|
| Status |
Public on Mar 04, 2019 |
| Title |
Active Mycobacterium tuberculosis regulatory networks from alveolar macrophages of in vivo mouse infection uncovered by Path-seq |
| Organisms |
Mycobacterium tuberculosis; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Transcriptional profiling of Mycobacterium tuberculosis mRNA enriched from host-pathogen samples from in vivo alveolar macrophages (Mus musculus).
|
| |
|
| Overall design |
A mid log-phase stock of M. tuberculosis H37Rv was used to infect mice in an aerosol infection chamber. At 24 h after infection, bronchoalveolar lavage was performed on euthanized mice. Cells from BAL were filtered, spun down and resuspended in 96-well plate for antibody staining. Cell sorting was performed on a FACS Aria and the entire alveolar macrophage was resuspended in TRIzol (Invitrogen) where total RNA was isolated from mixed host-pathogen sample. MTB from bacterial culture in 7H9 media was also collected at 24 h as a control. Samples were processed by Path-seq, for enrichment of MTB transcripts. The sequence reads that passed quality filters were aligned to a combined M. tuberculosis and M. musuclus genome with Bowtie2 and processed using the R package DuffyNGS.
|
| |
|
| Contributor(s) |
Peterson EJ, Baliga NS |
| Citation(s) |
30833303 |
| |
| Submission date |
Jun 28, 2018 |
| Last update date |
Jun 03, 2019 |
| Contact name |
Eliza Peterson |
| Organization name |
Institute for Systems Biology
|
| Lab |
Baliga
|
| Street address |
401 Terry Ave N
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL22688 |
Illumina NextSeq 500 (Mycobacterium tuberculosis) |
| GPL25252 |
Illumina NextSeq 500 (Mus musculus; Mycobacterium tuberculosis) |
|
| Samples (6)
|
|
| Relations |
| BioProject |
PRJNA478391 |
| SRA |
SRP151570 |
Less...
More...