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Global gene expression profiles from PBMCs treated with reference tobacco product preparations.

ABSTRACT: This Data in Brief article describes global gene expression profiles from human peripheral blood mononuclear cells (PBMCs) that were treated with preparations from reference combustible and non-combustible tobacco products (TPPs). PBMCs isolated from non-smokers were treated with three non-cytotoxic doses of aqueous preparations from 3R4F cigarettes, termed Whole Smoke-Conditioned Medium (WS-CM) and a single dose of 2S3 moist snuff, termed smokeless tobacco extract (STE). PBMCs were treated with the test articles for 3 hours and the extracted total RNA was reverse transcribed and hybridized to HTA 2.0 Genechip® arrays and scanned using an Affymetrix GeneChip® Scanner 3000. CEL files and CHP files were generated using an Affymetrix Expression console. The CEL files were submitted to the NCBI database with GEO accession number GSE110027. The results of the microarray analyses are found in this Data in Brief article. Ingenuity Pathway Analysis (IPA; Qiagen) was used to conduct core analyses of genes that were differentially expressed by high WS-CM or STE based on the Ingenuity Gene knowledge. Expression of several of the differentially expressed genes was confirmed by RT-PCR. Analyses of these data can be found in the article "Distinct gene expression changes in human peripheral blood mononuclear cells treated with different tobacco product preparations" [1].

SUBMITTER: Arimilli S

PROVIDER: S-EPMC6598865 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

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Global gene expression profiles from PBMCs treated with reference tobacco product preparations.

Arimilli Subhashini S Makena Patrudu P Liu Gang G Prasad G L GL

Data in brief 20190503

This Data in Brief article describes global gene expression profiles from human peripheral blood mononuclear cells (PBMCs) that were treated with preparations from reference combustible and non-combustible tobacco products (TPPs). PBMCs isolated from non-smokers were treated with three non-cytotoxic doses of aqueous preparations from 3R4F cigarettes, termed Whole Smoke-Conditioned Medium (WS-CM) and a single dose of 2S3 moist snuff, termed smokeless tobacco extract (STE). PBMCs were treated with ...[more]

PMID: 31297406

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Project description:BACKGROUND: As an in vitro model porcine peripheral blood mononuclear cells (PBMCs) is frequently used as for immunogenetic research with the stimulation of bacterial antigens. To investigate the immunocompetence of PBMCs for recognition of Gram-positive and Gram-negative bacteria and in order to dissect the pathogenesis of diseases, gene expression assay is most commonly used. The gene expressions are required to normalize for reference genes which have tremendous effect on the results of expression study. The reference genes should be stably expressed between different cells under a variety of experimental conditions, but recent influx of data showed that expression stability of reference genes are varied under different experimental conditions. But data regarding the expression stability of reference genes in porcine PBMCs are limited. Therefore, this study was aimed to know whether the expression stability of commonly used reference genes in PBMCs is affected by various bacterial antigens under different experimental conditions in pigs. RESULTS: The mRNA expression stability of nine commonly used reference genes (B2M, BLM, GAPDH, HPRT1, PPIA, RPL4, SDHA, TBP and YWHAZ) was determined by RT-qPCR in PBMCs that were stimulated by LPS and LTA in vitro as well as cells un-stimulated control and non-cultured were also consider for this experiment. mRNA expression levels of all genes were found to be affected by the type of stimulation and duration of the stimulation (P?<?0.05). geNorm software revealed that in case of irrespective of stimulation (without considering the type of stimulation), RPL4, PPIA and B2M were the most stable reference genes in PBMCs; in case of the control group, PPIA, BLM and GAPDH were the most stable reference genes. PPIA, B2M and RPL4 were the most stable reference genes in LPS stimulated PBMCs; and YWHAZ, RPL4 and PPIA were the most stably expressed reference genes in the case of LTA stimulated PBMCs. When LPS was used combined with LTA for the stimulation, YWHAZ, B2M and SDHA remained the most stable genes. PPIA, BLM and GAPDH were found to be most stably expressed reference genes when PBMCs were not cultured. NormFinder revealed different sets of stably expressed reference genes in PBMCs under different experimental conditions. Moreover, geNorm software suggested that the geometric mean of the three most stable genes would be the suitable combination for accurate normalization of gene expression study. CONCLUSION: There was discrepancy in the ranking order of reference genes obtained by different analysing algorithms (geNorm and NormFinder). In conclusion, the geometric mean of the RPL4, B2M and PPIA seemed to be the most appropriate combination of reference genes for accurate normalization of gene expression data in porcine PBMCs without knowing the type of bacterial pathogenic status of the animals and in the case of mixed infection with Gram-negative and Gram-positive bacteria. In case of PBMCs without any stimulation, PPIA, BLM and GAPDH could be suggested as suitable reference genes.

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Global gene expression profiles from PBMCs treated with reference tobacco product preparations.

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Global gene expression profiles from PBMCs treated with reference tobacco product preparations.

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