|
| Status |
Public on Sep 01, 2007 |
| Title |
B73 19 DAP endosperm tissue biological replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Zea mays 19 day after pollination endosperm tissue
|
| Organism |
Zea mays |
| Characteristics |
Stage: 19 day after pollination endosperm; Genotype: B73
|
| Growth protocol |
Endosperm tissues were isolated from kernels of inbreds Mo17 and B73, and hybrids Mo17xB73 and B73xMo17 for gene expression analysis. Samples were collected during August 2005 from field-grown maize plants grown on the St. Paul campus Agricultural Experiment Station. Inbred and hybrid crosses were performed at three different dates to produce biological replicates. The crosses for all genotypes within a biological replicate were performed within 30 minutes of each other. Six ears of each genotypes were harvested at 19 DAP. Six endosperms were collected from each of the six ears and pooled for a total of 36 endosperms from each genotype by biological replicate combination. All tissues were flash frozen in a dry-ice cooled ethanol bath, and subsequently stored at −80˚C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Initial isolation of 19 DAP endosperm RNAs involved a combination of phenol/chloroform extraction and the TRIzol procedure, and essentially followed published methods (Leiva-Neto et al. 2004). Briefly, powders for 19 DAP endosperm were homogenized in extraction buffer (50mM TRIS pH 8.0, 150mM LiCl, 5mM EDTA pH 8.0, 1% SDS), extracted twice with an equal volume of 1:1 phenol chloroform, extracted with an equal volume of chloroform, and then extracted with TRIzol according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA). The 19 DAP endosperm RNAs were further purified using the RNeasy protocol (Qiagen Corp., Valencia, CA). All purified RNA samples were quantified and qualified using the Nanodrop spectrophotometer (Nanodrop Technologies, Montchanin, DE) and agarose gel electrophoresis.
|
| Label |
biotin
|
| Label protocol |
Eight ug of total RNA was labeled for each hybridization using the One-Cycle cDNA Synthesis Kit, according to the manufacturer’s instructions (Affymetrix, Santa Clara CA).
|
| |
|
| Hybridization protocol |
Hybridization was performed according to the recommended Affymetrix protocols at the University of Minnesota Microarray facility.
|
| Scan protocol |
The Genechip 3000 scanner was used to scan each array
|
| Description |
No other relevant details
|
| Data processing |
MAS5.0 values are reported; the .cel file is also available
|
| |
|
| Submission date |
Jun 25, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Nathan M Springer |
| E-mail(s) |
springer@umn.edu
|
| Phone |
6126246241
|
| Fax |
6126251738
|
| Organization name |
University of Minnesota
|
| Department |
Plant Biology
|
| Street address |
1445 Gortner Ave
|
| City |
Saint Paul |
| State/province |
MN |
| ZIP/Postal code |
55108 |
| Country |
USA |
| |
|
| Platform ID |
GPL4032 |
| Series (2) |
| GSE8278 |
Non-additive and imprinted gene expression in hybrid maize endosperm_19DAP |
| GSE8308 |
Non-additive and imprinted gene expression in hybrid maize endosperm_13DAP and 19DAP |
|
