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| Status |
Public on Apr 24, 2018 |
| Title |
NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence [ATAC-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We describe the accessible chormatin landscape in RAS-induced (RIS) and NOTCH induced senescence (NIS) using ATAC-seq. By expressing active NOTCH (N1ICD) in the context of RIS, we find that N1ICD antagonizes the formation of accessible regions in RIS. By performing co-cultures, we demonstrate that cells expressing a NOTCH1 ligand, JAGGED1, can antagonize the formation of RIS specific accessible regions.
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| Overall design |
Interrogation of accessible regions in RIS and NIS cells using ATAC-seq in IMR90 cells expressing ER:HRAS(G12V) and infected with a control (pWZL) vector or pWZL FLAG-N1ICD, and treated with 100nM 4OHT for 6 days or untreated. In co-culture experiments, IMR90 cells expressing ER:HRAS(G12V) and mRFP1 are cultured at a ratio of 1:1 with tumour cell lines for 6 days with 4OHT before isolating red (IMR90 cells) using flow cytometry to perform ATAC-seq. To determine the effect of HMGA1 depletion on the distribution of nucleosome free regions in RIS cells, IMR90 cells expressing ER:HRAS(G12V) were retrovirally infected with a short hairpin targetting HMGA1 (shHMGA1) and treated for 6 days with 4OHT before ATAC-seq.
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| Contributor(s) |
Parry AJ, Bihary D, Samarajiwa SA, Narita M |
| Citation(s) |
29743479 |
| |
| Submission date |
Sep 07, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Shamith Samarajiwa |
| Organization name |
Imperial College London
|
| Department |
Genetics and Genomics Section Department of Metabolism, Digestion and Reproduction
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| Lab |
Computational Biology & Data Science
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| Street address |
ICTEM Building, Hammersmith Campus, Du Cane Road,
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| City |
London |
| ZIP/Postal code |
W12 0NN |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (24)
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| This SubSeries is part of SuperSeries: |
| GSE103590 |
NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence |
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| Relations |
| BioProject |
PRJNA402015 |
| SRA |
SRP117024 |
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