Microarray dataset on the genome-wide expression profile of an M. smegmatis amtR mutant (JR258) compared to M. smegmatis mc2155.

The dataset presented here describes a microarray experiment to identify the AmtR regulon of Mycobacterium smegmatis comparing the transcription profile of a M. smegmatis amtR mutant to M. smegmatis wild-type. The raw and processed microarray data are available in the ArrayExpress database under Accession Number E-MTAB-4857 and interpretation of this data is found in the research article "Structure and function of AmtR in Mycobacterium smegmatis: implications for post-transcriptional regulation of urea metabolism through a small antisense RNA" (Petridis et al., in press) [1].

Specifications Table

Value of the data

Description of the AmtR regulon gives insight into its role in the regulation of nitrogen metabolism in actinomycetes.

Our data can be used to further clarify gene regulation through the two canonical transcription regulators AmtR and GlnR in response to nitrogen availability.

The data can be used to characterize global regulatory networks in mycobacteria.

Data

Both raw and processed microarray data have been deposited in ArrayExpress with the Accession Number E-MTAB-4857 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4857/). The dataset summarize changes in the transcription profile of a Mycobacterium smegmatis amtR mutant compared to M. smegmatis wild-type. Raw data files are the result of four independent biological replicates including two dye swaps and the columns IA and IB in the raw data files correspond to Cy3 and Cy5 values, respectively. The processed data file contains the combined differential gene expression data including statistical analysis.

Experimental design, materials and methods

Construction of amtR deletion mutant

For a detailed description for the amtR deletion mutant construction, see Petridis et al. [1].

Microarray analysis and quantitative real-time PCR

Total RNA from M. smegmatis wild-type and M. smegmatis JR258 ∆amtR was extracted as previously described [2]. The quality of the RNA (RIN>9) was confirmed with the Bioanalyzer 2100 and the concentration was determined using a NanoDrop ND-100 spectrophotometer. RT-PCR was performed using SuperScript III (Invitrogen) according to the manufacturers instructions for cDNA synthesis and Phusion High-Fidelity PCR Kit (New England Biolabs) for PCR. Microarray analysis was performed using arrays provided by the Pathogen Functional Genomics Research Center (PFGRC) funded by the National Institute of Allergy and Infectious Diseases using protocols SOP# M007 and M008 from The Institute of Genomic Research (TIGR) [3]. The arrays were scanned using a Genepix 4000 A scanner and images were quantified using Spotfinder (TIGR) [3]. Total normalization and LOWESS normalization of the data were performed with the MIDAS software (TIGR) [3]. All data have been deposited in ArrayExpress with the Accession Number E-MTAB-4857.

Subject area	Biology
More specific subject area	Molecular biology
Type of data	Text file,.xlsx file (Excel)
How data was acquired	Scanned Genepix 4000A scanner. Images were quantified using Spotfinder (TIGR). Total normalization and LOWESS normalization with MIDAS software (TIGR)
Data format	Raw, processed
Experimental factors	A markerless deletion of the amtR gene in the background of M. smegmatis mc2155 was created.
Experimental features	Expression profiles of a M. smegmatis amtR mutant and M. smegmatis mc2155 were determined during aerobic growth in Hartmans de Bont minimal medium.
Data source location	Not applicable
Data accessibility	Data within this article are available in the ArrayExpress database (https://www.ebi.ac.uk/arrayexpress/) under Accession NumberE-MTAB-4857.