Genomics

Dataset Information

35

A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression array: Transcript and Genome Hybridizations


ABSTRACT: The publicly available genome sequence information of two rice strains, japonica cultivar Nipponbare and indica cultivar 93-11, opens a great opportunity for investigation of performances DNA genotyping by high-density oligonucleotide arrays. Here, we compare single feature polymorphism (SFP) detection performances between whole genome hybridization and transcript hybridization using Affymetrix Rice Expression Array and the two rice cultivars. Overall design: Total RNA from 3-4 week shoots and genomic DNA both Nipponbare and 93-11 were analyzed.

INSTRUMENT(S): [Rice] Affymetrix Rice Genome Array

SUBMITTER: Nori Kurata  

PROVIDER: GSE16341 | GEO | 2010-06-01

SECONDARY ACCESSION(S): PRJNA115273

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
GSE16341_RAW.tar Raw
filelist.txt Txt
Items per page:
1 - 2 of 2
altmetric image

Publications

A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays.

Horiuchi Youko Y   Harushima Yoshiaki Y   Fujisawa Hironori H   Mochizuki Takako T   Kawakita Masanori M   Sakaguchi Takayuki T   Kurata Nori N  

BMC genomics 20100520


<h4>Background</h4>High-density oligonucleotide arrays are effective tools for genotyping numerous loci simultaneously. In small genome species (genome size: < approximately 300 Mb), whole-genome DNA hybridization to expression arrays has been used for various applications. In large genome species, transcript hybridization to expression arrays has been used for genotyping. Although rice is a fully sequenced model plant of medium genome size (approximately 400 Mb), there are a few examples of the  ...[more]

Similar Datasets

| S-EPMC2885369 | BioStudies
| S-EPMC2435114 | BioStudies
| S-EPMC5507442 | BioStudies
| S-EPMC6350333 | BioStudies
| S-EPMC4261965 | BioStudies
| S-EPMC4131834 | BioStudies
| E-GEOD-36272 | BioStudies
| E-GEOD-38480 | BioStudies
| S-EPMC6397267 | BioStudies
| S-EPMC1808426 | BioStudies