|
| Status |
Public on Apr 19, 2011 |
| Title |
WT-seedling |
| Sample type |
SRA |
| |
|
| Source name |
total seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedling
smrna: total small RNAs
|
| Growth protocol |
Flowers were collected from 6-week-old plants grown on soil in a growth chamber under 12 hr light/12 hr dark at 21°C. Leaves and roots were harvested from 4-week-old plants grown hydroponically under 12 hr light/12 hr dark at 21°C in the MGRL medium. Seedlings were grown on MS plates in a growth chamber under 16 hr light/8 hr dark at 21°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For two-step purification of AGO/smRNA complexes, cleared extracts were fractioned on Superdex 200 10/300 columns (Akta-FPLC, GE) and further immunoprecipitated. After size-fractionation, total RNA or RNA recovered from the purified AGO-smRNA complexes were ligated to 3'² adapter (AppTCGTATGCCGTCTTCTGCTTG-L) and 5'² adapter (rGrUrUrCrArGrArGrUrUrCrUrArCrArGrUrCrCrGrArCrGrArUrC) sequentially. The ligated products were amplified by RT-PCR and used for Illumina's deep sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
smRNA sequencing data of total smRNAs in seedlings
|
| Data processing |
Adapters were removed by Perl script, if a hit with at most 1 mismatch to the first 4-nt of the adapter sequence could be found. After adapter removal, only 19-28 nt reads were aligned to the Arabidopsis thaliana genome (TAIR9) using C program. The small RNAs with perfect genomic matches are used for further analysis.
|
| |
|
| Submission date |
Apr 13, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Huan Wang |
| E-mail(s) |
hwang01@rockefeller.edu
|
| Organization name |
The Rockefeller University
|
| Lab |
Chua Nam-Hai
|
| Street address |
1230 York Avenue
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL9302 |
| Series (1) |
| GSE28591 |
Characterization of AGO1-/AGO4-associated smRNAs |
|
| Relations |
| SRA |
SRX058638 |
| BioSample |
SAMN00260307 |
