Country |
USA |
| |
|
| Platform ID |
GPL20818 |
| Series (1) |
| GSE151860 |
Variation in gene expression between two Sorghum bicolor lines differing in innate immunity response |
|
| Relations |
| BioSample |
SAMN15144528 |
| SRA |
SRX8478006 |
