|
| Status |
Public on Dec 22, 2010 |
| Title |
relative expression ratio of pupa to the fifth larva |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
RNA from the first day of pupation
|
| Organism |
Bombyx mori |
| Characteristics |
strain: Dazao P50
developmental stage: pupa
|
| Growth protocol |
Bombyx mori strain Dazao P50 were raised in 25 ℃ with light/dark 14/10h, 70% relative humidity after egg hatching.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent following manufacturer's instructions
|
| Label |
Cy5,Cy3
|
| Label protocol |
Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using YM30 column (Millipore) before hybridization.
|
| |
|
| Channel 2 |
| Source name |
RNA from the fifth instar larva
|
| Organism |
Bombyx mori |
| Characteristics |
strain: Dazao P50
developmental stage: larva, fifth instar
|
| Growth protocol |
Bombyx mori strain Dazao P50 were raised in 25 ℃ with light/dark 14/10h, 70% relative humidity after egg hatching.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent following manufacturer's instructions
|
| Label |
Cy3,Cy5
|
| Label protocol |
Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using YM30 column (Millipore) before hybridization.
|
| |
|
| |
| Hybridization protocol |
Labelled cDNA hybridized using the BioMixer™ Ⅱ system (Capitalbio). Slides placed in shaking water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1 % SDS), 1x SSC, 0.2x SSC and 0.1x SSC, each at 37 °C for 5 min prior to drying and scanning.
|
| Scan protocol |
Arrays scanned using an LuxScan-10K/A scanner (Capitalbio)
|
| Description |
Analysis used larva5 RNA as control sample for comparison to the sample of pupa
|
| Data processing |
Data analysis was carried out using Imagene version Genepix5.1 software. For each slide, spots flagged bad by Genepix were removed from the latter analysis step. Only those genes expressed at least two independent replications were kept for further analysis. Any intensity which was zero or negative after background subtraction was set equal to half the minimum of the positive corrected intensities for that array. Normalization of two channels of each array was done using global LOWESS method with R language. The vsn method was performed for normalization between arrays. R language was used.
|
| |
|
| Submission date |
Jul 13, 2010 |
| Last update date |
Jan 03, 2011 |
| Contact name |
Yunchao Kan |
| E-mail(s) |
yckan1974@nynu.edu.cn
|
| Organization name |
China-UK-NYNU-RRes Joint Libratory of insect biology
|
| Street address |
Wolong road 1638
|
| City |
Nanyang |
| State/province |
Henan |
| ZIP/Postal code |
473061 |
| Country |
China |
| |
|
| Platform ID |
GPL10677 |
| Series (2) |
| GSE22912 |
Expression of 50-500nt ncRNAs in silkworm Bombyx mori during two developmental transitions |
| GSE22913 |
Expression of 50-500nt ncRNAs in silkworm Bombyx mori: developmental time courses |
|
