|
| Status |
Public on Mar 01, 2020 |
| Title |
control RNA for 180 min treatment, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
RNA of yeast cells exposed to no NP for 180 minutes
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4742
|
| Treatment protocol |
Cultures at mid-exponential phase were treated with 1 mg/L and 5 mg/L NP prepared in ethanol while controls were treated with the same volume of ethanol for 120 and 180 minutes.
|
| Growth protocol |
YPD broth was inoculated with 1% of yeast pre-culture and incubated at 30⁰C, 180 RPM in incubator shaker
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total RNA was performed with RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
100 ng of total RNA was used to synthesize first-strand cDNA and the first-stranded cDNA was converted into a double-stranded DNA with GeneChip 3’ IVT Express Kit (Affymetrix Inc). In vitro transcription and synthesis of biotin-labelled aRNA were performed using the double-stranded DNA as a template.
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| |
|
| Hybridization protocol |
The purification and fragmentation steps were carried out using GeneChip reagents and fragmented aRNA was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies). A total of 5 µg of aRNA was hybridized on arrays for 16-h at 45⁰C.The arrays were then loaded into a fluidics station for washing and staining using Affymetrix Command Consoles Software (AGCC) 3.0.1 Fluidics Control Module with Mini_euk2v3.
|
| Scan protocol |
Arrays were scanned on an Affymetrix GeneChip Scanner 3000.
|
| Description |
NPK181
|
| Data processing |
CEL files obtained from the analyzed arrays were normalized via quantile normalization using RMA as applied in the affy package of R/Bioconductor suite of tools for the analysis of transcriptomics data. Significantly expressed genes were identified from the normalized log-expression values using the multiple testing option of LIMMA .
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| |
|
| Submission date |
Mar 15, 2017 |
| Last update date |
Mar 01, 2020 |
| Contact name |
Ceyhun Bereketoglu |
| E-mail(s) |
[email protected]
|
| Organization name |
Marmara University
|
| Street address |
Goztepe
|
| City |
Istanbul |
| ZIP/Postal code |
34722 |
| Country |
Turkey |
| |
|
| Platform ID |
GPL2529 |
| Series (1) |
| GSE96651 |
Genome reprogramming in Saccharomyces cerevisiae upon nonylphenol exposure |
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