|
| Status |
Public on Mar 01, 2016 |
| Title |
M1 |
| Sample type |
genomic |
| |
|
| Source name |
activated sludge sample collected at System MBR
|
| Organism |
activated sludge metagenome |
| Characteristics |
wastewater treatment system: Wastewater treatment system of MBR
collection timepoint: Day 1
|
| 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 1.
|
| 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 1.
|
| 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 1
|
| 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 |
Mar 26, 2015 |
| Last update date |
Mar 01, 2016 |
| Contact name |
Yu Xia |
| E-mail(s) |
xia-y11@mails.tsinghua.edu.cn
|
| Organization name |
Tsinghua Univeristy
|
| Department |
Environmental school
|
| Street address |
Tsinghua University, Haidian District
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL18128 |
| Series (1) |
| GSE67307 |
Comparison of overall functional gene structures of a membrane bioreactor (MBR) and an oxidation ditch (OD) running parallelly at full-scale |
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