GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM1180003

Query DataSets for GSM1180003

Status

Public on Aug 31, 2013

Title

OsWRKY53 over-expressing rice leaves (line 8) replicate 1

Sample type

RNA

Source name

OsWRKY53 over-expressing rice leaves (line 8)

Organism

Oryza sativa

Characteristics

genotype/variation: OsWRKY53 over-expressing rice leaves (line 8)

Treatment protocol

Fourth leaves were harvested from WT, OsWRKY53-overexpressing rice plants and OsWRKY53SD-overexpressing rice plants at the four-leaf stage.

Growth protocol

Rice plants were grown in a chamber under a 14-h-light (28℃) and 10-h-dark (24℃) cycle in hydroponic culture.

Extracted molecule

total RNA

Extraction protocol

RNeasy Plant Mini Kit (Qiagen)

Label

Cy3

Label protocol

Low RNA input Linear Amplification/Labeling Kit (Agilent)

Hybridization protocol

Agilent protocol G4140-90040

Scan protocol

Agilent scanner model G2565

Description

Biological replicate 1 of 4.

Data processing

After data was analyzed by Fearure Extraction software (version 11, Agilent), data normalization was performed using Partek Genomics Suite software (ver. 6.5; Partek software) by quantile normalization method.

Submission date

Jul 02, 2013

Last update date

Nov 04, 2013

Contact name

Kazunori Okada

E-mail(s)

ukokada@mail.ecc.u-tokyo.ac.jp

Phone

+81-3-5841-3070

Organization name

The University of Tokyo

Department

Biotechnology Research Center

Lab

Laboratory of Environmental Biochemistry

Street address

1-1-1, Yayoi, Bunkyo-ku

City

Tokyo

ZIP/Postal code

113-8657

Country

Japan

Platform ID

GPL8852

Series (1)

GSE48500

Effect of overexpression of the OsWRKY53 or phospho-mimicking mutant of OsWRKY53 in rice

Data table header descriptions
ID_REF
VALUE	Normalized signal intensity (log 2)

Data table
ID_REF	VALUE
Os01g0100100\|COMBINER_EST\|CI448596\|0	11.4655
Os01g0100200\|mRNA\|AK059894\|CDS+3'UTR	4.02191
Os01g0100400\|mRNA\|AK101455\|CDS+3'UTR	7.47157
Os01g0100500\|mRNA\|AK067316\|CDS+3'UTR	11.9974
Os01g0100600\|mRNA\|AK121362\|CDS+3'UTR	11.6889
Os01g0100700\|mRNA\|AK059844\|CDS+3'UTR	14.6173
Os01g0100700\|mRNA\|AK121523\|CDS+3'UTR	12.733
Os01g0100800\|mRNA\|AK122012\|CDS+3'UTR	10.9841
Os01g0100900\|COMBINER_EST\|CI015509\|0	12.6284
Os01g0101200\|mRNA\|AK067866\|CDS+3'UTR	11.6987
Os01g0101200\|mRNA\|AK104517\|CDS+3'UTR	13.8451
Os01g0101200\|mRNA\|AK104625\|CDS+3'UTR	13.8208
Os01g0101200\|mRNA\|AK104752\|CDS+3'UTR	13.8096
Os01g0101200\|mRNA\|AK119457\|CDS+3'UTR	9.01261
Os01g0101300\|COMBINER_EST\|CI016681\|6	9.99728
Os01g0101600\|mRNA\|AK099952\|CDS+3'UTR	7.35115
Os01g0101600\|mRNA\|AK103820\|CDS+3'UTR	12.4839
Os01g0101600\|mRNA\|AK122118\|CDS+3'UTR	12.4324
Os01g0101700\|COMBINER_EST\|CI525185\|3	14.5945
Os01g0101800\|mRNA\|AK103498\|CDS+3'UTR	10.2134

Total number of rows: 42477

Table truncated, full table size 1848 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM1180003_US90500268_251524114603_S01_GE1_105_Dec08_1_2.txt.gz	7.6 Mb	(ftp)(http)	TXT
Processed data included within Sample table