| Citation | Spencer WC, Zeller G, Watson JD, Henz SR, Watkins KL, McWhirter RD, Petersen SC, Sreedharan VT, Widmer C, Jo J, Reinke V, Petrella L, Strome S, Von Stetina S, Katz M, Shaham S, Raetsch G, Miller DM. A spatial and temporal map of C. elegans gene expression. Genome Res, 2011. |
| PubMed ID | 21177967 |
| Short Description | A spatial and temporal map of C. elegans gene expression. GEO Record: GSE23245 GSE23246 GSE23247 GSE23248 GSE23249 GSE23250 GSE23251 GSE23252 GSE23253 GSE23254 GSE23255 GSE23256 GSE23257 GSE23258 GSE23259 GSE23260 GSE23261 GSE23262 GSE23263 GSE23264 GSE23265 GSE23266 GSE23267 GSE23268 GSE23269 GSE23270 GSE23271 GSE23272 GSE23273 GSE23274 GSE23275 GSE23276 GSE23277 GSE23278 GSE23279 GSE23280 GSE23281 GSE23282 GSE23283 GSE23284 GSE23285 GSE23286 GSE23287 GSE23770 GSE25350 GSE25351 Platform: GPL5634 Download gene-centric, log2 transformed data: WBPaper00037950.ce.tr.csv |
| # of Conditions | 47 |
Full Description
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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. Experimental Details: TAR_early_embryo_20dC_0_4hrs_post_fertilization_N2 TAR_EE_Z1_Z4_male TAR_embryo_0hr_reference TAR_embryo_A_class_motor_neurons TAR_embryo_all_cells_reference TAR_embryo_AVA_neurons TAR_embryo_AVE_neurons TAR_embryo_BAG_neurons TAR_embryo_body_wall_muscle TAR_embryo_coelomocytes TAR_embryo_dopaminergic_neurons TAR_embryo_GABA_motor_neurons TAR_embryo_germline_precursor_cells TAR_embryo_hypodermal_cells TAR_embryo_intestine TAR_embryo_panneural TAR_embryo_pharyngeal_muscle TAR_embryo_PVC_neurons TAR_emb_Z1_Z4 TAR_gonad_from_young_adult_20dC_42hrs_post_L1_N2 TAR_L1_20dC_0hrs_post_L1_N2 TAR_L2_25dC_14hrs_post_L1_N2 TAR_L2_A_class_neuron TAR_L2_AFD TAR_L2_body_wall_muscle TAR_L2_coelomocytes TAR_L2_excretory_cell TAR_L2_GABA_alr_1 TAR_L2_GABA_neurons TAR_L2_glutamate_receptor_expressing_neurons TAR_L2_intestine TAR_L2_panneural TAR_L2_polyA_enriched_20dC_14hrs_post_L1_N2 TAR_L2_reference__mockIP TAR_L3_25dC_25hrs_post_L1_N2 TAR_L3_L4_dopaminergic_neuron TAR_L3_L4_hypodermal_cells TAR_L3_L4_PVD___OLL_neurons TAR_L3_L4_rectal_epithelial_cells TAR_L3_L4_reference__mockIP TAR_L4_25dC_36hrs_post_L1_N2 TAR_late_embryo_20dC_6_12hrs_post_fertilization_N2 TAR_male_L4_25dC_36hrs_post_L1_CB4689 TAR_soma_only_mid_L4_25dC_36hrs_post_L1_JK1107 TAR_young_adult_25dC_42hrs_post_L1_N2 TAR_Young_Adult_Cephalic_sheath__CEPsh TAR_Young_Adult_reference__mockIP. |
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