|
| Status |
Public on Feb 10, 2016 |
| Title |
Coxiella grown in Vero cells, time 14D, replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Coxiella grown in Vero cells, time 14D, early SCV
|
| Organism |
Coxiella burnetii |
| Characteristics |
strain/background: 493
cell type: bacterial cells
infected: Vero epithelial cells
time point (post-infection): 14 days
developmental stage: early SCV
|
| Treatment protocol |
C. burnetii was profiled at day 3, day 5, day 7, day 14 and day 21 post-infection of Vero cells.
|
| Growth protocol |
C. burnetii was grown in Vero cells for the time specified.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction followed by a MicrobEnrich kit (Applied Biosystems) was used to increase the relative level of C. burnetii RNA. Enriched RNA (~1 μg) was amplified using a MessageAmp II Bacteria kit (Applied Biosystems).
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled cRNA was then in vitro transcribed using cDNA as a template. Ten ug of labeled cRNA was fragmented using Ambion 10X fragmentation buffer (Invitrogen) and incubation at 75°C for 15 min.
|
| |
|
| Hybridization protocol |
All cRNAs were hybridized to a custom Affymetrix GeneChip.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.
|
| Description |
5099_KMS_2_Cb3_55_Vero-14-r2-848_01_8665
Gene expression data from Coxiella grown in Vero cells, time 14D replicate 2.
|
| Data processing |
The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Ft genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
|
| |
|
| Submission date |
Oct 29, 2015 |
| Last update date |
Feb 11, 2016 |
| Contact name |
Dan Sturdevant |
| E-mail(s) |
[email protected]
|
| Phone |
4063639248
|
| Organization name |
NIH
|
| Department |
NIAID
|
| Lab |
RTS
|
| Street address |
903 S 4th street
|
| City |
Hamilton |
| State/province |
MT |
| ZIP/Postal code |
59840 |
| Country |
USA |
| |
|
| Platform ID |
GPL4692 |
| Series (1) |
| GSE74489 |
Transcriptional profiling of Coxiella burnetii reveals extensive cell wall remodeling in the small cell variant developmental form |
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