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| Status |
Public on Feb 01, 2007 |
| Title |
Arabidopsis thaliana small RNAs sequences identified using high-throughput 454 sequencing technology |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
To determine the extent to which the major small RNA pathways functions across the Arabidopsis thaliana genome, small RNA populations from several tissues of wild-type (wt) and mutant plants were amplified by RT-PCR and sequenced using high-throughput 454 sequencing technology.
Keywords: small RNAs, high-throughput sequencing
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| Overall design |
Amplicons were prepared by 5' and 3' adaptor ligation and RT-PCR using small RNA fractions from inflorescence tissue (containing stage 1-12 flowers) of wt Col-0 plants, mutants with defects in each DCL gene (dcl1-7, dcl2-1, dcl3-1, dcl4-2), and mutants with defects in each RDR gene for which a function has been established (rdr1-1, rdr2-1, rdr6-15). Amplicons from whole seedlings (3 day post-germinations) were prepared from Col-0 and rdr6-15 plants. Small RNA preparations from leaf samples of Col-O that were either uninoculated or inoculated by Pseudomonas syringae pv tomato (DC3000hrcC) for 1 hr and 3 hr were also sequenced.
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| Web link |
http://asrp.cgrb.oregonstate.edu/db/
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| Contributor(s) |
Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, Carrington JC |
| Citation(s) |
17298187, 17299599, 17400893 |
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| Submission date |
Jan 08, 2007 |
| Last update date |
Mar 16, 2012 |
| Contact name |
James C Carrington |
| E-mail(s) |
jcarrington@danforthcenter.org
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| Phone |
314-587-1202
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| Organization name |
Donald Danforth Plant Science Center
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| Lab |
James C. Carrington
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| Street address |
975 North Warson Road
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| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63132 |
| Country |
USA |
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| Platforms (1) |
| GPL4732 |
Arabidopsis thaliana small RNAs sequences identified using high-throughput 454 sequencing technology |
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| Samples (14)
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| GSM154336 |
Col-0, inflorescence tissue (stage 1-12 flowers) |
| GSM154361 |
dcl1-7, inflorescence tissue (stage 1-12 flowers) |
| GSM154362 |
dcl2-1, inflorescence tissue (stage 1-12 flowers) |
| GSM154363 |
dcl3-1, inflorescence tissue (stage 1-12 flowers) |
| GSM154364 |
dcl4-2, inflorescence tissue (stage 1-12 flowers) |
| GSM154365 |
rdr1-1, inflorescence tissue (stage 1-12 flowers) |
| GSM154367 |
rdr2-1, inflorescence tissue (stage 1-12 flowers) |
| GSM154368 |
rdr6-15, inflorescence tissue (stage 1-12 flowers) |
| GSM154370 |
Col-0, leaf tissue |
| GSM154372 |
Col-0, leaf tissue, inoculated with Pseudomonas syringae pv. tomato (DC3000hrcC), 1 hr p.i. |
| GSM154374 |
Col-0, leaf tissue, inoculated with Pseudomonas syringae pv. tomato (DC3000hrcC), 3 hr p.i |
| GSM154375 |
Col-0, whole seedlings |
| GSM154376 |
rdr6-15, whole seedlings |
| GSM154377 |
Composite small RNA sequences |
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| Relations |
| BioProject |
PRJNA99059 |
| Supplementary data files not provided |
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