 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 19, 2011 |
| Title |
Characterization of AGO1-/AGO4-associated smRNAs |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
To fully characterize smRNAs associated with AGO1 and AGO4, we developed a two-step protocol to purify AGO/smRNA complexes from flowers, leaves, roots and seedlings with enhanced purity, and sequenced the smRNAs by Illuminaâs technology. We identified some additional miRNAs, collateral miRNAs encoded in known miRNA precursors, phased smRNA clusters and nat-siRNAs. Organ specific sequencing provided digital expression profiles of all obtained smRNAs, especially miRNAs.
|
| |
|
| Overall design |
We used extracts from Arabidopsis flowers, leaves and roots as well as ten-day old seedlings to purify smRNAs associated with AGO1 and AGO4 protein complexes using a two-step immunoprecipitation method.
|
| |
|
| Contributor(s) |
Wang H, Zhang X, Liu J, Kiba T, Woo J, Ojo T, Hafner M, Tuschl T, Chua N, Wang X |
| Citation(s) |
21457371 |
| 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 |
| |
|
| Platforms (1) |
| GPL9302 |
Illumina Genome Analyzer II (Arabidopsis thaliana) |
|
| Samples (14)
|
| GSM707681 |
WT-seedling |
| GSM707682 |
Two-step_purification_AGO1-associated_sRNAs_flower |
| GSM707683 |
Two-step_purification_AGO1-associated_sRNAs_leaf |
| GSM707684 |
Two-step_purification_AGO1-associated_sRNAs_root |
| GSM707685 |
Two-step_purification_AGO1-associated_sRNAs_seedling |
| GSM707686 |
Two-step_purification_AGO4-associated_sRNAs_flower |
| GSM707687 |
Two-step_purification_AGO4-associated_sRNAs_leaf |
| GSM707688 |
Two-step_purification_AGO4-associated_sRNAs_root |
| GSM707689 |
Two-step_purification_AGO4-associated_sRNAs_seedling |
| GSM707690 |
IP_AGO1-associated_sRNAs_flower |
| GSM707691 |
IP_AGO1-associated_sRNAs_root |
|
| Relations |
| SRA |
SRP006477 |
| BioProject |
PRJNA139119 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE28591_RAW.tar |
158.3 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...