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| Status |
Public on Jun 26, 2020 |
| Title |
FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues [human] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Fixed-Tissue ChIP-seq for H3K27Ac profiling (FiTAc-seq) is an epigenetic method for profiling active enhancers and promoters in FFPE tissues. We previously developed a modified ChIP-seq protocol (FiT-seq) for chromatin profiling in FFPE. FiT-seq produces high-quality chromatin profiles particularly for methylated histone marks but is not optimized for H3K27Ac profiling. FiTAc-seq is a modified protocol that replaces the proteinase K digestion applied in FiT-seq with extended heating at 65°C in more stringent detergent conditions and a minimized sonication step, to produce robust genome-wide H3K27Ac maps from clinical samples. We demonstrate FiTAc-seq suitability to generate high quality enhancer landscapes and SE annotation in a number of archived FFPE samples from distinct tumor types. This approach will be of great interest both for basic and clinical researchers. The entire protocol from FFPE blocks to sequence ready library can be accomplished within 4 days.
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| Overall design |
3 samples per tissue type for bladder, melanoma, and seminoma. 1 brain cancer breast metastasis sample. RT4 cell line open chromatin assessed to compare bladder.
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| Contributor(s) |
Font-Tello A, Kesten NG, Cejas P, Long HW |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Nov 21, 2019 |
| Last update date |
Jun 28, 2020 |
| Contact name |
Henry Long |
| E-mail(s) |
Henry_Long@DFCI.HARVARD.EDU
|
| Organization name |
Dana Farber Cancer Institute
|
| Street address |
450 Brookline ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
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| Platforms (2) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (13)
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| This SubSeries is part of SuperSeries: |
| GSE140808 |
FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues |
|
| Relations |
| BioProject |
PRJNA590996 |
| SRA |
SRP231165 |
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