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Transcriptional profiling of radiation damage and preventive treatments in a 3-dimensional (3D) human cell culture model of oral mucositis.

Lambros MP, DeSalvo MK, Moreno J, Mulamalla HC, Kondapalli L - Genom Data (2015)

Bottom Line: Here we provide detailed methods and analysis of microarray data for non-irradiated and irradiated human oral mucosal tissue with and without pretreatment with NAC, QYD and NAC-QYD.The microarray data been deposited in Gene Expression Omnibus (GEO): GSE62397.These data can be used to further elucidate the mechanisms of irradiation damage in oral mucosa and its prevention.

View Article: PubMed Central - PubMed

Affiliation: College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA.

ABSTRACT
Cancer patients who receive radiation are often afflicted by oral mucositis, a debilitating disease, characterized by mouth sores and difficulty in swallowing. Oftentimes, cancer patients afflicted with mucositis must stop life-saving therapies. Thus it is very important to prevent mucositis before it develops. Using a validated organotypic model of human oral mucosa, a 3-dimensional cell culture model of human oral keratinocytes, it has been shown that a mixture (NAC-QYD) of N-acetyl cysteine (NAC) and a traditional Chinese medicine, Qingre Liyan decoction (QYD), prevented radiation damage (Lambros et al., 2014). Here we provide detailed methods and analysis of microarray data for non-irradiated and irradiated human oral mucosal tissue with and without pretreatment with NAC, QYD and NAC-QYD. The microarray data been deposited in Gene Expression Omnibus (GEO): GSE62397. These data can be used to further elucidate the mechanisms of irradiation damage in oral mucosa and its prevention.

No MeSH data available.


Related in: MedlinePlus

Representative box plot of raw (R) and normalized (N) data from three technical replicate hybridizations of a single sample. For all samples, the box plots revealed median-centered raw data distributions, which were further refined during normalization. Overall, this points to high repeatability of technical replicate hybridizations.
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f0005: Representative box plot of raw (R) and normalized (N) data from three technical replicate hybridizations of a single sample. For all samples, the box plots revealed median-centered raw data distributions, which were further refined during normalization. Overall, this points to high repeatability of technical replicate hybridizations.

Mentions: Since three technical replicate hybridizations were performed and later averaged, care was taken to ensure high repeatability between technical replicates. First, raw and normalized log2 data for each sample were plotted using the R function boxplot. Control and flagged probes were not included. A representative box plot is shown in Fig. 1. While this analysis is designed to identify hybridizations that have intensity distributions different from those of their technical replicates, we did not find any instances of this. This analysis also ensures that the normalization has correctly centered the distributions of each replicate microarray.


Transcriptional profiling of radiation damage and preventive treatments in a 3-dimensional (3D) human cell culture model of oral mucositis.

Lambros MP, DeSalvo MK, Moreno J, Mulamalla HC, Kondapalli L - Genom Data (2015)

Representative box plot of raw (R) and normalized (N) data from three technical replicate hybridizations of a single sample. For all samples, the box plots revealed median-centered raw data distributions, which were further refined during normalization. Overall, this points to high repeatability of technical replicate hybridizations.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664678&req=5

f0005: Representative box plot of raw (R) and normalized (N) data from three technical replicate hybridizations of a single sample. For all samples, the box plots revealed median-centered raw data distributions, which were further refined during normalization. Overall, this points to high repeatability of technical replicate hybridizations.
Mentions: Since three technical replicate hybridizations were performed and later averaged, care was taken to ensure high repeatability between technical replicates. First, raw and normalized log2 data for each sample were plotted using the R function boxplot. Control and flagged probes were not included. A representative box plot is shown in Fig. 1. While this analysis is designed to identify hybridizations that have intensity distributions different from those of their technical replicates, we did not find any instances of this. This analysis also ensures that the normalization has correctly centered the distributions of each replicate microarray.

Bottom Line: Here we provide detailed methods and analysis of microarray data for non-irradiated and irradiated human oral mucosal tissue with and without pretreatment with NAC, QYD and NAC-QYD.The microarray data been deposited in Gene Expression Omnibus (GEO): GSE62397.These data can be used to further elucidate the mechanisms of irradiation damage in oral mucosa and its prevention.

View Article: PubMed Central - PubMed

Affiliation: College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA.

ABSTRACT
Cancer patients who receive radiation are often afflicted by oral mucositis, a debilitating disease, characterized by mouth sores and difficulty in swallowing. Oftentimes, cancer patients afflicted with mucositis must stop life-saving therapies. Thus it is very important to prevent mucositis before it develops. Using a validated organotypic model of human oral mucosa, a 3-dimensional cell culture model of human oral keratinocytes, it has been shown that a mixture (NAC-QYD) of N-acetyl cysteine (NAC) and a traditional Chinese medicine, Qingre Liyan decoction (QYD), prevented radiation damage (Lambros et al., 2014). Here we provide detailed methods and analysis of microarray data for non-irradiated and irradiated human oral mucosal tissue with and without pretreatment with NAC, QYD and NAC-QYD. The microarray data been deposited in Gene Expression Omnibus (GEO): GSE62397. These data can be used to further elucidate the mechanisms of irradiation damage in oral mucosa and its prevention.

No MeSH data available.


Related in: MedlinePlus