|
| Status |
Public on Feb 21, 2010 |
| Title |
antiAGO4 associated sRNAs (SL32) |
| Sample type |
SRA |
| |
|
| Source name |
IP floral
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: mixed stage inflorescence
fraction: IP
antibody: endogenous AGO4 Antibody
|
| Treatment protocol |
These samples are from immunopurifications of either AGO4, AGO6 and AGO9 in Arabidopsis thaliana or small RNAs isolated, cloned and sequenced from Arabidopsis.
|
| Growth protocol |
standard growth conditions (16hr light, 21 C)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The extract protocol varies for total sRNA and for immunopurifications (IP). If IP, proteins were purified with appropriate antibody and associated RNA was purified with Trizol reagent. If total sRNA, total RNA was extracted using Trizol reagent and small RNAs purified using mirVana (Ambion). For both of these types of samples, a 5' adapter was ligated, gel purified, followed by 3' adapter ligation, gel purification, 1st strand synthesis of RNA to create a cDNA library which was amplified with approximately 15 cycles of PCR. The PCR amplified library was then gel purified.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
small RNA sequencing
IP with endogenous AGO4 Antibody
raw data file: SL32.fq (fastq file)
|
| Data processing |
Small RNA adapters were removed using an exact match to the first 8bp of the 3' adapter (or the barcode + 3' adapter for multiplexed samples SL234B/C/F and SL235B/H). After adapter removal, reads were aligned to the Arabidopsis thaliana genome (TAIR v8) using SSAHA v3.1.
|
| |
|
| Submission date |
Jun 10, 2009 |
| Last update date |
Jun 11, 2013 |
| Contact name |
Krys Kelly |
| Organization name |
University of Cambridge
|
| Department |
Plant Sciences
|
| Lab |
Baulcombe Group
|
| Street address |
Downing Street
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 3EA |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9302 |
| Series (1) |
| GSE16545 |
Arabidopsis Argonaute4, Argonaute6 and Argonaute9 associated small RNAs |
|
| Relations |
| BioSample |
SAMN02198708 |
