Data in Brief ∎ (∎∎∎∎) ∎∎∎–∎∎∎
1 Contents lists available at ScienceDirect 2 3 4 5 6 journal homepage: www.elsevier.com/locate/dib 7 8 9 Data Article 10 11 12 13 14 2 15 Q2 16 a a,b,n 17 Q1 Michael Petridis , Gregory M. Cook 18 a Department of Microbiology and Immunology, Otago School of Medical Sciences, University of Otago, 19 Dunedin 9054, New Zealand b 20 Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand 21 22 23 24 a r t i c l e i n f o abstract 25 Article history: The dataset presented here describes a microarray experiment to 26 Received 13 September 2016 identify the AmtR regulon of Mycobacterium smegmatis comparing 27 Received in revised form the transcription profile of a M. smegmatis amtR mutant to 28 14 October 2016 M. smegmatis wild-type. The raw and processed microarray data 29 Accepted 15 November 2016 are available in the ArrayExpress database under Accession Num30 ber E-MTAB-4857 and interpretation of this data is found in the 31 research article “Structure and function of AmtR in Mycobacterium 32 smegmatis: implications for post-transcriptional regulation of urea 33 metabolism through a small antisense RNA” (Petridis et al., in 34 press) [1]. 35 & 2016 Published by Elsevier Inc. This is an open access article 36 under the CC BY license (http://creativecommons.org/licenses/by/4.0/). 37 38 39 40 Specifications Table 41 42 43 Subject area Biology 44 More specific sub- Molecular biology 45 ject area 46 47 48 DOI of original article: http://dx.doi.org/10.1016/j.jmb.2016.09.009 n 49 Correspondence to: Department of Microbiology and Immunology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand. 50 E-mail addresses:
[email protected] (M. Petridis),
[email protected] (G.M. Cook). 51 52 http://dx.doi.org/10.1016/j.dib.2016.11.049 53 2352-3409/& 2016 Published by Elsevier Inc. This is an open access article under the CC BY license 54 (http://creativecommons.org/licenses/by/4.0/).
Data in Brief
Microarray dataset on the genome-wide expression profile of an M. smegmatis amtR mutant (JR258) compared to M. smegmatis mc 155
Please cite this article as: M. Petridis, G.M. Cook, Microarray dataset on the genome-wide expression profile of an M. smegmatis amtR mutant (JR258) compared to M. smegmatis mc2155, Data in Brief (2016), http://dx.doi.org/10.1016/j.dib.2016.11.049i
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M. Petridis, G.M. Cook / Data in Brief ∎ (∎∎∎∎) ∎∎∎–∎∎∎
55 Type of data Text file,.xlsx file (Excel) 56 How data was Scanned Genepix 4000A scanner. Images were quantified using Spotfinder 57 acquired (TIGR). Total normalization and LOWESS normalization with MIDAS software 58 (TIGR) 59 Data format Raw, processed 60 Experimental A markerless deletion of the amtR gene in the background of M. smegmatis 61 factors mc2155 was created. 62 Experimental Expression profiles of a M. smegmatis amtR mutant and M. smegmatis mc2155 63 features were determined during aerobic growth in Hartmans de Bont minimal medium. 64 Data source Not applicable 65 location 66 Data accessibility Data within this article are available in the ArrayExpress database (https:// 67 www.ebi.ac.uk/arrayexpress/) under Accession Number E-MTAB-4857. 68 69 Value of the data 70 Description of the AmtR regulon gives insight into its role in the regulation of nitrogen metabolism 71 72 in actinomycetes. Our data can be used to further clarify gene regulation through the two canonical transcription 73 74 regulators AmtR and GlnR in response to nitrogen availability. The data can be used to characterize global regulatory networks in mycobacteria. 