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The following publications describe the data provided on this site.
- Galagan, J.E., Minch, K., Peterson, M., Lyubetskaya, A., Azizi, E., Sweet, L., Gomes, A., Rustad, T., Dolganov, G., Glotova, I., Abeel, T., Mahwinney, C., Kennedy, A.D., Allard, R., Brabant, W., Krueger, A., Jaini, S., Honda, B., Yu, W.H., Hickey, M.J., Zucker, J., Garay, C., Weiner, B., Sisk, P., Stolte, C., Winkler, J.K., Van de Peer, Y., Iazzetti, P., Camacho, D., Dreyfuss, J., Liu, Y., Dorhoi, A., Mollenkopf, H.J., Drogaris, P., Lamontagne, J., Zhou, Y., Piquenot, J., Park, S.T., Raman, S., Kaufmann, S.H., Mohney, R.P., Chelsky, D., Moody, D.B., Sherman, D.R., Schoolnik, G.K. (2013) The Mycobacterium tuberculosis regulatory network and hypoxia. Nature.499(7457):178-83
- Galagan, J., Lyubetskaya, A., Gomes, A. (2013) ChIP-Seq and the Complexity of Bacterial Transcriptional Regulation. Current topics in microbiology and immunology.363:43-68
- Jaini, S., Lyubetskaya, A., Gomes, A., Peterson, M., Park, S.T., Raman, S., Schoolnik, G., Galagan, J.E. Transcription Factor Binding Site Mapping Using ChIP-Seq. In: Hatfull G, Jacobs WR, Jr., editors. Molecular Genetics of Mycobacteria, 2nd Edition: ASM Press; In Press.
Use of these data should include the following acknowledgement:Data used was generated in whole or in part with Federal funds fromthe National Institute of Allergy and Infectious DiseasesNational Institute of Health, Department of Health and Human Services, under contract no. HHSN272200800059C
TF Induction Expression Data
Expression data following TF induction has been deposited in GEO under accession GSE43466
We have developed a number of software packages for data analysis.
CSDeconv is a computational method that determines the locations of transcription factor binding from ChIP-seq data. CSDeconv differs from prior methods in that it uses a blind deconvolution approach that allows multiple closely-spaced binding sites within a single promoter region to be called accurately. The method is described in Lun et al. (2009) . The source code is available here .
GenomeView is a stand-alone genome editor and viewer that provides fast and dynamic visualization of aligned short read data, genome sequences and annotations, and genome alignments. GenomeView allows users to load .bam files directly or through a URL. GenomeView was developed by a visiting graduate student in the Galagan lab, Thomas Abeel from Ghent University . It can be accessed and downloaded from its sourceforge page
E-Flux is novel method for modeling metabolic states using whole cell measurements of gene expression. The method extends the technique of Flux Balance Analysis (FBA) by modeling maximum flux constraints as a function of measured gene expression. The method is described in Colijn et al. (2009).
Experimental and computational protocols.
The following protocols are currently available:
(right-click on the links and choose "Save as..." to download the files)
In Vivo Culture Core
- THP-1 cell differentiation
- Mtb infection of THP-1 cell
- RNA and DNA isolation from Mtb infected THP-1 cells
- Sample prep for MS platforms
- Mtb enrichment MPIIB
- Mtb control for transcriptomics experiments
In Vitro Culture Core
- Protocol 1: in vitro Culture Protocol
- Protocol 1: ChIP in MTB
- Protocol 2: ChIP Library construction (from Illumina)
- ChIP of FLAG-tagged Atc-induced DNA binding proteins in MTB
- Sample sterilization for distribution to BL2 cores
- Detergent-free hypoxic model (SnowGlobe)
- Directional RNA Sequencing of rRNA-depleted MTB RNA
- Gene Expression Profiling using Two-Step MultiplexqRT-PCR
- Host RNA Isolation from MTB-infected Lung Tissue and Sputa
- MTB DNA Isolation from MTB-Infected Lung Tissue and Sputa
- MTB RNA Isolation from in vitro MTB Cultures
- MTB RNA Isolation from MTB-Infected Lung Tissue (Covaris Method)
- MTB Total RNAs Isolation (Alternative Qiagen Purification Method)
- Paired-End RNA Sequencing of rRNA-depleted MTB RNA
- rRNA Removal from Total RNA Using the EpicentreRibo-zero rRNA Removal Kit
- MPIB-0202-09VSBL (Fermentor and Snow Globe Model; cell pellets and culture medium)
- MPIB-0203-09SLBL (Fermentor Model; cell pellets and culture medium)
- MPIB-0204-09SLBL (Fermentor Model; cell pellets and culture medium)
- MPIB-0205-09SLBL (Snow Globe Model SG6; cell pellets and culture medium)
- MPIB-0206-09VSBL (Snow Globe Model SG7; cell pellets and culture medium)
- Protocol 1: Processing of Extracted Proteins
- Protocol 2: Protein Extraction from MTB by Bead Beating
- Protocol 3: Subcellular Fractionation of MTB Proteins
- Protocol 4: Protein Extraction for Secreted Proteome Analysis
- Protocol 5: Processing of Culture Filtrate for Secreted Proteome Analysis by Size Fractionation
- Protocol 6: Fractionation of Tryptic Digests of Extracted mTb Proteins/Peptides by Basic pH Reverse Phase Separation Method
- Protocol 7: Enrichment of Glycopeptides from Tryptic Mtb Digests
We use variety of third party software applications, publically available resources, and experimental methods.
Third Party Software
The Context Likelihood of Relatedness (CLR) algorithm is an extension of the relevance networks approach for identifying transcriptional regulatory interactions using gene expression data. The algorithm, developed by the lab of Tim Gardner, compares the mutual information between a transcription factor/gene pair to the background distribution of mutual information scores for all possible transcription factor/gene pairs that include either the transcription factor or its target. The algorithm is described in Faith et al. (2007) .
BioTapestry is an interactive tool for building, visualizing, and simulating genetic regulatory networks. BioTapestry was developed as a joint effort between the Bolouri Lab at the Institute for Systems Biology and the Davidson Lab at Caltech The tool provides a circuit diagram layout of genetic regulatory networks using a list of genetic interactions that can be manually our automatically generated. The software and example data sets can be downloaded here.
Cytoscape is a publically available open source software application for visualizing molecular interaction networks and integrating state information on the network. Cytoscape provides a general and flexible view of networks based on any type of underlying set of components and interactions, and is thus a standard tool for the initial visual interrogation of complex interaction maps. The software is available here.