|
| Status |
Public on Mar 11, 2010 |
| Title |
002194_3357_Koji_2d_3 |
| Sample type |
RNA |
| |
|
| Source name |
2 day wheat bran koji
|
| 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. A comaprison of gene expression between A. flavus NRRL3357 and A. oryzae RIB40 on wheat bran and field inoculated maize line B73. Wheat bran koji is commonly used for propagation of A. oryzae prior to fermentations. Opportunistic maize infection is part of the A. flavus lifestyle as a pathogen.
|
| 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 |
|
