Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0

A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies


ABSTRACT: Whole-genome transcriptional profiles of rice cell types, isolated by laser-capture microdissection. The first comprehensive multi-organ cell type transcriptome atlas from a plant, with 40 distinct cell types from several developmental stages of seeds, shoots and roots, reveals cell-specific promoter motifs, interaction partner candidates, hormone response centers, and other previously unrecognized cellular properties and patterns. Microarray experiments for 40 cell types and two organs were organized using a common reference statistical design, to assure data for all cells could be normalized for cross-comparison. In this design, the hybridization for each cell type sample included a second probe made from an RNA sample that served as a Common Reference, identically aliquoted from a single preparation, for all hybridizations, and including dye swaps for the two probe labels. The Common Reference RNA for all hybridizations was prepared from rice suspension cultures, selected as an undifferentiated cell type that expresses a relatively high percentage of its genome. Although this is an abundant source of RNA, the Common Reference RNA was amplified and labeled in identical fashion to other probes. At least four independent biological replicates for each cell type were collected and profiled; only microarray data sets with r >= 0.9 were retained. A dye swap was included, in which each cell type sample and the Common Reference were labeled with Cy3 and Cy5, respectively, on the two replicates and the reverse for two replicates.

ORGANISM(S): Oryza sativa

SUBMITTER: Nicole Clay 

PROVIDER: E-GEOD-13161 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

altmetric image

Publications

A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies.

Jiao Yuling Y   Tausta S Lori SL   Gandotra Neeru N   Sun Ning N   Liu Tie T   Clay Nicole K NK   Ceserani Teresa T   Chen Meiqin M   Ma Ligeng L   Holford Matthew M   Zhang Hui-yong HY   Zhao Hongyu H   Deng Xing-Wang XW   Nelson Timothy T  

Nature genetics 20090104 2


The functions of the plant body rely on interactions among distinct and nonequivalent cell types. The comparison of transcriptomes from different cell types should expose the transcriptional networks that underlie cellular attributes and contributions. Using laser microdissection and microarray profiling, we have produced a cell type transcriptome atlas that includes 40 cell types from rice (Oryza sativa) shoot, root and germinating seed at several developmental stages, providing patterns of cel  ...[more]

Similar Datasets

2006-10-12 | GSE4454 | GEO
2008-01-15 | GSE10173 | GEO
2003-03-18 | GSE344 | GEO
2010-06-12 | GSE22287 | GEO
2009-01-28 | GSE12933 | GEO
2022-06-03 | GSE39019 | GEO
2022-06-03 | GSE39008 | GEO
2013-05-01 | GSE42134 | GEO
2013-05-01 | E-GEOD-42134 | biostudies-arrayexpress
2005-02-21 | GSE2194 | GEO