|
| Status |
Public on Oct 01, 2008 |
| Title |
Pea_Shoot apical meristem 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Non-apical meristem tissues
|
| Organism |
Pisum sativum |
| Characteristics |
non-apical- meristem (NM) tissue consisted of primary stem, primary roots and mature leaves from 10-day-old garden pea (cultivar Torsdag) grown under greenhouse conditions in the uNiversity of Melbourne.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy Mini Kit was used for all RNA extraction
|
| Label |
Cy3
|
| Label protocol |
Target preparation and hybridization were performed in Australian Genome Research Facility Ltd (AGRF) according to the standard CombiMatrix protocol described in detail at www.combimatrix.com/docs/CustomArray4x2KProtocol.pdf. One microgram of total RNA from SAM or NM was labelled using the Kreatech’s ULS™ RNA ampULSe kit to generate Cy5 or Cy3 labelled targets.
|
| |
|
| Channel 2 |
| Source name |
Shoot apical meristem
|
| Organism |
Pisum sativum |
| Characteristics |
micro-dissected shoot apical mersietm from 10-day-old garden pea (cultivar Torsdag) grown under the greenhouse conditions in teh university fo Melbourne.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy Mini Kit was used for all RNA extraction
|
| Label |
Cy5
|
| Label protocol |
Target preparation and hybridization were performed in Australian Genome Research Facility Ltd (AGRF) according to the standard CombiMatrix protocol described in detail at www.combimatrix.com/docs/CustomArray4x2KProtocol.pdf. One microgram of total RNA from SAM or NM was labelled using the Kreatech’s ULS™ RNA ampULSe kit to generate Cy5 or Cy3 labelled targets.
|
| |
|
| |
| Hybridization protocol |
Carried out according to protocol at www.combimatrix.com
|
| Scan protocol |
The Cy5- and Cy3-hybridized chip was then scanned using Genepix 4000B microarray scanner (Axon Instruments, CA, USA) according to manufacturer’s instructions. The generated tiff image files were then imported into Combimatrix Microarray Imager to produce intensity data.
|
| Description |
The Cy5- or Cy3-labelled cDNA was then hybridized to different sector of the chip according to a balanced block design dual label experiment scheme (Cochran & Cox, 1992):
Sector 1: Cy3-SAM A vs Cy5-NM A
Sector 2: Cy5-SAM B vs Cy3-NM B
Sector 3: Cy3-SAM C vs Cy5-NM C
Sector 4: Cy5-SAM D vs Cy3-NM D
|
| Data processing |
The LimmaGUI software, which is an implementation of the Empirical Bayes linear modelling approach, was used for subsequent statistical analysis of the resulting data (Wettenhall & Smyth, 2004). A robust spline method was chosen for within array normalization and a least-square linear model fit was computed with the p-value adjusted using the Benjamini- Hochberg procedure.
|
| |
|
| Submission date |
Oct 11, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Chui E WONG |
| E-mail(s) |
acewong@unimelb.edu.au
|
| Organization name |
University of Melbourne
|
| Department |
Land and Food
|
| Lab |
Plant Molecular Biology and Biotechnology Group
|
| Street address |
University of Melbourne
|
| City |
Parkville |
| State/province |
Victoria |
| ZIP/Postal code |
3010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL5976 |
| Series (1) |
| GSE9278 |
Transcript profiling of the pea shoot apical meristem highlights processes underlying its function and maintenance |
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