|
| Status |
Public on Jul 01, 2017 |
| Title |
S. viridis A10.1 LLHC-F ZT28 REP1 |
| Sample type |
SRA |
| |
|
| Source name |
Leaf Tissue
|
| Organism |
Setaria viridis |
| Characteristics |
tissue: Leaf
accession: A10.1
sample age: 10 Days After Planting
treatment: 12 hour thermocycles (12h 32 deg C/ 12h 22 deg C)
|
| Growth protocol |
Plants were grown under either 12 hour photocycles (12h light/12h dark) or 12 hour thermocycles (12h 32 deg C/ 12h 22 deg C) then sampled every 2 hours for 48 hours under constant light and constant temperature conditions (32 deg C). Photocycle entrained samples are labeled LDHH-F, and thermocycle entrained samples are entrained LLHC-F.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Wang et al. 2012; http://dx.doi.org/10.1371/journal.pone.0026426
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
BBTools (v36.20) using parameters: ktrim=r k=23 mink=11 hdist=1 tpe tbo ktrim=l k=23 mink=11 hdist=1 tpe tbo qtrim=rl trimq=20 minlen=20 (Bushnell, 2016). Any parameters not specified were run as default.
Kallisto (v 0.42.4; (Bray et al., 2016)) was used to index the transcripts with the default parameters and the Setaria viridis transcripts fasta file (Sviridis_311_v1.1) from Phytozome (Goodstein et al., 2012).
Kallisto (v 0.42.4; (Bray et al., 2016)) was used to quantify reads with parameters:-t 40 -b 100. Any parameters not specified were run as default.
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Apr 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Malia Gehan |
| E-mail(s) |
mgehan@danforthcenter.org
|
| Organization name |
Donald Danforth Plant Science Center
|
| Street address |
975 N Warson Road
|
| City |
St. Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63132 |
| Country |
USA |
| |
|
| Platform ID |
GPL21478 |
| Series (1) |
| GSE97739 |
Setaria viridis (A10.1) circadian expression after light or temperature entrainment |
|
| Relations |
| BioSample |
SAMN06718785 |
| SRA |
SRX2734604 |
