|
| Status |
Public on Aug 17, 2017 |
| Title |
Sbi._R.07020_60DAP_internode_1.1 |
| Sample type |
SRA |
| |
|
| Source name |
Internode1
|
| Organism |
Sorghum bicolor |
| Characteristics |
line: R.07020
tissue: internode
|
| Treatment protocol |
Plants wereharvesteed at 60 days after planting. The top four succesive internodes below the apical dome were exicsed at the node thereby seperating each internode individually. The develpomental progression of internode represents the treatment in this expeirment.
|
| Growth protocol |
For microscopic and RNA-seq analysis of successive sub-apical internodes of sorghum stems, the photoperiod sensitive bioenergy genotype R.07020 was grown in a growth chamber for 60 days under long day conditions (14 h photoperiod) to prevent floral induction. The growth chamber’s temperature was 310C/220C day/night and at constant 50% relative humidity. The light in the growth chamber was supplied with fluorescent lamps at a light intensity of ~350 µMol m-2 s -1 of photosynthetically active radiation (PAR).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using TRIzol according to the manufacturer’s protocol (Invitrogen). About three µg of total RNA was used for RNA-seq library preparation using TruSeq™ RNA Sample Prep Kit v2 (Illumina, Inc.). RNA-seq library quality was assessed using a Bioanalyzer and sequenced on an Illumina HiSeq 2500 at the Texas A&M University Genomics and Bioinformatics Service Center.
The sequence template was prepped using the True-seq V2 kit from illumina which isolates polyadenylated RNA and preps it for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Read alingement to sorghum bicolor referance genome (CLC Genomics Workbench)
Qauntification of expression (CLC Genomics Workbench)
Statistical analysis of differential expression using the edge test (edgeR plugin for CLC Genomics Workbench)
Gene functional analysis and k-means clustering (Mapman)
Genome_build: Sorghum bicolor BTx623 V3.1
Supplementary_files_format_and_content: csv, RPKM data
|
| |
|
| Submission date |
May 11, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
brian adam mckinley |
| E-mail(s) |
brian.a.mckinley@ag.tamu.edu
|
| Phone |
4096796868
|
| Organization name |
texas A&M University
|
| Department |
biochemistry and biophysics
|
| Lab |
john mullet
|
| Street address |
2128 tamu
|
| City |
college station |
| State/province |
tx |
| ZIP/Postal code |
77802 |
| Country |
USA |
| |
|
| Platform ID |
GPL21615 |
| Series (1) |
| GSE98817 |
Dynamics of gene expression during devepolement and expansion of vegetative stem internodes of bioenergy sorghum |
|
| Relations |
| BioSample |
SAMN06928878 |
| SRA |
SRX2797305 |
