GSE24353-GSM600337-GPL10926-PMID:21503758.tsv
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"isolation source: Pure culture" "characteristics_ch1.1"
"Images were quantified using Agilent Feature Extraction Software (version 9.5.1.1 & 10.5.1.1) and obtained background subtracted and spatially detrended Processed Signal intensities." "data_processing.1"
"The total DNA to be used as target for microarray hybridization was isolated from soil/ sediment samples using the Mo Bio Power soil DNA kit (Mo Bio Inc., Carlsbad, CA, USA) as per manufacturer’s instructions. Before processing for DNA isolation, the soil/ sediments were mixed thoroughly using a mortar-pestle. One gm of soil/sediment was taken for DNA isolation, and during processing with the kit, lysozyme was added to facilitate the lysis of bacteria. The genomic DNA from pure bacterial cultures was isolated using the Wizard genomic DNA isolation kit (Promega corporation, Madison, USA) as per manufacturer's instructions. The concentration of DNA was analyzed by Nanodrop spectrophotometer (Nanodrop Technologies Inc, Rockland, USA), and quality was determined by analysis on DNA 12000 kit (Caliper Sciences, USA) using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA)." "extract_protocol_ch1.1"
"The Sphingomonas sp. strain NM-05 used in the study is a known degrader of γ-hexachlorocyclohexane (γ-HCH) and has been isolated from the vicinity of an industry India Pesticide Limited, Chinhat industrial area, Lucknow which is involved in manufacturing chlorinated pesticides for last 25 years. The strain was harvested in mineral salt medium with 0.34mM γ-HCH as sole source of carbon and energy. The strain Escherichia coli DH-5α was grown in Luria-Bertani medium to an O.D. of 0.4 at 37 degree centigrade with continuous shaking. The soil/sludge samples were collected in air tight vessels,transported on ice (4○C) to the laboratory and processed immediately for DNA isolation. At each sampling location multiple samples were collected from close (100m) to far (500m) from the industry, along the effluent channel and at the place where effluent channel from the industrial area falls into the river." "growth_protocol_ch1.1"
"Escherichia coli DH5[alpha]" "organism_ch1.1"
"Genomic DNA of Escherichia coli DH5α" "source_name_ch1.1"
"ECDH5_GD_RP1" "title.1"
"isolation source: Pure culture" "characteristics_ch1.1"
"The Sphingomonas sp. strain NM-05 used in the study is a known degrader of γ-hexachlorocyclohexane (γ-HCH) and has been isolated from the vicinity of an industry India Pesticide Limited, Chinhat industrial area, Lucknow which is involved in manufacturing chlorinated pesticides for last 25 years. The strain was harvested in mineral salt medium with 0.34mM γ-HCH as sole source of carbon and energy. The strain Escherichia coli DH-5α was grown in Luria-Bertani medium to an O.D. of 0.4 at 37 degree centigrade with continuous shaking. The soil/sludge samples were collected in air tight vessels,transported on ice (4○C) to the laboratory and processed immediately for DNA isolation. At each sampling location multiple samples were collected from close (100m) to far (500m) from the industry, along the effluent channel and at the place where effluent channel from the industrial area falls into the river." "growth_protocol_ch1.1"
"Escherichia coli DH5[alpha]" "organism_ch1.1"
"Genomic DNA of Escherichia coli DH5α" "source_name_ch1.1"