|
| Status |
Public on Mar 06, 2011 |
| Title |
Internode9_vs_Internode13_rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Internode 9
|
| Organism |
Zea mays |
| Characteristics |
line: B73
developmental stage: V13
tissue: internode 9
cell wall synthesis: secondary
|
| Treatment protocol |
No specific treatments.
|
| Growth protocol |
Maize inbred line B73 plants were grown in a greenhouse. Daylight was supplemented with overhead lighting using 400 W high-pressure sodium lamps for 16 h daily. Minimum temperatures were maintained at 25°C (day) and 18°C (night). Internode development was assessed using the vegetative identification system (Ritchie et al., 2005). At stage V13, the plants were harvested, the leaves and leaf sheath were removed and internodes 9 to 13 were excised, avoiding 1 cm either side of the node. The samples were frozen in liquid nitrogen and stored at -80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, Ca, USA) and purified using RNeasy MinElute Cleanup Kit columns (Qiagen, Valencia, CA, USA) according to a protocol recommended at www.maizearray.org.
|
| Label |
Cy3
|
| Label protocol |
1 μg RNA samples were used to make Cy3- and Cy5-labeled targets with a three-step protocol as follows: 1) cDNA was synthesized using an oligo-(d)T primer that incorporated the T7 promoter; 2) targets were amplified using in vitro transcription to produce aminoallyl-labeled cRNA; and 3) aminoallyl-labeled cRNA was coupled to Cy-labeled dyes. Details of these protocols can be found at: http://ag.arizona.edu/microarray/Microarraymethod1.doc
|
| |
|
| Channel 2 |
| Source name |
Internode 13
|
| Organism |
Zea mays |
| Characteristics |
line: B73
developmental stage: V13
tissue: internode 13
cell wall synthesis: primary
|
| Treatment protocol |
No specific treatments.
|
| Growth protocol |
Maize inbred line B73 plants were grown in a greenhouse. Daylight was supplemented with overhead lighting using 400 W high-pressure sodium lamps for 16 h daily. Minimum temperatures were maintained at 25°C (day) and 18°C (night). Internode development was assessed using the vegetative identification system (Ritchie et al., 2005). At stage V13, the plants were harvested, the leaves and leaf sheath were removed and internodes 9 to 13 were excised, avoiding 1 cm either side of the node. The samples were frozen in liquid nitrogen and stored at -80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, Ca, USA) and purified using RNeasy MinElute Cleanup Kit columns (Qiagen, Valencia, CA, USA) according to a protocol recommended at www.maizearray.org.
|
| Label |
Cy5
|
| Label protocol |
1 μg RNA samples were used to make Cy3- and Cy5-labeled targets with a three-step protocol as follows: 1) cDNA was synthesized using an oligo-(d)T primer that incorporated the T7 promoter; 2) targets were amplified using in vitro transcription to produce aminoallyl-labeled cRNA; and 3) aminoallyl-labeled cRNA was coupled to Cy-labeled dyes. Details of these protocols can be found at: http://ag.arizona.edu/microarray/Microarraymethod1.doc
|
| |
|
| |
| Hybridization protocol |
Labeled targets were mixed in hybridization buffer (2XSSC, Liquid Block, and 0.08% SDS). Arrays were hybridized at 55C for 8-12 hrs. The full hybridization protocol can be found at: http://ag.arizona.edu/microarray/Microarraymethod1.doc.
|
| Scan protocol |
Slides were scanned using a GenePix 4000 microarray scanner. Images were quantified using the Feature Extraction software GenePix Pro 6.0.
|
| Description |
Plant 2.
|
| Data processing |
LOESS normalizatizion was applied to log2 of processed Cy5/Cy3 signal. Bioconductor library limma was used.
|
| |
|
| Submission date |
Sep 07, 2010 |
| Last update date |
Mar 06, 2011 |
| Contact name |
Maurice Bosch |
| E-mail(s) |
mub@aber.ac.uk
|
| Organization name |
Aberystwyth University
|
| Department |
Institute of Biological, Environmental & Rural Sciences
|
| Street address |
Gogerddan
|
| City |
Aberystwyth |
| ZIP/Postal code |
SY23 3EB |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL6438 |
| Series (1) |
| GSE24014 |
Differential expression profiling between two maize internodes identifies genes involved in cell wall biogenesis |
|
