|
| Status |
Public on Mar 11, 2010 |
| Title |
001773_B73_Af_Rep2_48hrs |
| Sample type |
RNA |
| |
|
| Source name |
48 h maize B73 infection
|
| Organism |
Aspergillus flavus |
| Characteristics |
strain: NRRL3357
|
| Treatment protocol |
see description column
|
| Growth protocol |
see description column
|
| Extracted molecule |
total RNA |
| Extraction protocol |
see description column: For total RNA extraction the Qiagen RNeasy kit RNA cleanup protocol was typically used, for most samples a phenol chloroform extraction protocol preceeded use of the RNeasy kit. For some samples phenol chloroform extractions and LiCl precipitation was used to purify RNA, this protocol is available from http://www.aspergillusflavus.org/protocols/.
|
| Label |
biotin
|
| Label protocol |
Purdue Genomics Core Facility, Standard Affymetrix protocols were followed for hybridization of single-stranded cRNA to the single-stranded DNA oligonucleotides on the Affymetrix GeneChip® and to generate .DAT and .CEL files (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
|
| |
|
| Hybridization protocol |
Purdue Genomics Core Facility, Standard Affymetrix protocols were followed for hybridization of single-stranded cRNA to the single-stranded DNA oligonucleotides on the Affymetrix GeneChip® and to generate .DAT and .CEL files (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
|
| Scan protocol |
Purdue Genomics Core Facility, Standard Affymetrix protocols were followed for hybridization of single-stranded cRNA to the single-stranded DNA oligonucleotides on the Affymetrix GeneChip® and to generate .DAT and .CEL files (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).
|
| Description |
Investigator: Gary Payne. Inbred line B73 was planted at the Central Crops Research Station at Clayton, NC during the 2006, 2007, and 2008 growing season. The field was laid out in a randomized block design. Each block represented a biological rep; all experiments had a total of three replicates. Corn was hand pollinated to ensure all experimental ears were at the same stage of development. Ear selection for inoculation was based on date of pollination. Ears identified at the blister, milk, dough, and dent stages were used for each treatment. Ears within +/- 1 day of pollination were husked such that the husk remained attached. The exposed pin-bar needles were dipped into either a 1x106 spores/mL conidial suspension. The needles were then inserted into a row of kernels, introducing approximately 11-13 conidia into each kernel. Five rows were inoculated per ear. Using a rubber band, the husk was repositioned around the ear and a pollinating bag placed over the ear. At the late milk-early dough stage of development, kernels were inoculated with A.flavus. Harvesting took place 48, 60, 72, and 96 hours after inoculation. Only two replicates were used in the analysis due to the lack of infection in one of the replicates.
|
| Data processing |
RMA background correction, log2 transformation, quantile normalization, median polish probe summary, using JMP Genomics v3.0
|
| |
|
| Submission date |
May 11, 2009 |
| Last update date |
Mar 11, 2010 |
| Contact name |
David Ryan Georgianna |
| E-mail(s) |
[email protected]
|
| Phone |
919-515-6995
|
| URL |
http://www.aspergillusflavus.org
|
| Organization name |
North Carolina State University
|
| Department |
Plant Pathology
|
| Lab |
Center for Integrated Fungal Research - Gary Payne
|
| Street address |
851 Main Campus Dr
|
| City |
Raleigh |
| State/province |
NC |
| ZIP/Postal code |
27695 |
| Country |
USA |
| |
|
| Platform ID |
GPL8345 |
| Series (1) |
| GSE15435 |
Diverse expression patterns for secondary metabolism gene clusters from Aspergillus |
|
