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| Status |
Public on Mar 04, 2024 |
| Title |
ATAC-seq of TNF-alpha activation in HEK cells with or without TRAFTAC against NfkB |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
TRAnscription Factor TArgeting Chimeras (TRAFTACs) can downregulated specific transcription factors at the protein-level through their DNA-binding affinity. We tested a previously validated TRAFTAC (Samarasinghe et al., 2021) against NFkB in the context of TNF-alpha activation in HEK cells, and profiled DNA accessibility using ATAC-seq.
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| Overall design |
Replicating the experiments from (Samarasinghe et al., 2021), we transfected HEK cells with the dCas9-HT7 plasmid and DNA-RNA hybrids (NFkB or scrambled TRAFTAC, in duplicates) for 6h, before treating the cells with TNF-alpha (which triggers NFkB activation) and the PROTAC against the Halo tag (HP14) for 19h. We confirmed a 37% reduction in NFkB1/p50 levels before collecting the four samples for ATAC profiling.
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| Contributor(s) |
Frey SJ, Fischer V, Germain P, Gapp K |
| Citation missing |
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| Submission date |
Feb 28, 2024 |
| Last update date |
Mar 04, 2024 |
| Contact name |
Pierre-Luc Germain |
| Organization name |
ETH Zürich
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| Department |
D-HEST Institute for Neuroscience
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| Street address |
Winterthurerstrasse 190
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| City |
Zürich |
| ZIP/Postal code |
8057 Zürich |
| Country |
Switzerland |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (4)
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| GSM8118538 |
ATAC of HEK293 TNFa with scrambled TRAFTAC, rep1 |
| GSM8118539 |
ATAC of HEK293 TNFa with scrambled TRAFTAC, rep2 |
| GSM8118540 |
ATAC of HEK293 TNFa with TRAFTAC against NFkB, rep1 |
| GSM8118541 |
ATAC of HEK293 TNFa with TRAFTAC against NfkB, rep2 |
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| Relations |
| BioProject |
PRJNA1081902 |
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