|
| Status |
Public on Mar 05, 2019 |
| Title |
Leaf removed 3 h rep b |
| Sample type |
SRA |
| |
|
| Source name |
Leaf removed 3 h_first axillary bud
|
| Organism |
Sorghum bicolor |
| Characteristics |
cultivar: 100M
age: 7 days after sowing
treatment: 3h after leaf removal
tissue: First axillary bud
|
| Treatment protocol |
Treatments began 7 days after sowing. Plants were left intact, or leaf removal was conducted by peeling the entire coleoptile and first leaf from the culm to expose the axillary bud. The dissection was easily accomplished with minimal handling and without touching the bud. Axillary buds from the first leaf axil were harvested at 1, 3 and 6 h after leaf removal. Four replicates of 15 buds were harvested. The three highest quality replicates of each sample (by Bioanalyzer) were used for transcriptome analysis.
|
| Growth protocol |
Seeds were sown singly in 50 mL conical centrifuge tubes modified with a drain hole and filled with LC1 soilless medium supplemented with 7.5g/L 20-20-20 Osmocote fertilizer. Plants were grown in a growth chamber providing 575 mM m-2s-1 of PAR at a R:FR of 13.30 from t5 fluorescent lamps with a photoperiod of 16/8 light dark and 32/22oC day night temperatures.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol, the extracted RNA was digested with DNAseI and purified using an RNAeasy kit.
Libraries were constructed with the Illumina TruSeq kit and 125 bp reads were obtained from an Illumina HiSeq 2500 sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
LR 3 h - L3b (GE)
|
| Data processing |
Reads were mapped to the Phytozome 3.1 sorghum genome sequence using CLC Genomics Workbench 8.5.1 giving an average of 28 M unique exon reads per sample.
A multi-group comparison was created and expression differences were assessed using CLC Genomics Workbench 8.5.1’s Extraction of Differential Gene Expression (EDGE) algorithm.
Genome_build: Phytozome 3.1 sorghum genome sequence
Supplementary_files_format_and_content: Processed data is in Excel (xlsx) format. The data includes feature IDs, EDGE test of Leaf Removed vs Intact Leaf samples at 1, 3 and 6 h, annotations, exon lengths, total and unique gene, exon and intron reads, and RPKM.
|
| |
|
| Submission date |
Mar 04, 2019 |
| Last update date |
Mar 06, 2019 |
| Contact name |
Scott Andrew Finlayson |
| E-mail(s) |
sfinlayson@tamu.edu
|
| Organization name |
Texas A&M University
|
| Department |
SOil and Crop Sciences
|
| Street address |
370 Olsen Blvd
|
| City |
College Station |
| State/province |
Texas |
| ZIP/Postal code |
77843-2474 |
| Country |
USA |
| |
|
| Platform ID |
GPL21615 |
| Series (1) |
| GSE127822 |
Sorghum axillary bud transcriptome response to leaf removal |
|
| Relations |
| BioSample |
SAMN11053032 |
| SRA |
SRX5463950 |
