|
| Status |
Public on Jun 30, 2016 |
| Title |
N 8h_mRNA-seq (ht) |
| Sample type |
SRA |
| |
|
| Source name |
China
|
| Organism |
Gossypium hirsutum |
| Characteristics |
genotype: Nan Dan Ba Di Da Hua
phenotype: heat tolerant
tissue: leaf
culture condition: 1/2´ Hoagland’s solution
|
| Treatment protocol |
After about 20 days, when the seedlings had produced three leaves, they were randomly divided into three groups. In the middle of the day (about 6 h after the onset of light), two group was transferred into a plant growth chamber and subjected to a constant elevated temperature of 45 °C for 4 and 8 h, and the remaining one was the control (28 °C).
|
| Growth protocol |
Pre-germinated seeds of each genotype were sown in 20 pots (1-L volume) (6 seeds per pot) containing a sterile mixture of sand and gardening soil in a KR-III phytotron (Henan Ke-rui, Zhengzhou, China) under the following conditions: 28/22 °C day/night temperatures, 60–80% relative humidity, and a 14-h/10-h light/dark cycle under 450 µmol× m−2× s−1 light intensity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were harvested directly into liquid nitrogen and stored at −80°C until used for RNA extraction.Total RNA was isolated from cotton leaf samples treated with either high temperature or 28°C (as a control) for 4 or 8 h using a modified CTAB method and purified using Qiagen RNeasy columns (Qiagen, Hilden, Germany to use with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
After filtering of low-quality and dirty raw reads, transcriptome de novo assembly was carried out using the paired-end assembly method as implemented in Trinity (http://trinityrnaseq.sourceforge.net/; trinityrnaseq_r2012-10-05) [123]. After removal of repeats from the spliced sequences, transcripts were obtained of the expected length and size.
|
| |
|
| Submission date |
Jun 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Du Xiongming |
| E-mail(s) |
dujeffrey8848@hotmail.com
|
| Organization name |
Institute of cotton research of CAAS
|
| Street address |
38# Huanghe Avenue
|
| City |
Anyang |
| State/province |
Henan |
| ZIP/Postal code |
455000 |
| Country |
China |
| |
|
| Platform ID |
GPL16485 |
| Series (1) |
| GSE70205 |
Identification of candidate thermotolerance genes during early seedling stage in upland cotton (Gossypium hirsutum L.) revealed by comparative transcriptome analysis |
|
| Relations |
| BioSample |
SAMN03787752 |
| SRA |
SRX1070719 |
