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| Status |
Public on Jan 13, 2024 |
| Title |
Targeted Perturb-seq of regulators of the transcriptional network downstream of RAF-MAPK signaling [perturb_seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In this study we use a (targeted) perturb seq experiment in which we knock out 22 transcription factors downstream of MAPK signalling in order to reconstruct the transcriptional network downstream of RAF/MAPK signaling.
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| Overall design |
HEK-RAF-ER were transduced with a pooled CRISPR/Cas9 library targeting 22 transcription factors and the RAF-ER transgene with 4 guides each. Additionally, 10 non-targeting controls and 10 safe-cutters were included as negative controls. After a period of editing, the RAF/MAPK pathway was induced by 4OHT (tamoxifen), and single cell transcriptome gene expression and CRISPR libraries were generated using the 10x Chromium Single Cell 3' V3 with Feature Barcoding technology. Additionally, we performed targeted PCR amplification of 140 genes that yielded better coverage of these genes. These dial-out libraries were sequenced seperately.
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| Contributor(s) |
El GK, Klinger B, Sieber A, Böttcher M, Blüthgen N |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Dec 19, 2023 |
| Last update date |
Jan 15, 2024 |
| Contact name |
Nils Blüthgen |
| E-mail(s) |
nils.bluethgen@charite.de
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| Organization name |
Charite Universitätsmedizin Berlin
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| Department |
Institute of Pathology
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| Street address |
Chariteplatz 1
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| City |
Berlin |
| ZIP/Postal code |
10117 |
| Country |
Germany |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (18)
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| This SubSeries is part of SuperSeries: |
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| Relations |
| BioProject |
PRJNA1054533 |
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