|
| Status |
Public on Aug 18, 2011 |
| Title |
gDNA_Strain BAV1_rep1 |
| Sample type |
genomic |
| |
|
| Source name |
1 µg of gDNA
|
| Organism |
Dehalococcoides mccartyi BAV1 |
| Characteristics |
strain: Dehalococcoides sp. BAV1
bacterial culture: Pure culture
|
| Growth protocol |
For isolates, multiple 100 mL cultures were grown in parallel in order to obtain enough biomass. Pure cultures were provided with the appropriate chlorinated ethene, hydrogen and acetate. The enrichment culture was maintained in a semi-batch reactor with lactate and trichloroethene.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was extracted using either the Qiagen (Valencia, CA) DNeasy Blood & Tissue kit or the AllPrep DNA/RNA Mini Kit according to the manufacturers’ recommendations.
|
| 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).
|
| 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 |
Aug 19, 2010 |
| Last update date |
Aug 18, 2011 |
| 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) |
| GSE23707 |
The design and validation of a Dehalococcoides genus microarray and its application to two newly isolated Dehalococcoides strains for comparative genomics |
|
