|
| Status |
Public on Aug 22, 2018 |
| Title |
RhBMDMsinfected with M. tuberculosis H37Rv isogenic dosS deletion mutant strain for 4 hour- Replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
M. tuberculosis H37Rv isogenic dosS deletion mutant bacterial RNA isolated from infected RhBMDMs at 0 hour (0 hour means 4hr incubation of macrophages with M. tuberculosis H37Rv isogenic mutant strain of dosS gene deletion)
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
strain/genotype: H37Rv isogenic mutant strain of dosS gene deletion
source: Intraphagosomal M. tuberculosis H37Rv isogenic mutant bacterial RNA isolated from infected macrophages 4 hr post infection
|
| Growth protocol |
Rh-BMDMs were cultured as previously described (Mehra et al 2010 PMCID: PMC3052882 and Dutta et al 2012 PMCID: PMC3250399 and M. tuberculosis cultures were grwon following th eprotocol decribed by Gautam et al 2010 (PMID: 26270051 )
|
| Extracted molecule |
total RNA |
| Extraction protocol |
As described in previous publication Gautam et al 2010 PMID: 26270051
|
| Label |
Cy5
|
| Label protocol |
As described in previous publication Gautam et al 2010 PMID: 26270051
|
| |
|
| Channel 2 |
| Source name |
M. tuberculosis H37Rv isogenic dosS deletion mutant bacterial RNA isolated from in vitro grown cultures in 7H9 media and not in macrophages were used as baseline control
|
| Organism |
Mycobacterium tuberculosis |
| Characteristics |
strain/genotype: H37Rv isogenic mutant bacterial strain of dosS gene deletion
source: M. tuberculosis H37Rv isogenic mutant bacterial RNA isolated from in vitro grown cultures and not in macrophages
|
| Growth protocol |
Rh-BMDMs were cultured as previously described (Mehra et al 2010 PMCID: PMC3052882 and Dutta et al 2012 PMCID: PMC3250399 and M. tuberculosis cultures were grwon following th eprotocol decribed by Gautam et al 2010 (PMID: 26270051 )
|
| Extracted molecule |
total RNA |
| Extraction protocol |
As described in previous publication Gautam et al 2010 PMID: 26270051
|
| Label |
Cy3
|
| Label protocol |
As described in previous publication Gautam et al 2010 PMID: 26270051
|
| |
|
| |
| Hybridization protocol |
As described in previous publication Gautam et al 2010 PMID: 26270051
|
| Scan protocol |
As described in previous publication Gautam et al 2010 PMID: 26270051
As described in previous publication Gautam et al 2010 PMID: 26270051
|
| Description |
Biological replicate 1 of 3
|
| Data processing |
Data analysis procedures have been described in detail in the above referenced previous publications from our group. Briefly, data was extracted from 16 BIT TIFF files scanned using GenePix 4000B scanner (5um res) using GenePix pro 7.0 and then uploaded to Spotfire DecisionSite for Microarray Analysis. Array data was then filtered for abberant SNR, flags etc and normalized using the S+ ArrayAnalyzer LOWESS normalization script resident within Spotfire. Statistical significance was determined using Spotfire. Analyzed data were then exported to Excel.
|
| |
|
| Submission date |
Aug 21, 2018 |
| Last update date |
Aug 22, 2018 |
| Contact name |
Uma S Gautam |
| E-mail(s) |
ugautam@tulane.edu
|
| Phone |
9858716553
|
| Organization name |
TNPRC
|
| Department |
Bacteriology and Parasitology
|
| Lab |
B209 or RBL 20
|
| Street address |
18703 Three Rivers Road
|
| City |
Covington |
| State/province |
LA |
| ZIP/Postal code |
70433 |
| Country |
USA |
| |
|
| Platform ID |
GPL18320 |
| Series (2) |
| GSE118867 |
Mycobacterium tuberculosis Sensor Kinase DosS Modulates the Autophagosome in a DosR-independent Manner [II] |
| GSE118869 |
Mycobacterium tuberculosis Sensor Kinase DosS Modulates the Autophagosome in a DosR-independent Manner |
|
