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Experiment Name:

SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip

Accession No:

OS29

Microarray:

Rice57k

Visibility:

public

Experiment Type:

Experiment Factor(s):

cultivar: •Nipponbare •93-11

Quality Control:

Treatment summary:

cultivar	# replicates
Nipponbare	5
93-11	5

Total hybridizations: 10

Description:

This experiment has been imported by PLEXdb from NCBI GEO (GSE16265)

Series_summary:
Nucleotide polymorphisms can potentially influence the hybridization of mRNA to 25-mer oligonucleotides. Because Affymetrix Rice Genome Array was designated mainly for Nipponbare genome of Oryza sativa, the expression level of other varieties could not be estimated correctly. We tried to apply new approaches to estimate expression level by discerning the probe-level differential hybridization.

Series_overall_design:
Nipponbare and 93-11 replicates were analyzed.

Publication:

'SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip.', Fujisawa H, Horiuchi Y, Harushima Y, Takada T et al.
BMC Bioinformatics 2009 May 6;10:131.
pubmed: 19419536

Created:

2010-02-19 13:23:22

Last Update:

2010-02-19 13:48:16

GEO Accession

GSE16265

Submitter:

PLEXdb Curator

Experimenter:

Name:	Nori,,Kurata
Institution:	National Institute of Genetics
Head of Laboratory:	--
email(s):	nkurata@lab.nig.ac.jp
Homepage:


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