|
| Status |
Public on Mar 11, 2010 |
| Title |
WKRep1 |
| Sample type |
RNA |
| |
|
| Source name |
Autoclaved B73 maize whole kernel
|
| 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: Charles Woloshuk. Whole kernels (WK), endosperm (ENDO) and germs of B73 were autoclaved, placed in vials, inoculated with 1 X 105 conidia, and incubated at 29 C (+/- 1 C) for 5 days.
|
| 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) |
drgeorgi@ncsu.edu
|
| 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 |
|
