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| Status |
Public on May 08, 2024 |
| Title |
An epigenetic gene signature underlies phenotype switching in early stage melanomas [ChIP-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
A 122-epigenetic gene signature distinguished low- versus high-risk early stage melanomas. We sought to validate the signature, examined clinical correlates in a cohort of primary melanomas of the skin, and studied the underlying transcriptomic aberrations and changes in chromatin in cell lines representing these two groups.
H3K27Ac ChipSeq profiles of primary human melanoma cell lines (n=4) as well as corresponding input samples were generated by deep sequencing using Illumina NextSeq500.
Purpose: The goals of this study are to identify H3K27Ac differential peak expression between two groups of melanoma cell lines (Epgn1 and Epgn3) and relate this data to RNASeq.
Methods: H3K27Ac ChipSeq was performed on 4 melanoma cell lines by deep sequencing 75bp single end reads using Illumina NextSeq500. Reads were aligned and counts called using____. The sequence reads that passed quality filters were analyzed.
Results: Using an optimized data analysis workflow, we mapped about 40 million reads per Chip sample and 60 million reads per input sample to the human genome (build _____).
Conclusions: Our study allowed us to identify differentially expressed peaks between two classes of melanoma cell lines and relate this information to differential gene expression. Further in vitro and in vivo assays using some of the candidate genes identified will allow us to more fully understand primary melanoma progression.
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| Overall design |
H3K27Ac ChipSeq was performed on 4 melanoma cell lines by deep sequencing 75bp single end reads using Illumina NextSeq500.
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| Contributor(s) |
Mendelson K, Martin T, Nguyen C |
| Citation(s) |
38319712 |
| |
| Submission date |
Feb 22, 2022 |
| Last update date |
May 09, 2024 |
| Contact name |
Tiphaine Christiane Martin |
| E-mail(s) |
tiphaine.martin@mssm.edu
|
| Phone |
2128248403
|
| Organization name |
Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute
|
| Department |
Oncological Sciences
|
| Lab |
Parsons
|
| Street address |
1470 Madison Ave
|
| City |
New York |
| State/province |
75459 |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE198432 |
An epigenetic gene signature underlies phenotype switching in early stage melanomas. |
|
| Relations |
| BioProject |
PRJNA809401 |
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