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| Status |
Public on Mar 05, 2022 |
| Title |
Uterine fibroids patients gut microbiota Replicate 2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Uterine fibroids patient fecal microbiota
|
| Organism |
human feces metagenome |
| Characteristics |
age: 38
condition: Uterine fibroids
cell type: fecal microbiota
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA extracted following manufacturer's instructions
|
| Label |
cy5
|
| Label protocol |
10-20ng of DNA was amplified by PCR reaction with 16S universal primers.5ul PCR product was labelled with Bst enzyme and random primers at 45°C for 3 hours.The labeled product was stained with 20 μg of Cy5 dye and dissolved at 100 ng/ul after precipitation.
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| |
|
| Channel 2 |
| Source name |
Internal reference provided by the manufacturer
|
| Organism |
synthetic construct |
| Characteristics |
sample type: Internal reference (synthetic oligos)
concentration: 20ng/ul
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA extracted following manufacturer's instructions
|
| Label |
cy3
|
| Label protocol |
10-20ng of DNA was amplified by PCR reaction with 16S universal primers.5ul PCR product was labelled with Bst enzyme and random primers at 45°C for 3 hours.The labeled product was stained with 20 μg of Cy5 dye and dissolved at 100 ng/ul after precipitation.
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| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer provided by the manufacturer were added, and 500ng labeled sample DNA were applied to microarrays enclosed in the hybrid cassette. After hybridization, slides were washed sequential.
|
| Scan protocol |
Scans were performed on a GenePix4000B scanner.Images were quantified using Bluefuse software.
|
| Description |
Biological replicate 2 of 42.uterine fibroids patients gut microbiota
|
| Data processing |
LOWESS normalized, background subtracted data obtained from log10 of processed Red signal/processed Green signal. Bluefuse software was used.
The output.txt is the result from fluorescence array. All information about array was demonstrated in the head of output.txt file.
The output.xls.result.txt is the relative abundances of each identified species, which are calculated base on fluorescence value in output.txt.
The relative abundances of each identified species, which are calculated base on the program,which first calculated the mean intensities of the 3 replicated spots corresponding to each species for the Cy5 and Cy3 channels. The mean Cy5/Cy3 ratio was calculated from the mean intensity of the two channels. The species were ranked by their mean signal intensity from which the background fluorescent signal was calculated from the median of mean intensity of the lower 30% of the species. For a species to be judged as positive detection, its mean signal intensity must be 10 fold above the background fluorescent signal. To calculate the relative abundance of the positive species, we normalize the mean Cy5/Cy3 ratios of all the positive species and the percentage of each species multiply a fix factor 100000, and round up the result ,which is presented as the relative abundance value.
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| |
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| Submission date |
Mar 04, 2022 |
| Last update date |
Mar 05, 2022 |
| Contact name |
xuan peng |
| E-mail(s) |
206511008@csu.edu.cn
|
| Organization name |
Kaifu District, Changsha City, Hunan Province
|
| Street address |
88 Xiangya Road
|
| City |
Changsha City of Hunan Province |
| State/province |
Hunan |
| ZIP/Postal code |
421600 |
| Country |
China |
| |
|
| Platform ID |
GPL32019 |
| Series (1) |
| GSE197904 |
Gut microbiota: uterine fibroids patients vs. healthy control |
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