|
| Status |
Public on Mar 31, 2022 |
| Title |
DT0hRep1 |
| Sample type |
SRA |
| |
|
| Source name |
leaf tissue
|
| Organism |
Panicum virgatum |
| Characteristics |
developmental stage: E3
tissue: leaf
treatment: drought
biomaterial provider: Robert Nobel Foundation
|
| Treatment protocol |
The control and drought treated plants were arranged in one growth chamber and palnts with drought and heat treatment in a separate chamber
|
| Growth protocol |
The ramets of lowland ecotype Alamo, AP13 genotype of switcghrass were transplanted in 3GP nursery pots and later transferred to the green house for optimum conditions at the Samuel Roberts Noble Foundation in Ardmore, Oklahoma.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from all samples, contamination of genomic DNA removed by DNAase treatment, quality of RNA's checked, and 1 µg of RNA used for cDNA sythnesis.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA Sample Preparation Kit following manufacturers protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The libraries were sequenced on Illumina HiSeq 2500 platform with 101 bp paired-end reads.
FASTX-Toolkit was used to perform quality control for RNA-Seq data w8ith at least 30 base quality score and at least 50 bps of read length.
TopHat was used to align the reads to the switchgrass reference genome
FPKM values were calculated using the Cufflinks
Reads counts performed usign HTSeq
Genome_build: Pvirgatum_450_v4.1 (https://phytozome-next.jgi.doe.gov/info/Pvirgatum_v4_1)
Supplementary_files_format_and_content: txt
|
| |
|
| Submission date |
May 11, 2021 |
| Last update date |
Mar 31, 2022 |
| Contact name |
Shaojun Xie |
| E-mail(s) |
[email protected]
|
| Phone |
7657140672
|
| Organization name |
Purdue University
|
| Street address |
3135 Decatur Street
|
| City |
WEST LAFAYETTE |
| State/province |
Indiana |
| ZIP/Postal code |
47906 |
| Country |
USA |
| |
|
| Platform ID |
GPL24761 |
| Series (1) |
| GSE174278 |
RNA-Seq analysis of switchgrass transcriptome in response to single drought and combinations of drought and heat stress |
|
| Relations |
| BioSample |
SAMN19109886 |
| SRA |
SRX10861377 |
