|
| Status |
Public on Jan 25, 2013 |
| Title |
126421 Broth vs IC |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Intracellular
|
| Organism |
Francisella tularensis subsp. holarctica LVS |
| Characteristics |
sample type: Intracellular
growth substrate: hepatocytic cell line FL83B
|
| Treatment protocol |
The FL83B cells were co-incubated with the LVS for 24 h, washed, and incubate for another 24 h with gentamicin.
|
| Growth protocol |
The F. tularensis LVS cultured in MH broth overnight was used to infect FL83B cells or harvested as Broth control.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Intracellular bacteria were released by saponin in the presence of ethanol and phenol. Bacteria harvest from MH broth were treated the same way. Total RNA of bacteria were isolated with RNeasy Midi Kit.
|
| Label |
cy3
|
| Label protocol |
The cDNA of both the intracellular and broth-cultured LVS was synthsized from total RNA and labeled with cy3 or cy5, respectively.
|
| |
|
| Channel 2 |
| Source name |
Broth
|
| Organism |
Francisella tularensis subsp. holarctica LVS |
| Characteristics |
sample type: Broth
growth substrate: MH broth
|
| Treatment protocol |
The FL83B cells were co-incubated with the LVS for 24 h, washed, and incubate for another 24 h with gentamicin.
|
| Growth protocol |
The F. tularensis LVS cultured in MH broth overnight was used to infect FL83B cells or harvested as Broth control.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Intracellular bacteria were released by saponin in the presence of ethanol and phenol. Bacteria harvest from MH broth were treated the same way. Total RNA of bacteria were isolated with RNeasy Midi Kit.
|
| Label |
cy5
|
| Label protocol |
The cDNA of both the intracellular and broth-cultured LVS was synthsized from total RNA and labeled with cy3 or cy5, respectively.
|
| |
|
| |
| Hybridization protocol |
cDNA with 200 pmol Cy3 and cDNA with 200 pmol Cy5 were included in hybridization solution. Hybridization was performed on a TEcan hyrbridization station.
|
| Scan protocol |
Arrays were scanned with an Agilent 2505B scanner with laser power set to 100% and PMT gains set to auto.
|
| Data processing |
GenePix Pro 6 was used to grid arrays. Lossless image files were stored for later analysis. The microarray data was analyzed using the Limma module of the Bioconductor package for the R statistical environment. The normexp method was used for background correction, followed by print tip loess normalization and between-array normalization of intensities. The microarray data for each gene were fitted to a linear model, and statistics were generated using the lmFit and eBayes functions. The P values displayed were adjusted for multiple testing using the Benjamini and Hochberg method within Limma. Genes with P values of <0.05 were considered differentially regulated. Annotations for microarray data were derived from TIGR gal files.
|
| |
|
| Submission date |
Jan 24, 2013 |
| Last update date |
Jan 25, 2013 |
| Contact name |
Cindy A. Thomas |
| E-mail(s) |
cindya_thomas@yahoo.com
|
| Phone |
631-632-4226
|
| Fax |
631-632-4294
|
| Organization name |
Stony brook University
|
| Department |
Molecular Genetics and Microbiology
|
| Lab |
Martha B. Furie
|
| Street address |
280 CMM
|
| City |
Stony brook |
| State/province |
New York |
| ZIP/Postal code |
11794 |
| Country |
USA |
| |
|
| Platform ID |
GPL4250 |
| Series (1) |
| GSE43731 |
Gene Expression of F. tularensis LVS in hepatocytic cell line FL83B vs LVS cultured in MH broth |
|
