GEO DataSets

(Submitter supplied) Dehalococcoides mccartyi are functionally important bacteria that catalyze the reductive dechlorination of chlorinated ethenes. However, these anaerobic bacteria are fastidious to isolate, making downstream genomic characterization challenging. In order to facilitate genomic analysis, a fluorescence-activated cell sorting (FACS) method was developed in this study to separate D. mccartyi cells from a microbial community, and the DNA of the isolated cells was processed by whole genome amplification (WGA) and hybridized onto a D. more...

Organism:

Dehalococcoides mccartyi BAV1; Dehalococcoides mccartyi CBDB1; Dehalococcoides mccartyi VS; Dehalococcoides mccartyi 195

Type:

Genome variation profiling by array

Platform:

GPL10838

21 Samples

Download data: CEL, CHP

(Submitter supplied) 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. more...

Organism:

Dehalococcoides mccartyi BAV1; Dehalococcoides mccartyi CBDB1; Dehalococcoides sp. ANAS1; Dehalococcoides; Anaeromyxobacter dehalogenans 2CP-C; Dehalococcoides mccartyi VS; Dehalococcoides mccartyi 195; Dehalococcoides sp. ANAS2

Type:

Genome variation profiling by array

Platform:

GPL10838

24 Samples

Download data: CEL, CHP

(Submitter supplied) Microbial reductive dechlorination of trichloroethene (TCE) in groundwater often results in the accumulation of dichloroethenes (DCEs). Dehalococcoides mccartyi (Dhc) are the only known bacteria capable of dechlorination beyond DCE to non-toxic ethene. In this study, two newly isolated Dhc strains (11a and 11a5) with dissimilar functional abilities are described. Strain 11a reductively dechlorinates TCE, 1,1-DCE, cis-DCE, trans-DCE, and vinyl chloride (VC) to ethene, while strain 11a5 dechlorinates TCE and all three DCE isomers only to VC. more...

Organism:

Dehalococcoides; Dehalococcoides mccartyi 195; Dehalococcoides mccartyi VS; Dehalococcoides mccartyi BAV1; Dehalococcoides mccartyi CBDB1

Type:

Genome variation profiling by array

Platform:

GPL10838

6 Samples

Download data: CEL, CHP

(Submitter supplied) The aim of this study is to obtain a systems level understanding of the interactions between Dehalococcoides and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. more...

Organism:

Dehalococcoides mccartyi 195; Dehalococcoides mccartyi; Dehalococcoides mccartyi BAV1; Dehalococcoides mccartyi VS; Dehalococcoides mccartyi CBDB1

Type:

Expression profiling by array

Platform:

GPL10838

12 Samples

Download data: CEL

(Submitter supplied) Microarrays are useful tools for detecting and quantifying specific functional and phylogenetic genes in natural microbial communities. In order to track uncultivated microbial genotypes and their close relatives in an environmental context, we designed and implemented a “genome proxy” microarray that targets microbial genome fragments recovered directly from the environment. Fragments consisted of sequenced clones from large-insert genomic libraries from microbial communities in Monterey Bay, the Hawaii Ocean Time-series station ALOHA, and Antarctic coastal waters. more...

Organism:

uncultured crenarchaeote 4B7; Prochlorococcus marinus subsp. pastoris str. CCMP1986; Prochlorococcus marinus str. MIT 9312; uncultured marine gamma proteobacterium EBAC31A08; uncultured marine bacterium EB0_41B09; uncultured proteobacterium 60D04; Prochlorococcus marinus str. MIT 9313; Prochlorococcus marinus str. MIT 9515; uncultured marine bacterium 577; uncultured gamma proteobacterium eBACHOT4E07; uncultured marine alpha proteobacterium; uncultured Pseudomonadota bacterium; uncultured crenarchaeote 74A4; uncultured proteobacterium 65D09; uncultured marine group II euryarchaeote EF100_57A08; uncultured marine bacterium EB000_55B11; uncultured marine group II euryarchaeote 37F11; uncultured marine bacterium 440; uncultured marine bacterium 583; marine metagenome

Type:

Other

Platform:

GPL6012

28 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of Dehalococcoides mccartyi in the commercially available KB-1™ consortia comparing control standard TCE batch fed culture to treatments either introducing the culture to a standard batch feeding, stressful condition, or continous feed rate.

Organism:

Dehalococcoides mccartyi

Type:

Expression profiling by array

Platform:

GPL16261

36 Samples

Download data: TXT

(Submitter supplied) A cDNA-microarray was designed and used to monitor the transcriptomic profile of Dehalococcoides mccartyi strain 195 (in a mixed community) respiring various chlorinated organics, including chloroethenes and 2,3-dichlorophenol. The cultures were continuously fed in order to establish steady-state respiration rates and substrate levels. The organization of array data into a clustered heat map revealed two major experimental partitions. more...

Organism:

Dehalococcoides mccartyi 195

Type:

Expression profiling by array

Platform:

GPL10023

53 Samples

Download data: TXT