|
| Status |
Public on Sep 30, 2011 |
| Title |
Small RNAs from Zostera marina leaves |
| Sample type |
SRA |
| |
|
| Source name |
Leaves
|
| Organism |
Zostera marina |
| Characteristics |
tissue: Leaves
geographic location: All samples were harvested in the Indian River Bay, DE.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the Plant RNA Purification Reagent (Invitrogen). Quality of total RNA was evaluated by agarose gel electrophoresis, micro-electrophoresis (Agilent 2100 Bioanalyzer, Ambion) and O.D. measurements (Nanodrop ND-1000).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
ZMR1
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 |
Small RNA reads were analyzed after removal of 3' adapter (5' -TCGTATGCCGTCTTCTGCTTG) and filtering of 5' adapter (5'-GTTCAGAGTTCTACAGTCCGACGATC) or 3' adapter artefacts.
|
| |
|
| Submission date |
Sep 29, 2011 |
| Last update date |
Jun 11, 2013 |
| 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 |
GPL14640 |
| Series (2) |
| GSE28755 |
Comparative sequence analysis of plant small RNAs |
| GSE32480 |
High-throughput sequencing of small RNAs in Zostera marina |
|
| Relations |
| BioSample |
SAMN02198007 |
