|
| Status |
Public on May 14, 2015 |
| Title |
YS-Cold-24h |
| Sample type |
RNA |
| |
|
| Source name |
tea leaf
|
| Organism |
Camellia sinensis |
| Characteristics |
cultivar: Yingshuang
tissue: leaf
treatment: Cold-24h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each tissue sample was extracted using TRK-1001 kit (LC Sciences) according to the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
Labeling of total RNA was performed according to the protocol from LC Science for a single-color experiment with no modification.
|
| |
|
| Hybridization protocol |
Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.
|
| Scan protocol |
Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics)
|
| Data processing |
Data were analyzed by first subtracting the background, then the signals were normalized using a Lowess (locally weighted regression) filter. The raw microarray data set was filtered according to a standard procedure to exclude spots with minimum intensity. It was arbitrarily set to an intensity parameter of P100 for the miRNA microarray data. Spots with diameters less than 10 μm and flagged spots were also excluded from the analyses.
|
| |
|
| Submission date |
Dec 24, 2013 |
| Last update date |
May 14, 2015 |
| Contact name |
Yue Zhang |
| E-mail(s) |
2011204025@njau.edu.cn
|
| Organization name |
Nanjing Agricultural University
|
| Department |
Tea Science Research Institute
|
| Street address |
Weigang No.1
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL18106 |
| Series (2) |
| GSE53632 |
Identification and characterization of cold responsive microRNAs in tea plant (Camellia sinensis) based on high-throughput sequencing and their targets using degradome analysis [microarray] |
| GSE61719 |
Identification and characterization of cold responsive microRNAs in tea plant (Camellia sinensis) based on high-throughput sequencing and their targets using degradome analysis |
|
