Transcriptomics,Genomics

Dataset Information

24

Validation of gene expression from rice locus (self-hybridization)


ABSTRACT: Transcription from 23K TIGR–loci were confirmed by full–length cDNA mapping, but other 33K TIGR–loci were not confirmed. However, it was not natural to think that full–length cDNA libraries was included almost rice genes, because the transcription of 3K CDS–ANE were confirmed by other transcriptome resources in TIGR OSA1. So, for detection of gene expression from FL–locus and TIGR–locus, we designed about 82K 60mer oligo probes based on TIGR Pseudomolecules release 2. However, TIGR–locus was revised according to revised Pseudomolecules and other additional transcriptome resources. Therefore designed 82K probes were re-mapped on TIGR4 ,and 63455 probes were mapped on 43090 locus Keywords: tissue type comparison Overall design: organisms = Oryza sativa ssp. japonica (Nipponbare), and indica (IR64) tissues = shoot, root, panicle, callus hybridization = two dye method hybridization = self hybridization replication = two times

INSTRUMENT(S): Whole rice locus 44K array 1

SUBMITTER: Kouji Satoh 

PROVIDER: GSE7366 | GEO | 2007-11-28

SECONDARY ACCESSION(S): PRJNA100441

REPOSITORIES: GEO

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Publications

Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray.

Satoh Kouji K   Doi Koji K   Nagata Toshifumi T   Kishimoto Naoki N   Suzuki Kohji K   Otomo Yasuhiro Y   Kawai Jun J   Nakamura Mari M   Hirozane-Kishikawa Tomoko T   Kanagawa Saeko S   Arakawa Takahiro T   Takahashi-Iida Juri J   Murata Mitsuyoshi M   Ninomiya Noriko N   Sasaki Daisuke D   Fukuda Shiro S   Tagami Michihira M   Yamagata Harumi H   Kurita Kanako K   Kamiya Kozue K   Yamamoto Mayu M   Kikuta Ari A   Bito Takahito T   Fujitsuka Nahoko N   Ito Kazue K   Kanamori Hiroyuki H   Choi Il-Ryong IR   Nagamura Yoshiaki Y   Matsumoto Takashi T   Murakami Kazuo K   Matsubara Ken-ichi K   Carninci Piero P   Hayashizaki Yoshihide Y   Kikuchi Shoshi S  

PloS one 20071128 11


Rice (Oryza sativa L.) is a model organism for the functional genomics of monocotyledonous plants since the genome size is considerably smaller than those of other monocotyledonous plants. Although highly accurate genome sequences of indica and japonica rice are available, additional resources such as full-length complementary DNA (FL-cDNA) sequences are also indispensable for comprehensive analyses of gene structure and function. We cross-referenced 28.5K individual loci in the rice genome defi  ...[more]

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