NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1306261 Query DataSets for GSM1306261
Status Public on Jan 31, 2015
Title Amplified DNA_Strain 195 Sample 1_rep1
Sample type genomic
 
Source name 1 µg of DNA
Organism Dehalococcoides mccartyi 195
Characteristics bacteria: Pure culture
sample type: Amplified DNA
Growth protocol Replicate 100 mL cultures were grown in parallel with chlorinated ethene, hydrogen and acetate.
Extracted molecule genomic DNA
Extraction protocol gDNA from cultures was extracted using the Qiagen (Valencia, CA) DNeasy Blood & Tissue kit according to the manufacturers’ recommendations.The DNA of sorted cells were amplifed by the Qiagen REPLI-g midi kit (Valencia, CA).
Label Biotin
Label protocol One µg of gDNA was prepared for each microarray according to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).
 
Hybridization protocol According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).
Scan protocol According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).
Description Amplified DNA
Data processing Data analysis was performed using Affymetrix GeneChip software and the MAS5 algorithm. Each microarray was normalized by scaling the signal intensities of the positive control spike-mix to a target signal intensity of 2500 to allow comparison between microarrays.
 
Submission date Jan 13, 2014
Last update date Jan 31, 2015
Contact name Patrick Lee
E-mail(s) leep@berkeley.edu
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
 
Platform ID GPL10838
Series (1)
GSE54040 Development of a Fluorescence-Activated Cell Sorting Method Coupled with Whole Genome Amplification To Analyze Minority and Trace Dehalococcoides Genomes in Microbial Communities

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 9.97844 A 0.175328
AFFX-BioB-M_at 4.71045 A 0.470241
AFFX-BioB-3_at 0.613475 A 0.976071
AFFX-BioC-5_at 12.0976 A 0.327079
AFFX-BioC-3_at 5.00777 A 0.440646
AFFX-BioDn-5_at 0.717332 A 0.891021
AFFX-BioDn-3_at 12.8219 A 0.0956669
AFFX-CreX-5_at 0.794618 A 0.645572
AFFX-CreX-3_at 1.04124 A 0.891021
AFFX-DapX-5_at 4583.46 P 4.42873e-05
AFFX-DapX-M_at 5822.31 P 4.42873e-05
AFFX-DapX-3_at 4982.13 P 4.42873e-05
AFFX-LysX-5_at 1156.29 P 4.42873e-05
AFFX-LysX-M_at 1080.99 P 4.42873e-05
AFFX-LysX-3_at 1318.1 P 4.42873e-05
AFFX-PheX-5_at 1895.14 P 4.42873e-05
AFFX-PheX-M_at 1600.92 P 4.42873e-05
AFFX-PheX-3_at 1301.13 P 4.42873e-05
AFFX-ThrX-5_at 2739.98 P 4.42873e-05
AFFX-ThrX-M_at 2949.3 P 4.42873e-05

Total number of rows: 4789

Table truncated, full table size 159 Kbytes.




Supplementary file Size Download File type/resource
GSM1306261_Amplified_DNA_Strain_195_Sample_1_rep1.CEL.gz 724.1 Kb (ftp)(http) CEL
GSM1306261_Amplified_DNA_Strain_195_Sample_1_rep1.CHP.gz 1.2 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap