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Series GSE23707 Query DataSets for GSE23707
Status Public on Aug 18, 2011
Title The design and validation of a Dehalococcoides genus microarray and its application to two newly isolated Dehalococcoides strains for comparative genomics
Platform organisms Dehalococcoides mccartyi BAV1; Dehalococcoides mccartyi 195; Dehalococcoides mccartyi CBDB1; Dehalococcoides mccartyi VS
Sample organisms Dehalococcoides; Dehalococcoides mccartyi BAV1; Dehalococcoides mccartyi 195; Anaeromyxobacter dehalogenans 2CP-C; Dehalococcoides sp. ANAS1; Dehalococcoides sp. ANAS2
Experiment type Genome variation profiling by array
Summary The chlorinated ethene-respiring bacteria of the genus Dehalococcoides are important for bioremediation. A microarray targeting genes from all available sequenced genomes of the Dehalococcoides genus was designed with 4305 probe sets to target 98.6% of all genes from strains 195, CBDB1, BAV1, and VS. The microarrays were validated with genomic DNA (gDNA) of strains 195 and BAV1 and satisfactory analytical reproducibility, quantitative response and gene detection accuracy were obtained. These microarrays were applied to query the genomes of two recently isolated Dehalococcoides strains, ANAS1 and ANAS2. Strains ANAS1 and ANAS2 can both couple the reduction of TCE, cDCE and 1,1-DCE but not PCE and tDCE with growth while only strain ANAS2 couples VC reduction to growth. Analysis of the respective gDNA using the microarrays showed that the genomes of both strains are similar to each other and to strain 195, except for genes that are within the previously defined integrated elements (IEs) or high plasticity regions (HPRs). Similar results to the combined isolates were obtained when gDNA of ANAS, the enrichment culture from which the two Dehalococcoides isolates originated, was applied to the microarrays. The genome similarities, together with the distinct chlorinated ethene usage of strains ANAS1, ANAS2 and 195 demonstrate that closely phylogenetically related strains can be physiologically different. This incongruence between physiology and core genome phylogeny appears to be driven by the presence of distinct reductive dehalogenase (RDase)-encoding genes with characterized chlorinated ethene functions (pceA, tceA in strain 195; tceA in strain ANAS1; vcrA in strain ANAS2). Genes encoding central metabolic functions of strain 195 were all detected in strains ANAS1 and ANAS2, while interestingly, the tryptophan operon of these strains is similar to that of strain VS. Overall, the microarrays are a valuable high-throughput tool for comparative genomics of un-sequenced Dehalococcoides-containing samples.
Overall design The genomic DNA (gDNA) of each culture was analyzed in triplicate. gDNA from strain 195 and strain BAV1 was used as positive control, while gDNA from Anaeromyxobacter dehalogenans strain 2CP-C served as negative control in validating the microarray. gDNA from the two newly isolated strains ANAS1 and ANAS2 as well as the enrichment culture (ANAS) where the two strains originated was also analyzed.
Contributor(s) Lee PK, Cheng D, Hu P, West KA, Dick GJ, Brodie EL, Andersen GL, Zinder SH, He J, Alvarez-Cohen L
Citation(s) 21228894
Submission date Aug 19, 2010
Last update date Nov 29, 2012
Contact name Patrick Lee
Organization name University of California, Berkeley
Department Civil and Environmental Engineering
Street address 209 O'Brien Hall
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
Platforms (1)
GPL10838 [4dehalosa520666F] Affymetrix Dehalococcoides genus 4.8K array
Samples (24)
GSM585159 gDNA_Strain 195_rep1
GSM585160 gDNA_Strain 195_rep2
GSM585161 gDNA_Strain 195_rep3
BioProject PRJNA130891

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE23707_RAW.tar 47.7 Mb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file

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