GEO DataSets

(Submitter supplied) Transcriptional profiling of the Donna II mixed community containing Dehalococcoides mccartyi strain 195 comparing a batch starved control to the mixed community being fed 1,2,3,4-tetrachlorobenzene as an electron acceptor. The goal was to determine which transcripts are regulated in response to a shift in a different electron acceptor rather than the consistent tetrachloroethene (PCE) that the parent reactor was maintained on.

Organism:

Dehalococcoides mccartyi 195

Type:

Expression profiling by array

Platform:

GPL16121

8 Samples

Download data: TXT

(Submitter supplied) Bacteria of the group “Dehalococcoides” display the ability to respire recalcitrant chlorinated organic compounds in laboratory and field site applications. Though reductive dehalogenases (RDases) have been shown to directly catalyze dechlorination reactions, the respiratory pathways and function of most genome-encoded RDases in Dehalococcoides strains remain incompletely described. In order to broaden the understanding of the biological organization of “Dehalococcoides”, this study monitored the trancriptomic response of “Dehalococcoides ethenogenes” stain 195 through microarray technology. more...

Organism:

Dehalococcoides mccartyi 195; Dehalococcoides mccartyi

Type:

Expression profiling by array

Platform:

GPL11218

6 Samples

Download data: TXT

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

Type:

Expression profiling by array

Platform:

GPL10838

12 Samples

Download data: CEL

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

Type:

Genome variation profiling by array

Platform:

GPL10838

21 Samples

Download data: CEL, CHP

(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

(Submitter supplied) Differental gene expression of three consortia: Dhc195/DVH with exogenous cobalamin, Dhc195/DVH/PF with exogenous cobalamin, Dhc195/DVH/PF without exogenous cobalamin Acronyms: Dhc195: Dehalococcoides mccartyi strain 195; DVH: Desulfovibrio vulgaris Hildenborough; PF: Pelosinus fermentans strain R7

Organism:

Dehalococcoides mccartyi BAV1; Dehalococcoides mccartyi 195; Dehalococcoides mccartyi VS; Nitratidesulfovibrio vulgaris str. Hildenborough; Dehalococcoides mccartyi CBDB1; Pelosinus fermentans DSM 17108

Type:

Expression profiling by array

Platform:

GPL10838

9 Samples

Download data: CEL

(Submitter supplied) Four stable and robust TCE-dechlorinating microbial communities were enriched from TCE-contaminated groundwater under four different conditions exploring two parameters, high and low methanogenic activity (Meth and NoMeth), with and without vitamin B12 supplement (MethB12 and NoMethB12, Meth and NoMeth, respectively). Identical amounts of lactate (2.7 mmol) and TCE (20 μl) were supplied as electron donor and electron acceptor. more...

Organism:

Dehalococcoides mccartyi VS; environmental samples; Dehalococcoides mccartyi BAV1; Dehalococcoides mccartyi CBDB1; environmental samples; environmental samples; Dehalococcoides mccartyi 195

Type:

Genome variation profiling by array

Platform:

GPL10838

12 Samples

Download data: CEL

(Submitter supplied) A microarray targeting four sequenced strains in the Dehalococcoides (Dhc) genus was used to analyze gene expression in a robust long-term trichloroethene (TCE)-degrading microbial community (designated ANAS) during feeding cycles that involve conditions of periodic substrate supply. The Dhc transcriptome was examined at three time-points throughout a batch feeding cycle: T1 (27 h) when TCE, dichloroethene (DCE), and vinyl chloride (VC) were present; T2 (54 h) when only VC remained; and T3 (13 d) when Dhc had been starved of substrate for nine days. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL10838

9 Samples

Download data: CEL

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

Type:

Genome variation profiling by array

Platform:

GPL10838

6 Samples

Download data: CEL, CHP

(Submitter supplied) Bacteria of the genus Dehalococcoides play an important role in the reductive dechlorination of chlorinated ethenes. A systems level approach was taken in this study to examine the global transcriptomic and proteomic responses of exponentially growing D. ethenogenes strain 195 to fixed nitrogen limitation (FNL). As expected, the nitrogen-fixing (nif) genes were differentially up-regulated in the transcriptome and proteome of strain 195 during FNL. more...

