|
| Status |
Public on Mar 18, 2019 |
| Title |
Col-0_22C_ZT1_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Col-0_22C_ZT1
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype background: Col-0
genotype/variation: wild type
temperature: 22°C
time (hours): 1
tissue: 12-day-old whole seedling tissue
replicate: 3
|
| Treatment protocol |
Plants were exposed to temperature stress for 1 hour at 0 or 5 hours after lights on
|
| Growth protocol |
Arabidopsis plants were grown for 12 days in diurnal conditions at 22°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy plant mini kit were used to extract total RNA
Libraries were constructed using protocol adapted from: A high-throughput method for Illumina RNA-Seq library preparation. See Temporal dynamics of temperature stress responses in Arabidopsis for details.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
flowcell664_lane1_pair1_CGTGTGTT
processed data file:
cca1lhyData.xlsm
|
| Data processing |
Basic read processing
Filtering was performed with cutadapt with default settings
RNA-seqeuncing reads were aligned to the Araport11 gff file using TopHat2 (version 2.0.14) and Bowtie2 (version 2.2.5).
Relative gene expression was calculated using edgeR and limma
Genome_build: Araport 11 GFF (201606)
Supplementary_files_format_and_content: excel file with log2fold-change, false discovery rate, and counts per million by gene
|
| |
|
| Submission date |
Jun 19, 2018 |
| Last update date |
Mar 18, 2019 |
| Contact name |
Dawn Nagel |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Califonia, Riverside
|
| Department |
Botany and Plant Sciences
|
| Lab |
Dawn Nagel
|
| Street address |
3401 Watkins Avenue (Batchelor Hall Rm 1123)
|
| City |
Riverside |
| State/province |
CA |
| ZIP/Postal code |
92507 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE116004 |
Contribution of time of day and the circadian clock to the heat stress responsive transcriptome in Arabidopsis |
|
| Relations |
| BioSample |
SAMN09456140 |
| SRA |
SRX4240062 |
