TY  - JOUR
A1  - Spencer, W. Clay
A1  - Zeller, Georg
A1  - Watson, Joseph D.
A1  - Henz, Stefan R.
A1  - Watkins, Kathie L.
A1  - McWhirter, Rebecca D.
A1  - Petersen, Sarah
A1  - Sreedharan, Vipin T.
A1  - Widmer, Christian
A1  - Jo, Jeanyoung
A1  - Reinke, Valerie
A1  - Petrella, Lisa
A1  - Strome, Susan
A1  - Von Stetina, Stephen E.
A1  - Katz, Menachem
A1  - Shaham, Shai
A1  - Rätsch, Gunnar
A1  - Miller, David M.
T1  - A spatial and temporal map of C. elegans gene expression
Y1  - 2011/02/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 325 
EP  - 341 
DO  - 10.1101/gr.114595.110 
VL  - 21 
IS  - 2 
UR  - http://genome.cshlp.org/content/21/2/325.abstract 
N2  - The C. elegans genome has been completely sequenced, and the developmental anatomy of this model organism is described at single-cell resolution. Here we utilize strategies that exploit this precisely defined architecture to link gene expression to cell type. We obtained RNAs from specific cells and from each developmental stage using tissue-specific promoters to mark cells for isolation by FACS or for mRNA extraction by the mRNA-tagging method. We then generated gene expression profiles of more than 30 different cells and developmental stages using tiling arrays. Machine-learning–based analysis detected transcripts corresponding to established gene models and revealed novel transcriptionally active regions (TARs) in noncoding domains that comprise at least 10% of the total C. elegans genome. Our results show that about 75% of transcripts with detectable expression are differentially expressed among developmental stages and across cell types. Examination of known tissue- and cell-specific transcripts validates these data sets and suggests that newly identified TARs may exercise cell-specific functions. Additionally, we used self-organizing maps to define groups of coregulated transcripts and applied regulatory element analysis to identify known transcription factor– and miRNA-binding sites, as well as novel motifs that likely function to control subsets of these genes. By using cell-specific, whole-genome profiling strategies, we have detected a large number of novel transcripts and produced high-resolution gene expression maps that provide a basis for establishing the roles of individual genes in cellular differentiation. 
ER  -