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| Status |
Public on Jun 21, 2010 |
| Title |
Global identification of Arabidopsis thaliana ARGONAUTE1-associated small RNA. |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Small RNA from total RNA (input fraction) and immunoprecipitated HA-AGO1-complexes (IP fraction) were identified using high-throughput sequencing-by-synthesis.
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| Overall design |
Two replicate input fraction samples were used as controls for two replicate IP fraction samples. Total RNA from input fractions and small RNA that co-immunoprecipitated with HA-AGO1 complexes were size fractionated by polyacrylamide gel electrophoresis to recover 18-24 nucleotide small RNA. 3' and then 5' adaptors were serially ligated on to each small RNA followed by PAGE purification. RT-PCR was used to convert RNA to DNA amplicons. Amplicons were sequenced using the Illumina GAIIx platform. Resulting reads were parsed and mapped to the A. thaliana genome (TAIR9) using the CASHX pipeline.
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| Contributor(s) |
Cuperus JT, Carbonell A, Fahlgren N, Garcia-Ruiz H, Burke RT, Takeda A, Sullivan CM, Gilbert SD, Montgomery TA, Carrington JC |
| Citation(s) |
20562854 |
| |
| Submission date |
Jun 09, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
James C Carrington |
| E-mail(s) |
jcarrington@danforthcenter.org
|
| Phone |
314-587-1202
|
| Organization name |
Donald Danforth Plant Science Center
|
| Lab |
James C. Carrington
|
| Street address |
975 North Warson Road
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63132 |
| Country |
USA |
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| Platforms (1) |
| GPL9302 |
Illumina Genome Analyzer II (Arabidopsis thaliana) |
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| Samples (4)
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| Relations |
| SRA |
SRP002667 |
| BioProject |
PRJNA128651 |
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