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Status |
Public on Sep 16, 2008 |
Title |
Anther 1.0mm ND101 msca1-fs Rep2 |
Sample type |
RNA |
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Source name |
Anther 1.0mm ND101 msca1-fs X9-50E
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Organism |
Zea mays |
Characteristics |
background: ND101
|
Treatment protocol |
None
|
Growth protocol |
Plants were dissected after growth outdoors at the Stanford summer field; tissues were collected and frozen in liquid nitrogen immediately.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from 30 - 60 mg of frozen tissues with Qiagen RNeasy Mini kit, digested with DNase I, and cleaned up with RNeasy columns.
|
Label |
Cy5
|
Label protocol |
Total RNA (500 ng) was amplified & labeled with either Cy5 or Cy3 using Agilent Low RNA Input Fluorescent Linear Amplification Kit.
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Hybridization protocol |
750 ng of each labeled target cRNA were hybridized for 17 h at 60C.
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Scan protocol |
Slides were scanned on an Agilent G2565AA microarray scanner as indicated in the manual. Images were processed with the Agilent Feature Extraction software.
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Description |
compare msca1 fertile sib to mutant at Anther 1.0mm stage
|
Data processing |
After removal of spots flagged by Feature Extraction as below background or saturated or outliers, median intensity values were normalized using loess method in limma R package (within arrays) and then with the quantile method (between arrays). Values were normalized again to the median intensity of hybridized probes on an array by array basis.
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Submission date |
Sep 12, 2008 |
Last update date |
Sep 16, 2008 |
Contact name |
John F Fernandes |
E-mail(s) |
jfernand@stanford.edu
|
Phone |
650-533-9376
|
Organization name |
Stanford University
|
Department |
Bio Sci
|
Lab |
Walbot
|
Street address |
385 Serra Mall
|
City |
Stanford |
State/province |
CA |
ZIP/Postal code |
94305 |
Country |
USA |
|
|
Platform ID |
GPL7297 |
Series (1) |
GSE12756 |
Transcriptome profiling of maize anthers using genetic ablation to analyze pre-meiotic and tapetal cell types |
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