|
| Status |
Public on Mar 15, 2017 |
| Title |
WT LF3h rep1 |
| Sample type |
SRA |
| |
|
| Source name |
flower buds at stages 10-12
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: Wild-type
treatment: treated at 37C for 3h
tissue: flower bud
developmental stage: flower stages 10-12
ecotype: Col-0
|
| Treatment protocol |
Flowering plants were treated at 37 0C for 3 hours, and the control were taken at 22C. After heat shock, early flower (EF), late flower (LF) and rosette leaf (RL) were collected immediately and put into the liquid nitrogen.
|
| Growth protocol |
Seeds were sown into soil before stratified at 4 0C for two days, and cultivated under standard growth conditions (22 0C, 16/8 h day/night photoperiod, 60% humidity).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Plant materials were ground in liquid nitrogen, and total RNA was extracted with Trizol.
The cDNA libraries were constructed and sequenced with Illumina HiSeq3000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
RNA-seq reads were aligned to the Arabidopsis thaliana reference genome using TopHat (version 2.0.13)
Uniquely aligned reads were counted for each annotated gene using the program htseq-count from the python package HTSeq
Genome_build: TAIR10
Supplementary_files_format_and_content: gene_readCount.txt: Tab-delimited text file with each row representing a gene and each column a sample; sample names were shown on the head line (Abbr.: RL, rosette leaf; EF, early flower; LF, late flower)
|
| |
|
| Submission date |
Jan 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Hongxing Yang |
| E-mail(s) |
[email protected]
|
| Organization name |
Shanghai Chenshan Botanical Garden
|
| Street address |
3888 Chenhua Rd, Songjiang District
|
| City |
Shanghai |
| State/province |
- |
| ZIP/Postal code |
201602 |
| Country |
China |
| |
|
| Platform ID |
GPL21179 |
| Series (1) |
| GSE94015 |
Tissue-Specific Transcriptomics Reveals Role of the Unfolded Protein Response in Maintaining Fertility upon Heat Stress in Arabidopsis |
|
| Relations |
| BioSample |
SAMN06252782 |
| SRA |
SRX2513396 |
