|
| Status |
Public on Dec 19, 2018 |
| Title |
sM7 |
| Sample type |
genomic |
| |
|
| Source name |
antibiotic resistance genes and virulence genes in activated sludge of full-scale wastewater treatment systems
|
| Organism |
activated sludge metagenome |
| Characteristics |
tissue: activated sludge of full-scale wastewater treatment system
wastewater treatment system: Wastewater treatment system of MBR in the short term
|
| Treatment protocol |
MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 7.
|
| Growth protocol |
MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 7.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Microbial genomic DNA was extracted from the pellets of activated sludge samples through joint use of freezing and sodium dodecyl sulfate (SDS) for cell lysis (Zhou et al. 1996). The extracted products were then purified employing the Wizard® SV Genomic DNA Purification Kit (Promega, Madison WI). DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.
|
| Label |
Cy5
|
| Label protocol |
As previously described (Lu et al. 2012), 1000 ng of each DNA sample was labeled were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA) and then dried.
|
| |
|
| Hybridization protocol |
All labeled DNA was resuspended in 10 μl hybridization solution as previously described (Wu et al. 2006) and was hybridized with GeoChip 4.2 on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA) at 42℃ with 40% formamide for 16h.
|
| Scan protocol |
Microarrays were scanned by a ScanArray 5000 Microarray Analysis System (PerkinElmer, Wellesley, MA, USA) at 100% laser power.
|
| Description |
GeoChip data for activated sludge sample collected at System MBR, Day 7
raw data file: Activated sludge raw data1.txt
|
| Data processing |
Signal intensities of the spots were measured with ImaGene 6.0 (Biodiscovery Inc., El Segundo, CA, USA). Data pretreatment was performed online (ieg.ou.edu). The percentages of thermophile probes (negative controls) in each sample were made less than 5% by the removal of low quality spots. The genes detected in only one out of three samples from the same system were removed. The genes detected only in 3 or fewer samples out of 12 samples from the same system were removed to avoid potential noises. For each sample, intensities of the genes were then transformed to the natural logarithmic form and divided by the mean signal intensity.
|
| |
|
| Submission date |
Dec 18, 2018 |
| Last update date |
Dec 19, 2018 |
| Contact name |
Bing Zhang |
| E-mail(s) |
zhangbingwhu@126.com
|
| Phone |
+86 18610848200
|
| Organization name |
Tsinghua University
|
| Department |
School of Environment
|
| Street address |
Rm 437, School of Environment, Tsinghua University
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL25953 |
| Series (1) |
| GSE124018 |
Profiles of antibiotic resistance genes (ARGs) and virulence genes (VGs) and their temporal interactions in OD and MBR |
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