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Sample GSM357700

Query DataSets for GSM357700

Status

Public on Nov 11, 2010

Title

Anther at P1, biological rep1

Sample type

RNA

Source name

Anther, uni-nucleated gametopyte 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	0.7150419
Os02g0123600\|mRNA\|AK104814\|CDS+3'UTR	6.0415936
Os06g0727900\|COMBINER_EST\|Os06g0727900\|8	0.28509307
Os11g0205500\|mRNA\|AK072329\|CDS+3'UTR	5.027535
Os10g0580400\|mRNA\|AY463691\|CDS+3'UTR	0.01
Os03g0740600\|mRNA\|AK073852\|CDS+3'UTR	1.3312153
Os10g0573800\|COMBINER_EST\|CI421851\|0	3.9284484
Os09g0441900\|mRNA\|AK062809\|UTR	0.35099024
Os03g0226600\|mRNA\|AK121288\|CDS+3'UTR	0.8517257
Os02g0588400\|COMBINER\|CI265704\|6	0.01
Os07g0650600\|mRNA\|AB072978\|CDS+3'UTR	0.07569929
Os06g0716700\|mRNA\|AB037681\|CDS+3'UTR	41.541916
Os02g0208900\|mRNA\|AK066171\|CDS+3'UTR	0.69511884
Os03g0121200\|mRNA\|AK060028\|CDS+3'UTR	7.153345
Os03g0336700\|mRNA\|AK120611\|CDS+3'UTR	14.146328
Os01g0120800\|mRNA\|AK121302\|CDS+3'UTR	0.01
Os02g0650900\|mRNA\|AK103028\|CDS+3'UTR	3.4679778
Os01g0111900\|mRNA\|AK103326\|CDS+3'UTR	11.876925
Os07g0148800\|mRNA\|AK062246\|CDS+3'UTR	25.152306
Os10g0478200\|mRNA\|AF353203\|CDS+3'UTR	205.37816

Total number of rows: 42537

Table truncated, full table size 1923 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM357700.txt.gz	7.6 Mb	(ftp)(http)	TXT
Processed data included within Sample table