GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM357697

Query DataSets for GSM357697

Status

Public on Nov 11, 2010

Title

Anther at M2, biological rep3

Sample type

RNA

Source name

Anther, pollen mother cells at meiotic zygotene-pachytene 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	3.3090768
Os02g0123600\|mRNA\|AK104814\|CDS+3'UTR	7.589258
Os06g0727900\|COMBINER_EST\|Os06g0727900\|8	0.01
Os11g0205500\|mRNA\|AK072329\|CDS+3'UTR	2.859812
Os10g0580400\|mRNA\|AY463691\|CDS+3'UTR	0.06698102
Os03g0740600\|mRNA\|AK073852\|CDS+3'UTR	0.48543692
Os10g0573800\|COMBINER_EST\|CI421851\|0	5.1279254
Os09g0441900\|mRNA\|AK062809\|UTR	0.29107413
Os03g0226600\|mRNA\|AK121288\|CDS+3'UTR	0.92406934
Os02g0588400\|COMBINER\|CI265704\|6	0.01
Os07g0650600\|mRNA\|AB072978\|CDS+3'UTR	0.09132573
Os06g0716700\|mRNA\|AB037681\|CDS+3'UTR	54.902218
Os02g0208900\|mRNA\|AK066171\|CDS+3'UTR	0.55767125
Os03g0121200\|mRNA\|AK060028\|CDS+3'UTR	8.707424
Os03g0336700\|mRNA\|AK120611\|CDS+3'UTR	23.602741
Os01g0120800\|mRNA\|AK121302\|CDS+3'UTR	0.028831366
Os02g0650900\|mRNA\|AK103028\|CDS+3'UTR	0.42485425
Os01g0111900\|mRNA\|AK103326\|CDS+3'UTR	3.6844552
Os07g0148800\|mRNA\|AK062246\|CDS+3'UTR	15.098628
Os10g0478200\|mRNA\|AF353203\|CDS+3'UTR	88.80556

Total number of rows: 42537

Table truncated, full table size 1933 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM357697.txt.gz	7.6 Mb	(ftp)(http)	TXT
Processed data included within Sample table