|
| Status |
Public on Mar 04, 2019 |
| Title |
Active Mycobacterium tuberculosis regulatory networks from in vitro infection of mouse macrophages 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 vitro bone marrow derived macrophages (Mus musculus).
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| Overall design |
Mouse bone marrow derived macrophages (BMDMs) were infected with MTB H37Rv strain (MOI 10), followed by washing 3x with RPMI at 2 h post infection. At 2 h, 8 h, and 24 h MTB infected BMDMs were lysed with TRIzol (Invitrogen) and total RNA was isolated from mixed host-pathogen sample. MTB from bacterial culture in 7H9 media and uninfected BMDMs were also collected at the same time points. Samples were either processed by Path-seq, RNA-seq or and profiled by Illumina sequencing, in triplicate. 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.
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| |
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| Contributor(s) |
Peterson EJ, Baliga NS |
| Citation(s) |
30833303 |
| |
| Submission date |
Jun 27, 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 |
| |
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| Platforms (3) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL22688 |
Illumina NextSeq 500 (Mycobacterium tuberculosis) |
| GPL25252 |
Illumina NextSeq 500 (Mus musculus; Mycobacterium tuberculosis) |
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| Samples (36)
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| Relations |
| BioProject |
PRJNA478245 |
| SRA |
SRP151491 |
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