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| Status |
Public on Jun 23, 2022 |
| Title |
PrrA modulation of Mycobacterium tuberculosis response to acidic pH and high chloride levels is critically regulated by serine/threonine protein kinases |
| Organism |
Mycobacterium tuberculosis |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The purpose of this study was to understand how prevention of serine/threonine protein kinase (STPK) phosphorylation of PrrA impacts PrrA modulation of M. tuberculosis transcriptional response to acidic pH and high chloride levels.
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| Overall design |
Mtb strain CDC1551 with a deletion of the native copy of prrA, and harboring a prrA-FLAG-DAS4 (wild type prrA allele - prrA-DUC/∆prrA) or prrA-T6A-FLAG-DAS4 (T6A STPK-phosphoablative prrA allele - prrA-T6A-DUC/∆prrA) construct was grown to an OD600 of ~0.6 in standing, filter-capped T-75 flasks. Bacteria were then subcultured to an OD600 = 0.3 in standing, filter-capped T-25 flasks in 7H9, pH 7 media ± 250 mM NaCl, or 7H9, pH 5.7 media ± 250 mM NaCl. Exposure to the different media conditions was for 4 hours in a humidified, 37°C, 5% CO2 incubator before RNA was extracted. RNA was prepared by removing the rRNA and library prepping with a TruSeq Stranded kit (Illumina) before high-throughput sequencing with an Illumina HiSeq 2500 (High Output v4) (100 bp single end reads, one lane). Two biological samples per condition were sequenced.
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| Contributor(s) |
Giacalone D, Tan S |
| Citation(s) |
35913986 |
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| Submission date |
Mar 19, 2022 |
| Last update date |
Aug 24, 2022 |
| Contact name |
Shumin Tan |
| Organization name |
Tufts University School of Medicine
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| Department |
Molecular Biology and Microbiology
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| Street address |
150 Harrison Ave
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02111 |
| Country |
USA |
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| Platforms (1) |
| GPL17879 |
Illumina HiSeq 2500 (Mycobacterium tuberculosis) |
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| Samples (8)
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| GSM5962199 |
pH 7, prrA-DUC/∆prrA, replicate 1 (prrA T6A pH NaCl) |
| GSM5962200 |
pH 7, prrA-DUC/∆prrA, replicate 2 (prrA T6A pH NaCl) |
| GSM5962201 |
pH 7, prrA-DUC/∆prrA, 250 mM NaCl, replicate 1 (prrA T6A pH NaCl) |
| GSM5962202 |
pH 7, prrA-DUC/∆prrA, 250 mM NaCl, replicate 2 (prrA T6A pH NaCl) |
| GSM5962203 |
pH 7, prrA-T6A-DUC/∆prrA, replicate 1 (prrA T6A pH NaCl) |
| GSM5962204 |
pH 7, prrA-T6A-DUC/∆prrA, replicate 2 (prrA T6A pH NaCl) |
| GSM5962205 |
pH 7, prrA-T6A-DUC/∆prrA, 250 mM NaCl, replicate 1 (prrA T6A pH NaCl) |
| GSM5962206 |
pH 7, prrA-T6A-DUC/∆prrA, 250 mM NaCl, replicate 2 (prrA T6A pH NaCl) |
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| Relations |
| BioProject |
PRJNA817807 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE199000_PrrA_DUC_del_prrA_pHCl_vs_PrrA_DUC_del_prrA_pH7.csv.gz |
199.7 Kb |
(ftp)(http) |
CSV |
| GSE199000_PrrA_T6A_DUC_del_prrA_pH7_vs_PrrA_DUC_del_prrA_pH7.csv.gz |
202.5 Kb |
(ftp)(http) |
CSV |
| GSE199000_PrrA_T6A_DUC_del_prrA_pH7_vs_PrrA_T6A_DUC_del_prrA_pHCl.csv.gz |
200.8 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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