|
| Status |
Public on Dec 05, 2012 |
| Title |
earlyJK31_28_D5 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Bartonella quintana culture from blood agar
|
| Organism |
Bartonella quintana |
| Characteristics |
temperature: 28C
day: 5
|
| Treatment protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Growth protocol |
Bartonella quintana cultures were passaged from thawed stocks on blood agar plates
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cDNA was generated from 0.5 mg of total RNA using random hexamer primers (Invitrogen) and SuperScriptä III (Invitrogen) following the manufacturer’s instructions
|
| Label |
Cy5
|
| Label protocol |
Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
|
| |
|
| Channel 2 |
| Source name |
pooled samples
|
| Organism |
Bartonella quintana |
| Characteristics |
sample type: pooled from all samples
|
| Treatment protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Growth protocol |
Bartonella quintana cultures were passaged from thawed stocks on blood agar plates
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cDNA was generated from 0.5 mg of total RNA using random hexamer primers (Invitrogen) and SuperScriptä III (Invitrogen) following the manufacturer’s instructions
|
| Label |
Cy3
|
| Label protocol |
Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
|
| |
|
| |
| Hybridization protocol |
Hybridization mix was comprised of 10 ml of Cy5 labeled sample, 10 ml of Cy3 labeled pooled reference sample, 5 ml blocking buffer, and 25 ml of Agilent Gene Expression Buffer. Hybridizations were carried out at 65°C for 16-19 h in Agilent hybridization chambers rotating at 10 rpm in a convection oven
|
| Scan protocol |
scanned on a Genepix 4000B scanner, adjusting PMT gains to balance the global dye signal balance ratio to 1.0 +/- 0.1
|
| Description |
Biological replicate. 28C timepoint day 5
|
| Data processing |
gridded using Genepix6.0 software, background subtracted Cy5/Cy3 ratios were log2 transformed and zero centered
|
| |
|
| Submission date |
Dec 03, 2012 |
| Last update date |
Dec 05, 2012 |
| Contact name |
Christopher S Nelson |
| E-mail(s) |
christopher.nelson@ucsf.edu
|
| Organization name |
UCSF
|
| Street address |
1700 4th St.
|
| City |
San Francisco |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL16349 |
| Series (1) |
| GSE42685 |
Bartonella quintana: growth phase and temperature response |
|
