|
| Status |
Public on Apr 24, 2014 |
| Title |
Small RNAs from Petunia leaves |
| Sample type |
SRA |
| |
|
| Source name |
Leaves
|
| Organism |
Petunia x hybrida |
| Characteristics |
tissue: Leaves
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the Plant RNA Purification Reagent (Invitrogen). Low molecular weight RNA was gel-sized in the ~18-33 nt range. Quality of total RNA was evaluated by agarose gel electrophoresis, micro-electrophoresis (Agilent 2100 Bioanalyzer, Ambion) and O.D. measurements (Nanodrop ND-1000).
Small RNA libraries were constructed at Illumina using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Total RNA was submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. Low molecular weight RNA was gel-sized in the ~18-33 nt range. The small RNA library was sequenced with the Sequencing-by-synthesis (SBS) technology by Illumina.
|
| Data processing |
A custom script was designed to trim 3' adapters from native illumina short reads as well as detect and remove 5' or 3' adapter artefacts.
|
| |
|
| Submission date |
Apr 24, 2014 |
| Last update date |
Apr 24, 2014 |
| Contact name |
Emanuele De Paoli |
| E-mail(s) |
emanuele.depaoli@gmail.com
|
| Phone |
00390432558676
|
| Organization name |
University of Udine
|
| Department |
Agricultural, Food, Environmental and Animal Sciences
|
| Lab |
E. De Paoli
|
| Street address |
via delle Scienze 206
|
| City |
Udine |
| State/province |
UDINE |
| ZIP/Postal code |
33100 |
| Country |
Italy |
| |
|
| Platform ID |
GPL9397 |
| Series (2) |
| GSE28755 |
Comparative sequence analysis of plant small RNAs |
| GSE57052 |
High-throughput sequencing of small RNAs in Petunia |
|
| Relations |
| BioSample |
SAMN02736849 |
