|
| Status |
Public on Jan 31, 2015 |
| Title |
Amplified DNA_AD14_rep1 |
| Sample type |
genomic |
| |
|
| Source name |
1 µg of DNA
|
| Organism |
Dehalococcoides mccartyi 195 |
| Characteristics |
bacteria: Enrichment 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) |
[email protected]
|
| 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 |
|
