|
| Status |
Public on Jun 21, 2010 |
| Title |
smallRNA-total_RNA-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Flowers (stage 1-12)
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
strain: Col-0 pAGO1:HA-AGO1
tissue: Flowers
developmental stage: stage 1-12
sample source: Total RNA
ChIP-seq antibody: none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNA were extracted from total RNA or HA-AGO1 complexes immunoprecipitated with anti-HA antibody (Roche clone 12CA5, catalog # 11583816001) by size fractionation using polyacrylamide gel electrophoresis. Small RNA were converted to DNA amplicons by serial adaptor ligation to both ends followed by RT-PCR. DNA amplicons were sequenced using an Ilumina Genome Analyzer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Small RNA from IP input sample
library selection: RT-PCR
|
| Data processing |
Small RNA sequences were parsed from Illumina sequencing data files through identification of the 3' adaptor boundary (the first six nucleotides of the 3' adaptor: CTGTAG) and mapped to the A. thaliana genome (TAIR9) using the CASHX pipeline. Only sequences that mapped perfectly to the A. thaliana genome were included in the analysis.
Processed data presented in .gff files. A .gff README file is linked to Series GSE22252 record.
|
| |
|
| 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 |
| |
|
| Platform ID |
GPL9302 |
| Series (1) |
| GSE22252 |
Global identification of Arabidopsis thaliana ARGONAUTE1-associated small RNA. |
|
| Relations |
| SRA |
SRX022363 |
| BioSample |
SAMN00016414 |
