Transcriptomics

Dataset Information

21

Analysis of RNA Based Transcriptome of Mycobacterium leprae genome from Environmental and Clinical Samples


ABSTRACT: BACKGROUND: This study was conducted to analyse M. leprae gene expression profiles in biopsy of leprosy patient and in environmental soil samples. Investigation was carried out to find out the expression profile for the minimal gene set necessary for growth of environmental M. leprae and its genes potentially require for infection and pathogenesis of leprosy. METHOD: RNA was extracted from human biopsy and environmental soil samples and total RNA obtained by subtractive hybridization of rRNA, was reverse transcribed and amplified using random primers. The whole genome was tiled at 10bp to obtain probes having 60 mer oligonucleotides in sense orientation. 179963 probes were designed in both sense and antisense orientation. Blast was performed against the mRNA sequence databases to check the specificity of the probes. Finally, 359926 probes were designed and 56579 specific probes were replicated to fill the remaining spots. RESULTS: Up regulation of several functional genes of M. leprae genome were observed from soil samples responsible for metabolism of Carbon compounds [9], Amino acids and amines [4] , Fatty acids synthesis [21], Lipid Biosynthesis [33], Phosphorous compounds [2]. Up regulation of genes were observed from soil samples in energy metabolism function such as Glycolysis [6], Pyruvate dehydrogenase [1], TCA cycle [12], Glyoxylate bypass [12]. In up regulation of respiration function [11] genes were observed and some of genes responsible for miscellaneous oxidoreductases and oxygenases [22] function, ATP-proton motive force [4] were also observed. Up regulation of genes for cell envelope function [65], conserved membrane proteins [107], cell processes [62], central intermediary metabolism [79], polyamine synthesis[38], biosynthesis of cofactors, prosthetic groups and carriers [36], broad regulatory functions [35], macromolecule metabolism[103], degradation of macromolecules [25], miscellaneous transferases [36], conserved hypothetical [204] and unknowns [101] were observed. Significant up regulation of Virulence genes [9], PE and PPE families [3] were also observed from soil samples. CONCLUSION: Transcriptome analysis indicated that up regulation of essential genes of M. leprae transcripts in environmental samples as compared to M. leprae from human biopsy samples which strongly suggested that several M. leprae genes are expressed more in environment for its survival and may act as source of infection. Overall design: RNA was extracted from human biopsy and environmental soil samples and total RNA obtained by subtractive hybridization of rRNA, was reverse transcribed and amplified using random primers. The whole genome was tiled at 10bp to obtain probes having 60 mer oligonucleotides in sense orientation. 179963 probes were designed in both sense and antisense orientation. Blast was performed against the mRNA sequence databases to check the specificity of the probes. Finally, 359926 probes were designed and 56579 specific probes were replicated to fill the remaining spots.

INSTRUMENT(S): Agilent-061379 Custom Mycobacterium Leprae, 2x400K designed by Genotypic Technology Private Limited. (AMADID: 061379)

ORGANISM(S): Mycobacterium leprae  

SUBMITTER: Genotypic technology  

PROVIDER: GSE68192 | GEO |

SECONDARY ACCESSION(S): PRJNA282025

REPOSITORIES: GEO

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