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Table 1 Genes identified as differentially expressed# between IMS sorted E. coli cells versus unsorted E. coli cells* by the method of cDNA microarray and their differential expression confirmed with another method of qPCR

From: Separation of the bacterial species, Escherichia coli, from mixed-species microbial communities for transcriptome analysis

   Fold-change of expression (sorted/unsorted)   
Gene Locus Tag Microarray study I Microarray study II qPCR (sorted/unsorted) Annotation
tldD b3244 2.7 ± 1.4Ψ 2.7 ± 1.4 1.1 (0.8, 1.48)& Predicted peptidase
proW b2678 2.4 ± 1.1 3.3 ± 1.3 -1.6 (-1.1, -2.3) Glycine betaine transporter subunit
ansP b1453 2.2 ± 1.1 2.5 ± 1.1 1.2 (0.9, 1.48) L-asparagine transporter
ydhB b1659 -2.2 ± 1.1 -2.9 ± 1.2 -5.0 (-4.4, -5.7) Predicted DNA-binding transcriptional regulator
yhhN b3468 -2.6 ± 1.3 -3.1 ± 1.2 -3.1 (-2.8, -3.4) Conserved inner membrane protein
ygeV b2869 -2.7 ± 1.1 -3.3 ± 1.4 -1.6 (-1.4, -1.7) Predicted DNA-binding transcriptional regulator
flhE b1878 -2.7 ± 1.2 -3.2 ± 1.2 -1.8 (-1.7, -2.0) Conserved protein
yicG b3646 -3.0 ± 1.2 -4.6 ± 1.3 -3.7 (-3.3, -4.1) Conserved inner membrane protein
  1. #Fold-changes of gene expression were significantly different from 2, with one-tail t-tests performed (p < 0.05).
  2. *Sorted E. coli cells: E. coli cells treated with dispersion/homogenization and IMS cell sorting after pre-stored in RNAlater; Unsorted E. coli cells: E. coli cells continuously stored in RNAlater without any treatment.
  3. Annotations are updated according to records of E. coli K-12 MG1655 in NCBI Entrenz Gene Database.
  4. ΨMean ± geometric standard deviation from two replicate slides, with three built-in replicates in each slide; positive and negative values indicate up- and down-regulation, respectively, in dispersed and IMS sorted cells. Geometric standard deviation is 2SD, where SD is standard deviation of log2 transformation of fold-change.
  5. &Mean of the fold change in gene expression from four replicates (ranges of fold change are given in parentheses), positive and negative values indicate up- and down- regulation, respectively, in dispersed and IMS sorted cells quantified by the method of qPCR.