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Sample GSM357694 Query DataSets for GSM357694
Status Public on Nov 11, 2010
Title Anther at M1, biological rep1
Sample type RNA
 
Source name Anther, pollen mother cells at meiotic leptotene stage
Organism Oryza sativa
Characteristics cultivar: Nipponbare
Treatment protocol Tissue samples were collected on July - October. Collected biological samples were frozen in liquid nitrogen and kept -80C until RNA extraction.
Growth protocol Plants were grown in paddy fields under normal condition at Mishima, Japan.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with RNeasy plant mini kit (Qiagen) according to manufacturer's protocol.
Label Cy3
Label protocol Cy3-labeled cRNA were prepared from 100 ng total RNA using Low RNA Input Linear Amp Kit (Agilent) according to manufacturer's protocol .
 
Hybridization protocol Fragmentation and hybridization was carried out with Gene Expression Hybridization Kit (Agilent). 400 ng of labeled and fragmented cRNA was hybridized to microarray using hybridization oven G2545A (Agilent), and wash step was performed with Gene Expression Wash Buffer Kit (Agilent). All operations were performed according to manufacturer's protocol.
Scan protocol Microarrays were scanned using Agilent DNA microarray scanner G2565BA.
Description Gene expression data from developing anther.
Data processing Scanned tiff image files were analyzed with FeatureExtraction 9.5.1 (Agilent). We slightly modified manufacturer's default extraction protocol called 'GE1-v5_95_Feb07' as follows: 'Background Subtraction Method' was set to 'Average of Negative Control Features', and 'Use Surrogates' was set to 'False'. Then 'gBGSubSignal' columns were extracted from the text data files produced by FeatureExtraction, and introduced into GeneSpring 7.3.1 (Agilent). Positive and negative control features (such as spike-in or dark corner) were removed before data introduction into GeneSpring. Introduced signal intensities were scaled to median per chip, and the lowest value of scaled signal intensity was set to 0.01. Normalized signal intensities of some probes locating multiple positions on a array were average values of all corresponding probes.
 
Submission date Jan 06, 2009
Last update date Feb 25, 2011
Contact name Nori Kurata
E-mail(s) nkurata@nig.ac.jp
Phone +81-55-981-6808
Organization name National Institute of Genetics
Lab Plant genetics Lab.
Street address 1111 Yata
City Mishima
State/province Shizuoka
ZIP/Postal code 411-8540
Country Japan
 
Platform ID GPL8852
Series (2)
GSE14301 Rice expression atlas (5): Anther development (Agilent data)
GSE14304 Rice expression atlas: Plant reproductive process

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
Os12g0531300|COMBINER|CI260116|6 2.6366289
Os02g0123600|mRNA|AK104814|CDS+3'UTR 6.25086
Os06g0727900|COMBINER_EST|Os06g0727900|8 0.01
Os11g0205500|mRNA|AK072329|CDS+3'UTR 2.025249
Os10g0580400|mRNA|AY463691|CDS+3'UTR 0.01
Os03g0740600|mRNA|AK073852|CDS+3'UTR 0.92358893
Os10g0573800|COMBINER_EST|CI421851|0 3.7189248
Os09g0441900|mRNA|AK062809|UTR 0.4660371
Os03g0226600|mRNA|AK121288|CDS+3'UTR 0.6340921
Os02g0588400|COMBINER|CI265704|6 0.01
Os07g0650600|mRNA|AB072978|CDS+3'UTR 0.06265572
Os06g0716700|mRNA|AB037681|CDS+3'UTR 65.86334
Os02g0208900|mRNA|AK066171|CDS+3'UTR 0.663707
Os03g0121200|mRNA|AK060028|CDS+3'UTR 3.529418
Os03g0336700|mRNA|AK120611|CDS+3'UTR 13.240222
Os01g0120800|mRNA|AK121302|CDS+3'UTR 0.06021273
Os02g0650900|mRNA|AK103028|CDS+3'UTR 0.01
Os01g0111900|mRNA|AK103326|CDS+3'UTR 2.6443546
Os07g0148800|mRNA|AK062246|CDS+3'UTR 10.173522
Os10g0478200|mRNA|AF353203|CDS+3'UTR 127.02994

Total number of rows: 42537

Table truncated, full table size 1932 Kbytes.




Supplementary file Size Download File type/resource
GSM357694.txt.gz 7.5 Mb (ftp)(http) TXT
Processed data included within Sample table
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