 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 26, 2017 |
| Title |
Genomic binding for cAMP responsive transcription factors, CRP (Rv3676) and Cmr (Rv1675c) in TB complex mycobacteria |
| Organism |
Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We identified the genome-wide binding sites of CRP/FNR family transcription factors CRP and Cmr in M. bovis BCG using ChIP-seq, and cross-referenced these binding sites to orthologous regions in M. tuberculosis. Selected binding sites for each transcription factor were further characterized for their importance to gene regulation.
|
| |
|
| Overall design |
Chromatin immunoprecipitation was performed in M. bovis BCG Pasteur strain using antibodies to CRP or Cmr. Genome-wide binding profiles for each transcription factor were compared with and without elevated levels of cAMP. CRP studies were performed with native CRP expression levels, while Cmr binding was analyzed in the presence of cmr overexpression using the tuf promoter. cAMP levels were elevated exogenously by addition of dibutyryl cAMP treatment, or endogenously by expression of the Rv1264 catalytic domain. Bacteria were analyzed in late log phase during growth in ambient air (21% O2) or hypoxia (1.3% O2) supplemented with 5% CO2.
Please note that polyclonal antisera were generated in New Zealand white rabbits against CRP, as described in Bai et al. 2007. Infect Immun 75(11): 5509-5517, and against Cmr, as described in Ranganathan et al. 2016. Nucleic Acids Res 44(1):134-151.
|
| |
|
| Contributor(s) |
McDonough K, Ranganathan S |
| Citation(s) |
29165665 |
| |
| Submission date |
Oct 25, 2017 |
| Last update date |
Jun 12, 2019 |
| Contact name |
Kathleen McDonough |
| E-mail(s) |
[email protected]
|
| Organization name |
Wadsworth Center, NYSDOH
|
| Street address |
120 New Scotland Ave
|
| City |
Albany |
| State/province |
NY |
| ZIP/Postal code |
12208 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL24180 |
Illumina Genome Analyzer IIx (Mycobacterium bovis BCG str. Pasteur 1173P2) |
|
| Samples (10)
|
| GSM2830260 |
54_3; Native Cmr, basal cAMP levels |
| GSM2830261 |
33_4; Cmr overexpression, basal cAMP levels |
| GSM2830262 |
33_3; Cmr overexpression, exogenous cAMP supplementation |
| GSM2830263 |
33_1; Native CRP, exogenous cAMP supplementation |
| GSM2830264 |
33_2; Native CRP, basal cAMP |
| GSM2830265 |
34_1; Native CRP, endogenous cAMP supplementation |
| GSM2830266 |
49_3; Native CRP, basal cAMP levels |
| GSM2830267 |
49_4; Native CRP, basal cAMP levels, starvation |
| GSM2830268 |
54_1; Native CRP, basal cAMP |
| GSM2830269 |
54_2; Native CRP, endogenous cAMP supplementation |
|
| Relations |
| BioProject |
PRJNA415712 |
| SRA |
SRP121406 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE106135_CRP_Binding_Sites_GEO_Sub.txt.gz |
29.2 Kb |
(ftp)(http) |
TXT |
| GSE106135_Cmr_Binding_sites_GEO_Sub_b.txt.gz |
4.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...