|
| Status |
Public on Feb 17, 2017 |
| Title |
OG1RF/rnjB Cy3/cy5 #2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Steady-state continuous cultured experimental samples after 15 min oxygen depletion.
|
| Organism |
Enterococcus faecalis |
| Characteristics |
strain: OG1RF
|
| Treatment protocol |
None
|
| Growth protocol |
Enterococcus faecalis cells were grown in BHI to mid-exponential phase at 37˚C 250rpm
|
| Extracted molecule |
total RNA |
| Extraction protocol |
An equavelent of 1 OD600 cells were collected. RNAs were extracted from collected cells using NucleoSpin RNA II kit with on-colume DNase digestion
|
| Label |
Cy3
|
| Label protocol |
Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.
|
| |
|
| Channel 2 |
| Source name |
Steady-state continuous cultured control samples in presence of oxygen
|
| Organism |
Enterococcus faecalis |
| Characteristics |
strain: rnjB deletion
|
| Treatment protocol |
None
|
| Growth protocol |
Enterococcus faecalis cells were grown in BHI to mid-exponential phase at 37˚C 250rpm
|
| Extracted molecule |
total RNA |
| Extraction protocol |
An equavelent of 1 OD600 cells were collected. RNAs were extracted from collected cells using NucleoSpin RNA II kit with on-colume DNase digestion
|
| Label |
Cy5
|
| Label protocol |
Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.
|
| |
|
| |
| Hybridization protocol |
Labelled cDNA hybridised using the MWG Gene-Frame system. Slides placed in shaking water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1 % SDS), 1x SSC, 0.2x SSC and 0.1x SSC, each at 37 °C for 5 min prior to drying and scanning.
|
| Scan protocol |
Microarray slides were scanned using an GenePix 4000b scanner with GENPIXPRO 5.0 software
|
| Description |
Cy3/Cy5 dye swap hybridized wildtype and mutant strain RNAs with microarray silde
|
| Data processing |
Data analysis was carried out using Genepix Pro 5.0 and Genesight version 4 (Biodiscovery Inc).After quantitation and global normalization using the average spot intensity, Ratios of OG1RF to the rnjB mutant were calculated for each spot. For each open reading frame (ORF), ratios for each culture were calculated by averaging ratios for spots within a chip that met quality criteria and their averaging dye-swap hybridizations. The P value from a one-sample t test, testing whether the grand mean log ratio was different from 0.0, was significant at the 0.05 level or better
|
| |
|
| Submission date |
Feb 16, 2017 |
| Last update date |
Feb 17, 2017 |
| Contact name |
Peng Gao |
| E-mail(s) |
peng.gao@uth.tmc.edu
|
| Phone |
7135003482
|
| Organization name |
UTHealth
|
| Department |
IMM
|
| Street address |
SRB 301V, 1825 Pressler Street
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL23076 |
| Series (1) |
| GSE95005 |
Comparison of transcriptome between E .faecalis OG1RF and rnjB deletion mutant |
|
