|
| Status |
Public on Feb 15, 2011 |
| Title |
wheat_leaf_insensitive_1H |
| Sample type |
SRA |
| |
|
| Source name |
wheat young leaf
|
| Organism |
Triticum aestivum |
| Characteristics |
line: TAM (insensitive to heat stress)
age: two week old
tissue: leaf
stress: 40°C (heat stress)
time: 1 hour
|
| Treatment protocol |
For powdery mildew infection, one isolate of Erysiphe graminis f. sp. tritici (Egt) (Isolate E09) was maintained on the wheat cultivar Fidel by weekly transfer to new plants. Inoculations were performed at a density of 100-150 conidia/mm2 by brushing plants. Leaves were collected at 12 hours after infection. For heat stress,the seedlings were subjected to 40°C (heat stress) for 1 hour and returned to normal conditions for 2 hours.
|
| Growth protocol |
Hexaploid wheat (Triticum aestivum L.) line ‘8866’ (S)(susceptible to wheat powdery mildew), ‘Pm30’ (Resistant to wheat powdery mildew), and ‘TAM’ (tolerant to heat stress) were grown in a growth chamber at a relative humidity of 75% and 26/20℃ day and night temperature with light intensity of 3000 lx. 2 week-old plants were used for all experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the frozen leaves by using Trizol agent (TaKaRa, Inc., Dalian, China) according to the manufacturer’s instructions. Cloning of the small RNAs was performed as described by Sunkar and Zhu. Briefly, low molecular weight RNA was enriched by 0.5 M NaCl and 10% PEG8000 precipitation. About 100 μg low molecular weight RNA was separated on a denaturing 15% polyacrylamide gel. Labeled RNA oligonucleotides with 18 and 26 nt were used as size standards. The nucleotides from 18 to 26 nt were excised, and RNA was eluted overnight with 0.4M NaCl at 4˚C. The RNA was dephosphorylated by alkaline phosphatase (New England Biolabs Inc, Beijing China) and recovered by ethanol precipitated. The small RNAs were then ligated sequentially to RNA/DNA chimeric oligonucleotide adapters, and then reverse transcription was preformed, followed by PCR amplification. The resulting PCR products were sequenced using Solexa technology.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
TAM
|
| Data processing |
Automated base calling of the raw sequence and vector removal were performed with PHRED and CROSS MATCH programs. Trimmed 3′ and 5′ adapters sequences, removed RNAs less than 17 nt and polyA , only sequences longer than 17 nt with a unique ID were used for further analysis.
Processed data represents clean tags, 18-30 nt, tab delimited, sequence | count | length.
|
| |
|
| Submission date |
Feb 15, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
mingming xin |
| E-mail(s) |
xmmlyac@126.com
|
| Phone |
86-010-62731353
|
| Organization name |
China Agricultrual University
|
| Department |
plant genetics and breeding
|
| Lab |
wheat genetics and genomics
|
| Street address |
YUAN MING YUAN WEST ROAD 2, HAIDIAN DISTRICT
|
| City |
BEIJING |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL10467 |
| Series (2) |
| GSE27327 |
Genome-wide sequencing small RNAs in response to powdery mildew and heat stress in wheat |
| GSE27339 |
Wheat response to powdery mildew infection and heat stress |
|
| Relations |
| SRA |
SRX043495 |
| BioSample |
SAMN00215987 |
