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Rideout JR, Chase JH, Bolyen E, Ackermann G, González A, Knight R, Caporaso JG. Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets. Gigascience 2016; 5:27. [PMID: 27296526 PMCID: PMC4906574 DOI: 10.1186/s13742-016-0133-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 06/01/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bioinformatics software often requires human-generated tabular text files as input and has specific requirements for how those data are formatted. Users frequently manage these data in spreadsheet programs, which is convenient for researchers who are compiling the requisite information because the spreadsheet programs can easily be used on different platforms including laptops and tablets, and because they provide a familiar interface. It is increasingly common for many different researchers to be involved in compiling these data, including study coordinators, clinicians, lab technicians and bioinformaticians. As a result, many research groups are shifting toward using cloud-based spreadsheet programs, such as Google Sheets, which support the concurrent editing of a single spreadsheet by different users working on different platforms. Most of the researchers who enter data are not familiar with the formatting requirements of the bioinformatics programs that will be used, so validating and correcting file formats is often a bottleneck prior to beginning bioinformatics analysis. MAIN TEXT We present Keemei, a Google Sheets Add-on, for validating tabular files used in bioinformatics analyses. Keemei is available free of charge from Google's Chrome Web Store. Keemei can be installed and run on any web browser supported by Google Sheets. Keemei currently supports the validation of two widely used tabular bioinformatics formats, the Quantitative Insights into Microbial Ecology (QIIME) sample metadata mapping file format and the Spatially Referenced Genetic Data (SRGD) format, but is designed to easily support the addition of others. CONCLUSIONS Keemei will save researchers time and frustration by providing a convenient interface for tabular bioinformatics file format validation. By allowing everyone involved with data entry for a project to easily validate their data, it will reduce the validation and formatting bottlenecks that are commonly encountered when human-generated data files are first used with a bioinformatics system. Simplifying the validation of essential tabular data files, such as sample metadata, will reduce common errors and thereby improve the quality and reliability of research outcomes.
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Affiliation(s)
- Jai Ram Rideout
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - John H Chase
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Evan Bolyen
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | - Antonio González
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, CA, 92093, USA.,Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, 92093, USA
| | - J Gregory Caporaso
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA. .,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA.
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Laubitz D, Harrison CA, Midura-Kiela MT, Ramalingam R, Larmonier CB, Chase JH, Caporaso JG, Besselsen DG, Ghishan FK, Kiela PR. Reduced Epithelial Na+/H+ Exchange Drives Gut Microbial Dysbiosis and Promotes Inflammatory Response in T Cell-Mediated Murine Colitis. PLoS One 2016; 11:e0152044. [PMID: 27050757 PMCID: PMC4822813 DOI: 10.1371/journal.pone.0152044] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 02/16/2016] [Indexed: 12/26/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are associated with functional inhibition of epithelial Na+/H+ exchange. In mice, a selective disruption of NHE3 (Slc9a3), a major apical Na+/H+ exchanger, also promotes IBD-like symptoms and gut microbial dysbiosis. We hypothesized that disruption of Na+/H+ exchange is necessary for the development of dysbiosis, which promotes an exacerbated mucosal inflammatory response. Therefore, we performed a temporal analysis of gut microbiota composition, and mucosal immune response to adoptive T cell transfer was evaluated in Rag2-/- and NHE3-/-/Rag2-/- (DKO) mice with and without broad-spectrum antibiotics. Microbiome (16S profiling), colonic histology, T cell and neutrophil infiltration, mucosal inflammatory tone, and epithelial permeability were analyzed. In adoptive T cell transfer colitis model, Slc9a3 status was the most significant determinant of gut microbial community. In DKO mice, NHE3-deficiency and dysbiosis were associated with dramatically accelerated and exacerbated disease, with rapid body weight loss, increased mucosal T cell and neutrophil influx, increased mucosal cytokine expression, increased permeability, and expansion of CD25-FoxP3+ Tregs; this enhanced susceptibility was alleviated by oral broad-spectrum antibiotics. Based on these results and our previous work, we postulate that epithelial electrolyte homeostasis is an important modulator in the progression of colitis, acting through remodeling of the gut microbial community.
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Affiliation(s)
- Daniel Laubitz
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
| | - Christy A. Harrison
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
| | - Monica T. Midura-Kiela
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
| | - Rajalakshmy Ramalingam
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
| | - Claire B. Larmonier
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
| | - John H. Chase
- Department of Biological Sciences, Center for Microbial Genetics and Genomics at Northern Arizona University, Flagstaff, Arizona, United States of America
| | - J. Gregory Caporaso
- Department of Biological Sciences, Center for Microbial Genetics and Genomics at Northern Arizona University, Flagstaff, Arizona, United States of America
| | - David G. Besselsen
- University Animal Care, University of Arizona, Tucson, Arizona, United States of America
| | - Fayez K. Ghishan
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
| | - Pawel R. Kiela
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
- * E-mail:
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