Organism:

Dehalococcoides mccartyi 195

Type:

Expression profiling by array

Platform:

GPL6336

6 Samples

Download data: CEL

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

Type:

Genome variation profiling by array

Platform:

GPL10838

24 Samples

Download data: CEL, CHP

(Submitter supplied) The syntrophic growth of strain 195 with Desulfovibrio vulgaris Hildenborough (DVH) and/or Methanobacterium congolense (MC) enhanced TCE dechlorination process by faster dechlorination rate and more robust growth. Transcriptomes of strain 195 grown in isolation, co- and tri-cultures were obtained by microarray experiments to find out the differential expressed genes corresponding to the syntrophic growth. more...

Organism:

Dehalococcoides mccartyi 195; Nitratidesulfovibrio vulgaris str. Hildenborough; Methanobacterium congolense

Type:

Expression profiling by array

Platform:

GPL6116

12 Samples

Download data: CEL

(Submitter supplied) Tetrachloroethene (PCE) and trichloroethene (TCE) are prevalent groundwater contaminants that can be completely reductively dehalogenated by Dehalococcoides organisms. A Dehalococcoides-containing microbial consortium (ANAS) with the ability to degrade TCE to ethene, an innocuous end-product, was previously enriched from contaminated soil. A whole-genome photolithographic microarray was developed based on the genome of Dehalococcoides ethenogenes 195 (strain 195). more...

Organism:

Dehalobacter restrictus; Dehalococcoides; Dehalococcoides mccartyi 195

Type:

Genome variation profiling by array

Platform:

GPL6116

9 Samples

Download data: CEL

(Submitter supplied) Dehalococcoides bacteria can reductively dehalogenate a wide range of halogenated organic pollutants. In this study, DNA microarrays were applied to monitor dynamic changes in the transcriptome as Dehalococcoides ethenogenes strain 195 transitioned from exponential growth into the stationary phase. In total, 415 non-redundant genes were identified as differentially expressed. As expected, genes involved with translation and energy metabolism were down-regulated while genes involved with general stress response, transcription, and signal transduction were up-regulated. more...

Organism:

Dehalococcoides mccartyi 195

Type:

Expression profiling by array

Platform:

GPL6336

15 Samples

Download data: CEL

(Submitter supplied) "Dehalococcoides ethenogenes" strain 195 with additional community members and luciferase. Arrays of this design have barcodes that begin with 16023019 or 2523019. Orientation: Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent. The ID column represents the Agilent Feature Extraction feature number. Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface). more...

Organism:

Dehalococcoides mccartyi 195

1 Series

1 Related Platform

8 Samples

Download data

(Submitter supplied) 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. Protocol: Affymetrix Prokaryotic Sample and Array Processing protocol; 100 Format (Midi)

Organism:

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

7 Series

93 Samples

Download data: CDF

(Submitter supplied) "Dehalococcoides ethenogenes" strain 195 with additional community members and luciferase. Arrays of this design have barcodes that begin with 16021465 or 2521465. Orientation: Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent. The ID column represents the Agilent Feature Extraction feature number. Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface). more...

Organism:

Dehalococcoides mccartyi 195

1 Series

6 Samples

Download data

(Submitter supplied) "Dehalococcoides ethenogenes" strain 195 with additional community members and luciferase. Arrays of this design have barcodes that begin with 16023019 or 2523019. Orientation: Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent. The ID column represents the Agilent Feature Extraction feature number. Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface). more...

Organism:

Dehalococcoides mccartyi 195

1 Series

1 Related Platform

53 Samples

Download data

(Submitter supplied) Manufacturer's protocol used: Affymetrix Prokaryotic Sample and Array Processing protocol; 100 Format (Midi)

Organism:

Dehalococcoides mccartyi 195

2 Series

21 Samples

Download data: CDF

(Submitter supplied) Prokaryotic midi format (format 100) Affymetrix control probe-sets: 45 Dehalococcoides ethenogenes specific probe-sets: 1560

Organism:

Dehalococcoides mccartyi 195

2 Series

21 Samples

Download data: CDF