|
| Status |
Public on Jun 30, 2013 |
| Title |
LoTCE gDNA_rep2 |
| Sample type |
genomic |
| |
|
| Source name |
TCE-dechlorinating enrichment with methanogenesis without the addition of cobalamin grown after 15 days
|
| Organism |
environmental samples |
| Characteristics |
bacteria: enrichment
|
| Growth protocol |
MethB12 was enriched from groundwater and maintained using defined medium amended with 20mM lactate, 100ug/L vitamin B12 and 2uL TCE. Meth was constructed using the same growth condition as MethB12 but without the addition of vitamin B12. NoMethB12 was constructed from MethB12 by adding 7ul TCE initially instead of 2uL. NoMeth was constructed from NoMethB12 without adding vitamin B12. Lactate and TCE were re-amended in all four enrichments resulting in a total of 2.7mmol lactate and 20uL TCE added. On day 15 for MethB12 and Meth, day 13 for NoMethB12 and NoMeth, when all TCE was dechlorinated, ~40mL cells were collected by centrifugation as one biological replicate. Three biological replicates were prepared.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using a DNeasy Blood & Tissue 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 DNA 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 |
gene presence/absence data
Dehalococcoides-containing mixed culture
|
| 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 |
Nov 08, 2011 |
| Last update date |
Jun 30, 2013 |
| 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) |
| GSE33530 |
Characterization of four TCE-dechlorinating microbial enrichments grown with different cobalamin stress and methanogenic conditions |
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