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Sample GSM600336 Query DataSets for GSM600336
Status Public on Apr 15, 2011
Title NM-05_GD_1250_RP1
Sample type genomic
 
Source name Genomic DNA of Sphingomonas sp. strain NM-05
Organism Sphingomonas sp. NM05
Characteristics isolation source: Pure culture
Growth protocol 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.
Extracted molecule genomic DNA
Extraction protocol 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).
Label Cy3
Label protocol The samples for Comparative Genomic DNA Hybridization were labeled using Agilent Genomic DNA labeling Kit (Part Number: 5190-0453). DNA of each sample was digested using Alu1 and Rsa1. This restricted DNA was then labeled with Cy3 dUTP using random primer labeling method. The labeled DNA was then concentrated and quality assessed for yields
 
Hybridization protocol 1.25 micrograms of cy3 labeled samples were hybridized. Hybridizations were done using the aCGH Hybridization kit of Agilent (Part Number: 5190-0404). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 24 hours
Scan protocol The hybridized slides were washed using Agilent aCGH wash buffers (Part No: 5188-5221/22) and scanned using the Agilent Microarray Scanner G2505C
Description Comparative genomic hybridization for pure genomic DNA of strain NM-05 (used as biological positive control)
Data processing 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.
 
Submission date Sep 24, 2010
Last update date Apr 15, 2011
Contact name Natesan Manickam
E-mail(s) nmanickam@iitr.res.in
Phone +91-522-2620107
Fax +91-522-2628227
Organization name Indian Institute of Toxicology Research
Department Department Environmental Biotechnology Division
Lab Environmental Biotechnology Lab
Street address Mahatma Gandhi Marg
City Lucknow
State/province Uttar Pradesh
ZIP/Postal code 226001
Country India
 
Platform ID GPL10926
Series (1)
GSE24353 Development and evaluation of a 60-mer oligonucleotide microarray for profiling of biodegradation and bacterial 16S rRNA genes in diverse contaminated ecosystems

Data table header descriptions
ID_REF
VALUE Normalized Cy3 signal intensity

Data table
ID_REF VALUE
1 6.431941e+002
2 1.994594e+000
3 1.994594e+000
4 1.994594e+000
5 1.994594e+000
6 6.316044e+000
7 1.247277e+001
8 1.994594e+000
9 1.994594e+000
10 1.186512e+001
11 1.994594e+000
12 2.142645e+000
13 6.311664e+000
14 7.909681e+001
15 2.407222e+000
16 1.994594e+000
17 3.282598e+002
18 1.994594e+000
19 2.563892e+001
20 1.994594e+000

Total number of rows: 15743

Table truncated, full table size 296 Kbytes.




Supplementary file Size Download File type/resource
GSM600336_US83000164_251715910007_S01-2_GE1_105_Dec08_2_1.txt.gz 2.3 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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