|
| Status |
Public on Aug 01, 2011 |
| Title |
tri-culture fed by 40µmol TCE_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
195/DVH/MC tri-culture grown on 3rd day
|
| Organisms |
Nitratidesulfovibrio vulgaris str. Hildenborough; Methanobacterium congolense; Dehalococcoides mccartyi 195 |
| Characteristics |
bacteria: tri-culture
agent: TCE
tce concentration: 40µmol
time: 3rd day
|
| Growth protocol |
15 replicates of 100mL culture were grown to early exponential phase when 90% of the given amount of trichloroethene was dechlorinated. For strain 195 on 7th day, for co-culture fed by 78µmol TCE on 5th day, for co-culture fed by 40µmol TCE on 3rd day, and for tri-culture fed by 40µmol TCE on 3rd day. 500mL cells were collected by filtration as one biological replicate. Three biological replicates were prepared.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen RNeasy Mini Kit (Qiagen,Valencia, CA) according to the manufacturer’s instructions. cDNA was synthesized according to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).
|
| Label |
biotin
|
| Label protocol |
One 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).
|
| Description |
Tri_3
|
| Data processing |
Data analysis was performed using the MAS5 algorithm and R statistical program . Each microarray was normalized by global scaling the signal intensities to a value of 2500.
|
| |
|
| Submission date |
Jan 24, 2011 |
| Last update date |
Aug 01, 2011 |
| 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 |
GPL6116 |
| Series (1) |
| GSE26815 |
Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analysis |
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