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| Status |
Public on Feb 10, 2022 |
| Title |
monthly_1_3C |
| Sample type |
genomic |
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| Source name |
soil DNA, Jan, control, replicate 1
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| Organism |
uncultured soil bacterium |
| Characteristics |
collection time: collected in Jan
condition: control
replicate: replicate 1
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted by MoBio PowerSoil DNA isolation kit (MoBio Laboratories, Carlsbad, CA, USA). DNA concentrations were quantified with PicoGreen using a FLUOstar OPTIMA fluorescence plate reader (BMG LabTech, Jena, Germany), and DNA purity was determined by the ratios of O.D. 260/280 nm and O.D. 260/230 nm using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA).
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| Label |
Cy3
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| Label protocol |
Purified DNA was first labeled with the fluorescent dye Cy-3 (GE Healthcare, CA, USA) using random priming as described previously (Cong et al., 2015), then purified by a QIAquick Purification kit (Qiagen, Valencia, CA, USA), and dried in a SpeedVac (Thermo Savant, NY, USA) at 45 °C for 45 min. The dried DNA was then resuspended into ??? μl of DNase/RNase-free distilled water and evenly mixed with ??? μl of hybridization solution, which contains 1 × Acgh blocking, 1 × HI-RPM hybridization buffer, 10 pM universal standard DNA, 0.05 μg/μl Cot-1 DNA, and 10% formamide (final concentrations).
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| Hybridization protocol |
The mixed solution was kept at 90 °C for 3 min for denaturation, and incubated at 37°C for 30 min before GeoChip hybridization was carried out at 67 °C for 24 hrs with a rotation at 20rpm in Agilent hybridization oven.
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| Scan protocol |
After hybridization, Agilent Wash Buffers were applied to wash away unbounded DNA at ordinary temperature, and the arrays were scanned with a NimbleGen MS200 Microarray Scanner (Roche NimbleGen, Madison, WI, USA) at 633 nm. Eventually the images data were extracted by Agilent Feature Extraction program.
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| Description |
collected in Jan, control, replicate 1
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| Data processing |
Raw signals were uploaded to Microarray Data Manager (http://ieg.ou.edu/microarray) for data quality control and normalization. Samples from January to June and from July to December were hybridized in separate batches. The signal-to-noise ratio (SNR) was set to 7 for Jan to Jun samples or 3.5 for Jul to Dec samples to minimize the batch effect. Spots with minimum intensity < 100 or detected in < 50% replicate samples were removed before statistical analyses. Both the universal standard and functional gene spot intensities are used to normalize the signals among arrays. Data were logarithmically transformed after quality control and normalization.
Probe names and detailed info for PROBE_ID in raw data and proteinGI in the data matrix are provided seperately. One shall be able to easily process the raw data, get normalized data, and complete annotations using http://ieg.ou.edu/microarray/.
Processed data file includes: Normalized signal intensity
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| Submission date |
Jan 26, 2022 |
| Last update date |
Feb 11, 2022 |
| Contact name |
Jiesi Lei |
| E-mail(s) |
leijs20@mails.tsinghua.edu.cn
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| Organization name |
Tsinghua University
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| Street address |
School of Environment, Tsinghua
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platform ID |
GPL22866 |
| Series (1) |
| GSE195490 |
Monthly dynamics of microbial functional diversity and composition in a tall-grass prairie, 2012 |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM5839184_255755310399_a01_532_635_converted_GE2_1105_Oct12_1_1.txt.gz |
46.8 Mb |
(ftp)(http) |
TXT |
| Processed data are available on Series record |
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