|
| Status |
Public on Jan 11, 2019 |
| Title |
Stem_B1b5_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Wheat stem tissue
|
| Organism |
Triticum aestivum |
| Characteristics |
cultivar/background: Fortuna (spring wheat)
genotype/variation: Rht-B1b
age: 14 days past anthesis
tissue: stem
|
| Treatment protocol |
Plants either carried the mutant semi-dwarfing allele, Rht-B1b, or the wildtype tall allele, Rht-B1a.
|
| Growth protocol |
Plants were grown under field conditions near Bozeman, MT (latitude 45.6N, longitude 111.00W). Plants were irrigated with 5cm of water on week pre- and post-anthesis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted in accordance with the QIAGEN RNeasy Plant Mini kit and quantified using an Agilent Bioanalyzer.
Libraries were prepared according to Illumina's TruSeq Stranded mRNA Library prep.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
5-B1b-2
processed data file: RNA_SEQ_edited_7.19.xlsx
|
| Data processing |
The sequence data were analyzed using ArrayStar (DNASTAR, Madison, Wisconsin), with the parameters set as: match setting at 100% for a minimum 50 bp, and all other settings left as default. The resultant data were presented as reads per kilobase of transcript for million mapped reads (RPKM) (Mortazavi et al., 2008) and normalized to Act-2, an actin like protein which was similarly expressed in both genotypes, and previously reported as a reliably expressed gene for normalization (Tenea et al., 2011). The data was analyzed globally against the available rice genome. Specific wheat genes of interest were also analyzed. Genes central to either carbon or nitrogen metabolism were identified based on expression profiling done in rice by Hirose (2006) and adapted in Schlosser (2014) to identify the most prevalent form of the gene in green tissue during development. Wheat genome orthologs were identified using NCBI BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi) and used for expression analysis.
Genome_build: Not provided
Supplementary_files_format_and_content: 9.30.2016_Select_Genes_Default.astar
Supplementary_files_format_and_content: RNA_SEQ_edited_7.19.xlsx: Excel file
|
| |
|
| Submission date |
Jan 10, 2019 |
| Last update date |
Jan 14, 2019 |
| Contact name |
Michael Giroux |
| E-mail(s) |
mgiroux@montana.edu
|
| Organization name |
Montana State University
|
| Department |
Plant Sciences
|
| Street address |
119 Plant Bioscience Building
|
| City |
Bozeman |
| State/province |
Montana |
| ZIP/Postal code |
59717 |
| Country |
USA |
| |
|
| Platform ID |
GPL18862 |
| Series (1) |
| GSE124940 |
The Impact of Wheat Rht-B1b Semi-Dwarfing Allele on Photosynthesis and Seed Development under Field Conditions |
|
| Relations |
| BioSample |
SAMN10724010 |
| SRA |
SRX5237895 |
