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| Status |
Public on Jul 29, 2020 |
| Title |
Next generation sequencing to reveal the transcriptome of a DUX4 inducible FSHD model |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Bulk RNA sequencing was performed on a CML derived cell line, which contains an TET-ON inducible system for DUX4 inducible expression (DIE). Due to the unconventional cellular background used for the generation of an inducible FSHD cell line, bulk RNA seq was performed to determine if, and otherwise to what extend, this cellular background inteferes with the transcriptional program DUX4 is known to activate in muscle cells.
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| Overall design |
The transcriptomes of induced DIE cells were compared to uninduced or DIE cells, to identify differentially expressed genes or pathways that change upon DUX4 induction. Induced and uninduced DIE cells in which the DUX4 transgene was knocked-out (DIE_KO) served as controls. Samples were sequenced using Illumina Nextseq 500, 2x75 kit, high output. Four technical replicates per samples were send for sequencing.
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| Contributor(s) |
Ashoti A, Geijsen N, Vivié J, Creyghton M, Baak M |
| Citation missing |
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| |
| Submission date |
Jul 17, 2020 |
| Last update date |
Jul 29, 2020 |
| Contact name |
Niels Geijsen |
| Organization name |
Hubrecht institute
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| Lab |
Geijsen
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| Street address |
Uppsalalaan, 8
|
| City |
Utrecht |
| State/province |
Utrecht |
| ZIP/Postal code |
3584CT |
| Country |
Netherlands |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (20)
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| Relations |
| BioProject |
PRJNA646952 |
| SRA |
SRP272388 |
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