|
| Status |
Public on Feb 13, 2018 |
| Title |
S. aureus, treated, 6.25 µM C162, biological replicate1 |
| Sample type |
RNA |
| |
|
| Source name |
C162-treated, S. aureus
|
| Organism |
Staphylococcus aureus |
| Characteristics |
growth phase: overnight culture (16-18 hours, lag phase)
treatment: C162
|
| Treatment protocol |
The samples were treated with 2.5 mg/mL lysozyme (Sigma-Aldrich) for 30 minutes at 37°C and proteinase K for 15 minutes at 65°C.
|
| Growth protocol |
S. aureus was cultured for 16 - 18 hours in the presence and absence of benzimidazole compound C162 (6.25 µM) at 37°C with agitation 250 rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total bacterial RNA was extracted using Epicentre MasterPureTM Complete DNA and RNA purification kit, followed by Qiagen's RNeasy Mini Kit and DNase treatment using Qiagen's RNase-Free DNase Set according to the manufacturers' instructions.
|
| Label |
biotin
|
| Label protocol |
50 ng of total RNA was processed using SensationPlusTM FFPE Amplification and 3' IVT Labeling Kit (Affymetrix) according to manufacturer's protocol to produce biotinylated cDNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, the cDNA were hybridized for 16 hour at 45°C with rotation at 60 rpm to Affymetrix GeneChip S. aureus Genome Array. GeneChips were washed and stained using the FS450_0005 fluidics protocol on fluidics station.
|
| Scan protocol |
GeneChips were scanned using an Affymetric 3000 7G scanner.
|
| Description |
Gene expression data of S. aureus in the presence of 6.25 µM C162.
|
| Data processing |
To perform data quality control (QC), feature intensity (CEL) files generated from GeneChip® Command Console® Software (AGCC) were imported into Affymetrix Expression Console (EC) 1.4 software. MAS5 algorithm were used for normalizing probe-level intensity. Gene expression analysis was performed using three independent mRNA samples for each group. To perform statistical analysis and obtain a list of differentially expressed genes, the resultant data (CHP files) were subjected to Affymetrix® Transcriptome Analysis Console (TAC) software for Gene Level Differential Expression Analysis.
|
| |
|
| Submission date |
Jul 18, 2016 |
| Last update date |
Feb 13, 2018 |
| Contact name |
Cin Kong |
| E-mail(s) |
kong_cin@hotmail.com
|
| Organization name |
Universiti Kebangsaan Malaysia
|
| Department |
School of Bioscience and Biotechnology
|
| Street address |
Faculty of Science and Technology
|
| City |
UKM Bangi |
| State/province |
Selangor |
| ZIP/Postal code |
43600 |
| Country |
Malaysia |
| |
|
| Platform ID |
GPL1339 |
| Series (1) |
| GSE84485 |
Effect of benzimidazole derivative C162 on Staphylococcus aureus virulence |
|
