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Table 1 Description of the datasets used for the analysis

From: Widespread uncoupling between transcriptome and translatome variations after a stimulus in mammalian cells

Short namea Description Biological source Reference Data IDb Chipc Cluster
+serum.0-2 h serum starvation release Mus musculus PMID: 17405863 GSE7363 MG_U74Av2 extracellular signalling
+EPO.0-2 h erythroid EPO deprivation release Mus musculus PMID: 18625885 E-MEXP-1689 MG_U74Av2  
-LIF.0-5d stem cell differentiation through LIF removal Mus musculus PMID: 18462695 GSE9563 Mouse430_2  
+LPS.0-1 h macrophage LPS treatment (1 h) Mus musculus PMID: 18230670 GSE4288 Mouse430_2  
+LPS.0-2 h macrophage LPS treatment (2 h) Mus musculus PMID: 18230670 GSE4288 Mouse430_2  
+LPS.0-4 h macrophage LPS treatment (4 h) Mus musculus PMID: 18230670 GSE4288 Mouse430_2  
+diff.WT.hepa differentiation of WT hepatocytes Homo sapiens PMID: 18221535 E-MEXP-958 HG-U133A differentiation
+diff.mTOR.hepa differentiation of mTOR activated hepatocytes Homo sapiens PMID: 17483347 E-MEXP-958 HG-U133A  
+diff.testis.P17-P22 testis differentiation (5d) Mus musculus PMID: 16682651 GSE4711 MOE430A  
+diff.testis.P17-P70 testis differentiation (53d) Mus musculus PMID: 16682651 GSE4711 MOE430A  
+diff.testis.P22-P70 testis differentiation (48d) Mus musculus PMID: 16682651 GSE4711 MOE430A  
+diff.lung.E19-E22 lung differentiation (3d) Rattus norvegicus PMID: 18952566 GSE12153 Rat230_2  
+diff.lung.E19-P1 lung differentiation (embrionic vs postnatal) Rattus norvegicus PMID: 18952566 GSE12153 Rat230_2  
+diff.lung.E22-P1 lung differentiation (embrionic vs postnatal) Rattus norvegicus PMID: 18952566 GSE12153 Rat230_2  
+eIF4E eIF4E overexpression Homo sapiens PMID: 17638893 GSE6043 HG-U133_Plus_2 translational machinery alteration
-eIF4GI eIF4GI depletion Homo sapiens PMID: 18426977 GSE11011 HG-U133A_2  
+v-Ki-ras v-Ki-ras transformation Homo sapiens PMID: 16446406 E-MEXP-461 HG_U95Av2  
+mTOR.no-diff mTOR activation of proliferative hepatocytes Homo sapiens PMID: 17483347 E-MEXP-958 HG-U133A  
+mTOR.diff mTOR activation of differentiated hepatocytes Homo sapiens PMID: 17483347 E-MEXP-958 HG-U133A  
  1. (a) short name specifying exposure to or subtraction from (+ or –) a broadly defined perturbation agent, perturbation agent name, experimental time.
  2. (b) dataset reference on GEO or ArrayExpress.
  3. (c) all the chips belong to the Affymetrix platform.
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BMC Genomics

ISSN: 1471-2164

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