|
| Status |
Public on Jan 01, 2013 |
| Title |
CosR-knockdown replicate 2. |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
C. jejuni wild type
|
| Organism |
Campylobacter jejuni |
| Characteristics |
genotype/variation: wild type
strain: NCTC 11168
|
| Treatment protocol |
For the CosR-knockdown condition, CosR specific PNA (CosR-PNA) was supplemneted into bacterial inoculum to a final concentration of 1.5 uM.
|
| Growth protocol |
C. jejuni cells adjusted final OD value to 0.08 at 600 nm were grown at 42°C in MH broth to the mid-exponential phase for approximately 8 hr with shaking under microaerphilic condition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted with Trizol reagent (Invitrogen) according to the manufacturer’s instructions from three independent bacterial cultures. After DNase treatment with the Turbo DNA-free™ kit (Ambion), total RNA was purified using acid-phenol solution.
|
| Label |
Cy3
|
| Label protocol |
Labeling reactions were performed with a Bioprime labeling kit (Invitrogen) in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60 μM dTTP; and 60 μM Cy5-dUTP (for CosR-knockdown) or Cy3-dUTP (for the wild type).
|
| |
|
| Channel 2 |
| Source name |
C. jejuni with CosR specific PNA
|
| Organism |
Campylobacter jejuni |
| Characteristics |
genotype/variation: CosR specific PNA (CosR-PNA)
strain: NCTC 11168
|
| Treatment protocol |
For the CosR-knockdown condition, CosR specific PNA (CosR-PNA) was supplemneted into bacterial inoculum to a final concentration of 1.5 uM.
|
| Growth protocol |
C. jejuni cells adjusted final OD value to 0.08 at 600 nm were grown at 42°C in MH broth to the mid-exponential phase for approximately 8 hr with shaking under microaerphilic condition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted with Trizol reagent (Invitrogen) according to the manufacturer’s instructions from three independent bacterial cultures. After DNase treatment with the Turbo DNA-free™ kit (Ambion), total RNA was purified using acid-phenol solution.
|
| Label |
Cy5
|
| Label protocol |
Labeling reactions were performed with a Bioprime labeling kit (Invitrogen) in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60 μM dTTP; and 60 μM Cy5-dUTP (for CosR-knockdown) or Cy3-dUTP (for the wild type).
|
| |
|
| |
| Hybridization protocol |
Labeled cDNAs were mixed with hybridization solution (MYcroarray.com), and the hybridization mixtures were heated at 65℃ for 5 min and then immediately cooled on ice for 5 min. Hybridization mixtures were directly loaded onto assembled MYcroarray.com microarray. The arrays hybridized at 50℃ for 16 hr using Agilent Hybridization oven (Agilent Technology, USA).
|
| Scan protocol |
The hybridization images were analyzed by GenePix Pro 6.0 (Axon Instruments, CA).
|
| Description |
Biological replication 2 of 3
|
| Data processing |
The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GeneSpring 7.3.1 (Agilent Technologies, USA).
|
| |
|
| Submission date |
Aug 17, 2012 |
| Last update date |
Jan 01, 2013 |
| Contact name |
Sunyoung Hwang |
| E-mail(s) |
skyborn7@snu.ac.kr
|
| Organization name |
Seoul National University
|
| Department |
Department of Food and Animal Biotechnology
|
| Lab |
Lab of Molecular Food Microbiology
|
| Street address |
599 Gwanak-ro
|
| City |
Seoul |
| ZIP/Postal code |
151921 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL15955 |
| Series (1) |
| GSE40201 |
Transcriptomic analysis of differential genetic expression under CosR-knockdown condition compared with wild-type |
|
