|
| Status |
Public on Jun 30, 2021 |
| Title |
CO2A_3 |
| Sample type |
SRA |
| |
|
| Source name |
Sorghum bicolor plants under normal concentration of CO2 and water deficit
|
| Organism |
Sorghum bicolor |
| Characteristics |
cultivar: cv. BRS330
tissue: prop roots tissue
treatment: A[CO2] + water deficit
|
| Treatment protocol |
60 DAP plants were submited to water deficit treatment based on reducing the irrigation to 0.45 L of water per day (70% of field capacity reduction). Control-plants were grown in ambient [CO2] (A[CO2], 400 µmol mol-1), and treated-plants in elevated [CO2] (E[CO2], 800 µmol mol-1), both submitted to chronic water-deficit (WD) for 30 days.
|
| Growth protocol |
Sorghum bicolor BRS330 was cultivated in soil, as described by De Souza et al. (2015). Plants received 1.5 L of water per day during the vegetative stage (0 - 60 days after planting, DAP).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed with 100 mg of grounded GPR tissue using the ReliaPrep RNA Tissue to fibrous tissues (Promega).
Libraries were constructed according to the manufacturer’s protocol of the Truseq Stranded mRNA Sample Prep LS Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The preprocessing step was carried out with Trimmomatic v0.36 to remove adapters and filter raw reads by quality.
The filtered quality reads were aligned to the most recent version (v3) of the Sorghum bicolor genome downloaded from the Phytozome database using the Hisat2 software with its default parameter values.
The aligned read counts, the fragments per kilobase of transcript per million mapped reads (FPKM) normalization values, and the differential expression analysis were carried out using the Cuffdiff package from Cufflinks v2.2.1 and its default parameter values. Genes with FDR value < 0.05 were considered differentially expressed genes (DEGs).
Genome_build: Sorghum bicolor ver. 3 from Phytozome
Supplementary_files_format_and_content: File in xlsx format
|
| |
|
| Submission date |
Jun 29, 2021 |
| Last update date |
Jul 01, 2021 |
| Contact name |
Luis Willian Pacheco Arge |
| Organization name |
UFRJ
|
| Department |
Genetica
|
| Lab |
LGMBV
|
| Street address |
Av. Carlos Chagas Filho, 373
|
| City |
Rio de Janeiro |
| State/province |
Rio de Janeiro |
| ZIP/Postal code |
21941-590 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL21615 |
| Series (1) |
| GSE179109 |
Integrative Analysis of Sorghum Bicolor Green Prop Roots Under Elevated CO2 and Water Deficit Conditions |
|
| Relations |
| BioSample |
SAMN19945314 |
| SRA |
SRX11248334 |
