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| Status |
Public on Sep 06, 2018 |
| Title |
Transcriptome Profiling of PanIN Cells Exposed to Tobacco Carcinogen |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: The goals of this study are to compare transcriptome profiling (RNA-seq) in pancreatic intraepithelial neoplasm (PanIN) cells exposed to tobacco-specific nitrosamine 4-(methyl nitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and to examine the upregulated pathways.
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| Overall design |
Methods: Total RNA was isolated from PanIN cells treated with tobacco specific nitrosamine 4-(methyl nitrosamino)-1-(3-pyridyl)-1-butanone (NNK) for 5 and 50 days. Samples were processed for RNA-seq using standard methods on the Illumina HiSeq 2000 platform. Sequencing was performed in two multiplexed lanes of 100-bp single-end sequencing, which resulted in 75 million mappable reads per lane. The Illumina pipeline was used for base calling and quality filtering of sequence reads. Transcript assembly and abundance estimates of transcripts in fragments per kilobase of exon per million fragments mapped (FPKM) were performed by Cufflinks. Significant differences in total gene and transcript expression, splice site, transcription start site (TSS) and promoter usage were determined using a false discovery rate (FDR)-adjusted P-value. This study provides a framework for understanding transcriptional changes when pancreas cells exposed to tobacco specific nitrosamine.
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| Contributor(s) |
Nagathihalli NS |
| Citation(s) |
30232221 |
| |
| Submission date |
Sep 05, 2018 |
| Last update date |
Mar 19, 2019 |
| Contact name |
Nagaraj Nagathihalli |
| E-mail(s) |
nnagathihalli@med.miami.edu
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| Phone |
(305) 243-3502
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| Organization name |
University of Miami
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| Department |
Surgery
|
| Street address |
1550 NW 10th Ave
|
| City |
Miami |
| State/province |
Florida |
| ZIP/Postal code |
33136 |
| Country |
USA |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA489448 |
| SRA |
SRP159661 |
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