|
| Status |
Public on Aug 16, 2008 |
| Title |
HA-AGO2 Input Fraction Small RNA |
| Sample type |
RNA |
| |
|
| Source name |
Inflorescence tissue: flower stages 1-12
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Col-0 ecotype transformed with AGO2:HA-AGO2
|
| Growth protocol |
Transgenic plants were grown on MS medium containing hygromycin (50 ug/ml) for 7 days, transferred to soil, and maintained in a standard greenhouse with 16 hr light/8 hr dark supplemental light cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Inflorescence tissue (flower stages 1-12) from zip-1 AGO7:HA-AGO7- or Col-0 AGO2:HA-AGO2-transformed plants was ground in lysis buffer. Cell debris was removed by centrifugation for 10 min at 12,000 g and the supernatant was partitioned into input and immunoprecipitation fractions. RNA was isolated immediately from the input fraction by phenol/chloroform extraction, followed by ethanol precipitation. HA-AGO7 and HA-AGO2 were immunoprecipitated using HA antibody and Protein A agarose beads. Beads were treated with proteinase K. RNA was isolated from the supernatant. Small RNA were fractionated on denaturing 17% polyacrylamide gels. Amplicons for sequencing were prepared by 5’ and 3’ adaptor ligations followed by RT-PCR. Sequencing-by-synthesis was done using an Illumina 1G Genome Analyzer.
|
| Label |
not applicable
|
| Label protocol |
not applicable
|
| |
|
| Hybridization protocol |
not applicable
|
| Scan protocol |
not applicable
|
| Description |
HA-AGO2 Input Fraction Small RNA
|
| Data processing |
Small RNA sequences were parsed from Illumina sequencing data files through identification of adaptor boundaries. Only sequences that mapped to the Arabidopsis thaliana Col-0 genome were included in the analysis.
|
| |
|
| Submission date |
Jul 08, 2008 |
| Last update date |
Aug 15, 2008 |
| 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 |
| |
|
| Platform ID |
GPL7029 |
| Series (1) |
| GSE12037 |
ARGONAUTE-small RNA Interactions in Arabidopsis thaliana Identified by High-Throughput Sequencing |
|
