|
| Status |
Public on Jun 26, 2012 |
| Title |
Lib 5 |
| Sample type |
SRA |
| |
|
| Source name |
whole rosette, three weeks old, strongly At-CHS silenced
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Ws-0 (CS915)
genotype: transgenic
ihprna construct: chss-guss^gusa-chsa
tissue: whole rosette
age: 3 weeks
|
| Treatment protocol |
Pooled 120 individual plants from ten independent T2 progenies.
|
| Growth protocol |
Light intensity of ~300 μE, 14h light/10h dark photoperiod, 15°C during the day and 5°C during the night.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The libraries were made using Small RNA Sample Prep Kits (Illumina Inc.; http://www.illumina.com/) following the manufacturer's protocol. 41 (Libs 0, 5 and 6) or 45 (Libs 1-4) cycles of Illumina sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Small RNA.
At-CHS silenced, strongly silenced.
|
| Data processing |
Sequences and intensity scores were extracted from the GAII image files using the standard Illumina IPAR pipeline.
Filtering for high-quality reads and adaptor trimming were done with a custom script.
FASTA files were generated based on analysis of calibrated peak intensities per channel in sig2 files.
All details of sig2 data processing are at http://atgc-illumina.googlecode.com/files/ILLUPA_Overview_AKozik_100108_A.pdf, slides 19-24, and in the script http://code.google.com/p/atgc-illumina/wiki/IlluminaFiltering .
Supplementary_files_format_and_content: FASTA files include clean trimmed high-quality reads that were used for the analysis and read counts.
|
| |
|
| Submission date |
Jun 25, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard Michelmore |
| Organization name |
University of California, Davis
|
| Department |
Genome Center
|
| Lab |
The Michelmore lab
|
| Street address |
Genome & Biomedical Sciences Facility, 451 East Health Sciences Drive
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL9302 |
| Series (1) |
| GSE38922 |
Distinctive profiles of small RNA couple inverted repeat-induced post-transcriptional gene silencing with endogenous RNA silencing pathways in Arabidopsis |
|
| Relations |
| SRA |
SRX155925 |
| BioSample |
SAMN01057697 |
