|
| Status |
Public on Mar 16, 2021 |
| Title |
KW7 cDNA |
| Sample type |
RNA |
| |
|
| Source name |
Environmental soil
|
| Organism |
soil metagenome |
| Characteristics |
geographic location: Sub-Arctic: Whapmagoostui-Kuujjuarapik
|
| Treatment protocol |
Soil samples were collected using a sterile scoop and placed into a 5 mL sampling tube containing RNAlater Stabilization Solution
|
| Growth protocol |
Samples collected directly from the environment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total DNA and RNA were extracted from each soil sample using ZymoBIOMICS DNA & RNA kit. The total RNA extracted were subjected to DNAse I treatment and cDNA was generated from the RNA template using SuperScript IV First-Strand Synthesis System for RT-PCR according to the manufacturer’s instruction.
|
| Label |
Cy3
|
| Label protocol |
The DNA from each sample (500 ng) was labelled with the fluorescent dye Cy-3 by random priming.
|
| |
|
| Hybridization protocol |
Each dried and labelled DNA sample was resuspended in 42 µL of hybridization solution. This solution consisted of 1 x HI-RPM hybridization buffer, 1 x comparative genome hybridization blocking agent, 0.05 µg・µL-1 Cot-1 DNA, 10 pM universal standard, and 10% formamide (final concentrations). The solution was later denatured by remaining at 95 ℃ for 3 min. To remove the bubbles created during the denaturation process, the conditions were maintained at 37 ℃ for 30 min. The hybridizations were carried out at 67 ℃ for 24 h
|
| Scan protocol |
The scanned images of the GeoChip hybridizations were obtained and converted by means of the Agilent Feature Extraction 11.5 software (Agilent Technologies, California, USA)
|
| Data processing |
The signal intensities, used as a proxy of abundances, were quantified and processed based on previous pipelines48 as follows: (i) removing probes with a signal-to-noise ratio of less than 2.0; (ii) normalizing the signal intensity of each probe by dividing the total signal intensity of a sample and multiplying by a constant
|
| |
|
| Submission date |
Mar 15, 2021 |
| Last update date |
Mar 16, 2021 |
| Contact name |
Shu-Kuan Wong |
| E-mail(s) |
wong.shu.kuan@nipr.ac.jp
|
| Organization name |
National Polar Research Institute
|
| Street address |
10-3, Midori-cho,
|
| City |
Tachikawa-shi, |
| State/province |
Tokyo |
| ZIP/Postal code |
190-8518 |
| Country |
Japan |
| |
|
| Platform ID |
GPL29739 |
| Series (1) |
| GSE168911 |
Survey of Functional Genes in the Arctic Soil of Whapmagoostui-Kuujjuarapik |
|
