|
| Status |
Public on May 10, 2011 |
| Title |
Small RNAs from Populus trichocarpa xylem |
| Sample type |
SRA |
| |
|
| Source name |
Xylem
|
| Organism |
Populus trichocarpa |
| Characteristics |
tissue: xylem
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the TriReagent (Molecular Research Center) for leaves and phloem sap and the Plant RNA Purification Reagent (Invitrogen) for flowers. 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 |
Xylem
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 |
Apr 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 |
GPL13473 |
| Series (2) |
| GSE28755 |
Comparative sequence analysis of plant small RNAs |
| GSE28984 |
High-throughput sequencing of small RNAs in Populus trichocarpa |
|
| Relations |
| BioSample |
SAMN02198373 |
