|
| Status |
Public on Mar 14, 2007 |
| Title |
ns1-R mutant vs wild-type (ns-wt-SAM3-high-rep5) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
RNA from nonmutant
|
| Organism |
Zea mays |
| Characteristics |
scan with high laser power and PMT gain settings
|
| Growth protocol |
Maize seedlings of the highly introgressed ns 1:1 line (segregation ratio at 50% ns1-R and 50% nonmutant) were grown under the same controlled condition and harvested for laser microdissection at two weeks after germination.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted using the PicoPure™ RNA extraction kit, and two rounds of RNA amplification were performed using T7-RNA polymerase as described (Nakozano et al., 2003) with changes described in Moll et al., 2004.
|
| Label |
Cy3
|
| Label protocol |
2µg of amplified RNA were indirectly labeled by amino allyl incorporation as described (Nakazono et al, 2003). To remove dye bias, Cy dyes were swapped between the RNA samples
|
| |
|
| Channel 2 |
| Source name |
RNA from ns1-R
|
| Organism |
Zea mays |
| Characteristics |
scan with high laser power and PMT gain settings
|
| Growth protocol |
Maize seedlings of the highly introgressed ns 1:1 line (segregation ratio at 50% ns1-R and 50% nonmutant) were grown under the same controlled condition and harvested for laser microdissection at two weeks after germination.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted using the PicoPure™ RNA extraction kit, and two rounds of RNA amplification were performed using T7-RNA polymerase as described (Nakozano et al., 2003) with changes described in Moll et al., 2004.
|
| Label |
Cy5
|
| Label protocol |
2µg of amplified RNA were indirectly labeled by amino allyl incorporation as described (Nakazono et al, 2003). To remove dye bias, Cy dyes were swapped between the RNA samples
|
| |
|
| |
| Hybridization protocol |
Fluorescent targets were hybridized as described in the “cDNA microarray protocol” file at Schnable Lab website at Iowa State University.
|
| Scan protocol |
Scanned on an ScanArray 5000™ scanner.
Images were quantified using Digital Genome™ software
|
| Description |
Biological replicate 5 of 6.
|
| Data processing |
LOWESS normalized, followed by median centering so that expression measures would be comparable across slides. The lowess normalized data from each scan was used for a mixed linear model analysis (Wolfinger et al., 2001).
|
| |
|
| Submission date |
Mar 12, 2007 |
| Last update date |
Mar 13, 2007 |
| Contact name |
Michael J Scanlon |
| E-mail(s) |
[email protected]
|
| Phone |
607-254-1156
|
| Fax |
(607) 255-5407
|
| Organization name |
Cornell University
|
| Department |
Department of Plant Biology
|
| Street address |
140 Emerson Hall
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL3538 |
| Series (1) |
| GSE7248 |
Transcriptome analyses of narrow sheath shoot apical meristem (SAM) vs non-mutant SAM |
|
