|
| Status |
Public on Jan 04, 2019 |
| Title |
NC567_24 h |
| Sample type |
SRA |
| |
|
| Source name |
Leaf
|
| Organism |
Nicotiana tabacum |
| Characteristics |
developmental stage: 5-6-leaf stage
tissue: the third leaf from the top
time point: 24 h
stress: cold
|
| Treatment protocol |
6 ℃ with humidity of 80% (16/8 h, light/dark).
|
| Growth protocol |
Both NC567 and Taiyan8 were cultured in plastic pots in a ventilated greenhouse. The seedlings with 6-8 leaves were moved into a growth chamber (Binder, Tuttlingen, Germany) and cultured at about 6 ℃ with humidity of 80% (16/8 h, light/dark).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The third leaf from the top from three plants were collected at 0 h (as control) and 24 h after cold treatment, washed carefully, and separately frozen in liquid nitrogen and stored at 80 ℃ prior to RNA extraction.
Approximately 5 µg of small RNA of each group was used for library preparation and sequencing. Small RNA sized at 18–30 nt was gel-purified. 59 and 39 Illumina RNA adapters were ligated to the small RNA molecules. The adapter-ligated small RNAs were then reversely transcribed and amplified for 15 cycles with PCR. Then 4 small RNA libraries were constructed and sequenced according to the Illumina HiSeq 2500 platform sequencing protocols.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
Filtering of adaptors and low-quality sequence with fastx_toolkit-0.0.13.2
Alignment with miRBase, ncRNA, piRNA and Rfam databases using CLC genomics_workbench 6.1
Prediction of novel miRNAs with sRNA Toolkit
Expression analysis with DEGseq R combined with perl
Supplementary_files_format_and_content: annonated and normalized abundance file
|
| |
|
| Submission date |
Jan 04, 2018 |
| Last update date |
Jan 04, 2019 |
| Contact name |
Xianwen Zhang |
| E-mail(s) |
xianwenzhang@hunau.edu.cn
|
| Phone |
08613875856138
|
| Organization name |
Hunan Agricultural University
|
| Street address |
1 Nongda Road Furong district
|
| City |
Changsha |
| State/province |
Hunan |
| ZIP/Postal code |
410128 |
| Country |
China |
| |
|
| Platform ID |
GPL22345 |
| Series (1) |
| GSE108733 |
Comparative analysis of miRNA transcriptome in tobacco under cold stress |
|
| Relations |
| BioSample |
SAMN08290860 |
| SRA |
SRX3530822 |
