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Sample GSM320079 Query DataSets for GSM320079
Status Public on Sep 16, 2008
Title Anther 1.0mm ND101 msca1-fs Rep2
Sample type RNA
 
Source name Anther 1.0mm ND101 msca1-fs X9-50E
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.
 
Hybridization protocol 750 ng of each labeled target cRNA were hybridized for 17 h at 60C.
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.
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.
 
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

Data table header descriptions
ID_REF
VALUE Median intensities for each channel were normalized within each array using loess and between arrays using quantile method. Normalized values were divided by the median intensity for the array.

Data table
ID_REF VALUE
1 0.115253437
2
3 0.518385396
4 0.562183803
5 0.675676695
6 -0.380067861
7
8
9 0.022036479
10 -0.220976065
11 0.316853797
12 -0.238012556
13 1.615013082
14
15 2.080133766
16 0.494886886
17 0.837821123
18 -0.163120484
19 0.521316242
20 -0.237064653

Total number of rows: 22575

Table truncated, full table size 374 Kbytes.




Supplementary file Size Download File type/resource
GSM320079.txt.gz 4.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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