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

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

		Fold-change of expression (sorted/unsorted)
Gene	Locus Tag	Microarray study I	Microarray study II	qPCR (sorted/unsorted)	Annotation^⊕
tldD	b3244	2.7 ± 1.4^Ψ	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

^#Fold-changes of gene expression were significantly different from 2, with one-tail t-tests performed (p < 0.05).
*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.
^⊕Annotations are updated according to records of E. coli K-12 MG1655 in NCBI Entrenz Gene Database.
^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 2^SD, where SD is standard deviation of log₂ transformation of fold-change.
^&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.

ISSN: 1471-2180