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| Status |
Public on May 10, 2024 |
| Title |
Soil sample 018 from Baltimore, USA |
| Sample type |
genomic |
| |
|
| Source name |
Soil samples from urban park green space
|
| Organism |
soil metagenome |
| Characteristics |
biome: Temperate
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA were extracted and qualified at AlmaLab (www.almalab.fi). Soils were extracted following the DNeasy PowerMax Soil Kit protocol (QIAGEN). The exact weight of each soil sample used for extraction was calculated by the mass difference between the 50 mL centrifuge tube (preservation solution preloaded) before and after soil addition. The DNA concentration was quantified using a Qubit 4 Fluorometer together with Qubit DNA IQ Assay Kit (Invitrogen). The DNA quality was verified by 1% agarose gel electrophoresis. DNA extracts were diluted to 1.5 ng uL-1 for amplicon sequencing.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled DNA was prepared from 1.0 ug DNA using the One-Color Low DNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by DNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and DNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
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| |
|
| Hybridization protocol |
1.0 ug of Cy3-labelled DNA (specific activity >10.0 pmol Cy3/ug DNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Geochip 5.0 180k Microarrays (G4112A) for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (GPL29739) using one color scan setting for 1x180k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
At each site, approximately 0.10 kg of soils was collected from surface (top 50 cm) for microbial Geochip analyses
|
| Data processing |
The purified DNA was analyzed using GeoChip 5.0 (Glomics Inc.). The total of 1.0 μg DNA per each plot received labelling, hybridization and imaging as previously described35, and the raw signal intensity data was then preprocessed by a standard analysis pipeline (http://ieg.ou.edu/microarray).
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| |
|
| Submission date |
Apr 16, 2021 |
| Last update date |
May 10, 2024 |
| Contact name |
Lantian Su |
| E-mail(s) |
lanter_shawn666@sjtu.edu.cn
|
| Organization name |
Shanghai Jiaotong University
|
| Department |
School of Agriculture and Biology
|
| Street address |
800 Dongchuan Rd.
|
| City |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
| |
|
| Platform ID |
GPL29739 |
| Series (1) |
| GSE172195 |
Geochip data of soil microbial community of biomes from three termperature zones |
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