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| Status |
Public on Jul 08, 2020 |
| Title |
Determine differences in gene expression between OPSCC cell lines with different sensitivity to IR |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
mRNA sequencing was performed on 10 oropharyngeal cancer cell lines (5 HPV-positive and 5 HPV-negative cell lines) for this project. Two cell lines (CU-OP-17 and CU-OP-20) were newly derived from HPV-negative and HPV-positive tonsil cancers, respectively (described in " Sensitivity of human papillomavirus-positive and -negative oropharyngeal cancer cell lines to ionizing irradiation" by Holzhauser et al. This study was performed with the goal to identify differences in gene expression between irradiated and non-irradiated cell line samples. Additionally, the aim was to identify possible changes in genes, involved in DNA repair or DNA damage response of the HPV-positive and HPV-negative cell lines. The data published showed an increase of HPV integration sites after irradiation. Additionally, all HPV-positive cell lines in this study showed expression of HPV encoded genes. However, no direct correlation of changes or expression of DNA repair genes was identified.
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| Overall design |
Identification of differences in gene expression by mRNA sequencing between non-irradiated and irradiated (2Gy) HPV-positive and HPV-negative OPSCC cell lines. Cells were grown under standard cell culture condition, mRNA was extracted and sequencing perfomed with 75bp PE (sequencing readlength)- TruSeq stranded total RNA with ribo-zero GOLD
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| Contributor(s) |
Holzhauser S, Powell N, Man S, Giles P |
| Citation missing |
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| |
| Submission date |
Jul 07, 2020 |
| Last update date |
Jul 10, 2020 |
| Contact name |
Peter Giles |
| E-mail(s) |
GilesPJ@Cardiff.ac.uk
|
| Organization name |
Cardiff University
|
| Street address |
Heath Park
|
| City |
CARDIFF |
| ZIP/Postal code |
CF14 4XN |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (20)
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| Relations |
| BioProject |
PRJNA644620 |
| SRA |
SRP270802 |
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