|
| Status |
Public on Feb 05, 2014 |
| Title |
Dhc195/DVH/PF (-) B12_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
tri-culture without exogenous cobalamin
|
| Organisms |
Nitratidesulfovibrio vulgaris str. Hildenborough; Dehalococcoides mccartyi 195; Pelosinus fermentans DSM 17108 |
| Characteristics |
consortia: Dehalococcoides mccartyi strain 195; Desulfovibrio vulgaris Hildenborough; Pelosinus fermentans strain R7
|
| Treatment protocol |
cell samples were taken when 70-80% TCE is degraded.
|
| Growth protocol |
Dhc195/DVH (+) B12 and Dhc195/DVH/PF (+) B12 were grown in defined medium with the amendement of 0.7mmol lactate, 100 µg/L vitamin B12 and ~77 µmol TCE; Dhc195/DVH/PF (-) B12 was grown in the same medium except that no vitamin B12 was added.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a acdic phenol-chloroform method.
|
| Label |
biotin
|
| Label protocol |
cDNA was synthesized using 9 µg total RNA according to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).~3-4 µg of cDNA 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. Analysis limited to Dhc195 probe sets.
|
| |
|
| Submission date |
Mar 27, 2013 |
| Last update date |
Feb 05, 2014 |
| Contact name |
Yujie Men |
| Organization name |
University of Illinois at Urbana-Champaign
|
| Street address |
205 N Mathews Ave
|
| City |
Urbana |
| ZIP/Postal code |
61801 |
| Country |
USA |
| |
|
| Platform ID |
GPL10838 |
| Series (1) |
| GSE45533 |
Corrinoid salvaging and remodeling by Dehalococcoides mccartyi strain 195 in a defined consortium containing a corrinoid-producer Pelosinus fermentans strain R7 |
|