75 76 77 78 1. Data 79 80 Q3 Both raw and processed microarray data have been deposited in ArrayExpress with the Accession 81 Number E-MTAB-4857 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4857/). The data82 set summarize changes in the transcription profile of a Mycobacterium smegmatis amtR mutant 83 compared to M. smegmatis wild-type. Raw data files are the result of four independent biological 84 replicates including two dye swaps and the columns IA and IB in the raw data files correspond to Cy3 85 and Cy5 values, respectively. The processed data file contains the combined differential gene 86 expression data including statistical analysis. 87 88 89 2. Experimental design, materials and methods 90 91 2.1. Construction of amtR deletion mutant 92 93 For a detailed description for the amtR deletion mutant construction, see Petridis et al. [1]. 94 95 2.2. Microarray analysis and quantitative real-time PCR 96 97 Total RNA from M. smegmatis wild-type and M. smegmatis JR258 ΔamtR was extracted as pre98 viously described [2]. The quality of the RNA (RIN 49) was confirmed with the Bioanalyzer 2100 and 99 the concentration was determined using a NanoDrop ND-100 spectrophotometer. RT-PCR was per100 formed using SuperScript III (Invitrogen) according to the manufacturers instructions for cDNA 101 synthesis and Phusion High-Fidelity PCR Kit (New England Biolabs) for PCR. Microarray analysis was 102 performed using arrays provided by the Pathogen Functional Genomics Research Center (PFGRC) 103 funded by the National Institute of Allergy and Infectious Diseases using protocols SOP# M007 and 104 M008 from The Institute of Genomic Research (TIGR) [3]. The arrays were scanned using a Genepix 105 4000 A scanner and images were quantified using Spotfinder (TIGR) [3]. Total normalization and 106 LOWESS normalization of the data were performed with the MIDAS software (TIGR) [3]. All data have 107 108 been deposited in ArrayExpress with the Accession Number E-MTAB-4857. Please cite this article as: M. Petridis, G.M. Cook, Microarray dataset on the genome-wide expression profile of an M. smegmatis amtR mutant (JR258) compared to M. smegmatis mc2155, Data in Brief (2016), http://dx.doi.org/10.1016/j.dib.2016.11.049i
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109 Acknowledgements 110 111 Q4 This work was supported by the Maurice Wilkins Centre for Molecular Biodiscovery and a 112 Marsden Grant from the Royal Society of New Zealand. G.M.C. was supported by a James Cook Fel113 lowship from the Royal Society of New Zealand. MP was supported by a University of Otago Doctoral 114 Scholarship, the Webster Center for Infectious Diseases and the Otago School of Medical Sciences. 115 116 117 Transparency document. Supplementary material 118 119 Q5 Transparency data associated with this article can be found in the online version at http://dx.doi. 120 org/10.1016/j.dib.2016.11.049. 121 122 123 Appendix A. Supplementary material 124 125 Supplementary data associated with this article can be found in the online version at http://dx.doi. 126 org/10.1016/j.dib.2016.11.049. 127 128 129 References 130 131 Q6 [1] M. Petridis, C. Vickers, J. Robson, J.L. McKenzie, M. Bereza, A. Sharrock, et al., Structure and function of AmtR in Mycobacterium smegmatis: implications for an AmtR/GlnR competitive binding mechanism for transcriptional regulation of urea 132 metabolism, J. Mol. Biol. (2016) (in press). 133 [2] M. Petridis, A. Benjak, G.M. Cook, Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using con134 tinuous culture, BMC Genom. 16 (2015) 821. [3] P. Hegde, R. Qi, K. Abernathy, C. Gay, S. Dharap, R. Gaspard, et al., A concise guide to cDNA microarray analysis, Bio135 techniques 29 (2000) 548–562.
Please cite this article as: M. Petridis, G.M. Cook, Microarray dataset on the genome-wide expression profile of an M. smegmatis amtR mutant (JR258) compared to M. smegmatis mc2155, Data in Brief (2016), http://dx.doi.org/10.1016/j.dib.2016.11.049i
