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| Status |
Public on Aug 15, 2017 |
| Title |
The Genomic Landscape of Atypical Fibroxanthoma |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In this study, we used exome sequencing and RNA sequencing to describe the genomic landscape of Atypical Fibroxanthoma (AFX). Using exome sequencing data, we identified several genes commonly mutated in our samples such as CSMD3, COL11A1, and FAT1. We also identified deletions in chr9p and chr13q in the AFX tumors. Using our RNA-sequencing data, we identified 8591 differentially expressed genes, of which 3524 genes had at least a 2 log fold change between AFX tumors and normal keratinocytes. We also identified several pathways that are dysregulated in AFX, such as epithelial to mesenchymal transition and tumor-associated macrophage response.
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| Overall design |
Eight atypical fibroxanthoma samples were collected during Mohs surgery and wide local excision. The samples were snap frozen and embedded in Tissue-Tek. Laser capture microdissection was used to isolate the tumor and normal keratinocytes. Exome sequence libraries were prepared with the Nimblegen SeqCap EZ Exome 3.0 capture kit. The RNA samples were reversed transcriped using the Nugen's Ovation RNA-Seq system-kit and prepared using Nugen's Ovation Ultralow kit. 101bp paired-end sequencing was performed on an Illumina HiSeq 2500 for the exome and RNA-Seq libraries. The normal keratinocytes were used as controls in this study when compared to the tumor.
RNA-seq data in this Series.
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| Contributor(s) |
Lai K, Harwood CA, Purdie K, Proby C, Mully T, Brooks L, Arron ST |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Aug 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Lai |
| E-mail(s) |
Kevin.Lai@ucsf.edu
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| Organization name |
University of California, San Fransico
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| Department |
Dermatology
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| Street address |
2340 Sutter Street
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA339046 |
| SRA |
SRP082197 |
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