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Browse RicePLEX Experiment Data

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SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip
Nori,,Kurata, National Institute of Genetics (nkurata@lab.nig.ac.jp)
Experiment design (10 hybridizations)
cultivar
•Nipponbare •93-11

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

Series_summary:
Nucleotide polymorphisms can potentially influen...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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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
Name: Nori,,Kurata
Institution: National Institute of Genetics
Head of Laboratory: --
email(s):
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