|
| Status |
Public on Dec 30, 2010 |
| Title |
soybean_degradome-library |
| Sample type |
SRA |
| |
|
| Source name |
soybean seed
|
| Organism |
Glycine max |
| Characteristics |
cultivar: Heinong44
tissue: seed
developmental stage: 15 days after flowering
|
| Growth protocol |
Soybean seeds of (Glycine max) cultivar Heinong44 were directly planted in the Experimental Station of Institute of Genetics and Developmental Biology, Chinese Academy of Sciences in Beijing on May. Soybean seeds of 15 days after flowering (DAF) were collected
|
| Extracted molecule |
total RNA |
| Extraction protocol |
In brief, poly(A) RNA was extracted from 200 μg of total RNA using the Oligotex kit (Qiagen). A 5’ RNA adapter containing a MmeI recognition site was ligated to the poly(A) RNA possessing a 5’-phosphate, by T4 RNA ligase (Ambion), and the ligated products were repurified using the Oligotex kit. Five PCR cycles were then performed to amplify the reverse transcription products. The PCR products were digested with MmeI and ligated to a 3’ double DNA adapter. The ligation products were amplified by 20 PCR cycles and gel-purified for SBS sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
construction of degradome library from mRNA in soybean seed
|
| Data processing |
Only 20-21 nt sequences with high quality were collected for subsequent analysis. The raw sequences were first normalized to “reads per 10 million” (RP10M). The distinct reads that perfectly matched soybean cDNA sequences remained. The 15 nt of sequence upstream and downstream of the 5’ end of matched reads were extracted to constitute 30-nt sequence tags for searching corresponding miRNA. The CleaveLand pipeline was used to align the 30 nt sequence to soybean known miRNAs from miRBase and our newly identified miRNAs. All alignments with scores up to 7 and no mismatches at the cleavage site (between the 10th and 11th nucleotides) were considered candidate targets.
|
| |
|
| Submission date |
Dec 29, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Jinsong Zhang |
| E-mail(s) |
jszhang@genetics.ac.cn
|
| Organization name |
IGDB
|
| Street address |
No.1 West Beichen Road,Chaoyang District
|
| City |
beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL11192 |
| Series (1) |
| GSE25260 |
Identification of miRNAs and their target genes in developing seeds of soybean by deep sequencing |
|
| Relations |
| SRA |
SRX037167 |
| BioSample |
SAMN00189460 |
