|
| Status |
Public on Sep 19, 2012 |
| Title |
Osmotic leaf |
| Sample type |
SRA |
| |
|
| Source name |
Osmotic leaf
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: leaf
|
| Treatment protocol |
Thirty-day-old plants were subjected to high osmotic stress by adding 0.3M mannitol to the basal MGRL medium for 3 hr in the light.
|
| Growth protocol |
Plants were grown at 22°C with a 150 μmol m-2 S-1 fluorescence rate and under 12 hour/12 hour light dark cycle in MGRL hydroponic medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
3 biological replicates were pooled and total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s protocol. Small RNAs (18 to 28 nt) from 40 μg total RNA were separated and then fractionated using 15% polyacrylamide urea gel. Subsequent steps were carried out by the protocol of Digital Gene Expression for Small RNA Sample Preparation (Illumina). Qualities and quantities of individual sRNA libraries were confirmed using Bioanalyzer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
base-call using Illumina's RTA package
adapter sequence was trimmed by Perl script
smRNA reads were aligned to Arabidopsis TAIR9 genome using C program
read counts are normalized to per million mapped reads
Genome_build: TAIR9
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each smRNA
|
| |
|
| Submission date |
Mar 16, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Huan Wang |
| E-mail(s) |
[email protected]
|
| 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 |
| |
|
| Platform ID |
GPL11221 |
| Series (1) |
| GSE36560 |
smRNA under high osmotic stress |
|
| Relations |
| SRA |
SRX130016 |
| BioSample |
SAMN00828849 |
