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| Status |
Public on May 04, 2021 |
| Title |
RNA-seq after DDX41 knockdown in U2OS cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: Investigating transcriptome changes after depletion of DDX41.
Methods: mRNA profiles after DDX41 knockdown compared to control knockdown were generated in 5 biological replicates. Samples were mapped using STAR (v2.7) against hg38 with the Gencode annotation. Reads per gene were counted using featureCounts (v.1.6). The differential expression analysis was performed using Bioconductor (v2.46)/DESeq2 (v1.26). Genes were deemed sign. diff. regulated with an FDR below 1%
Results: We were able to map 32,705 transcripts. Reactome pathway analysis revealed members of the NOTCH and TGFß family to be significantly upregulated when comparing a control knockdown to DDX41 knockdown. In addition, genes in chromatin organization were upregulated.
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| |
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| Overall design |
mRNA profiles 48 hours after a control knockdown or DDX41 knockdown in U2OS cells
|
| Web link |
https://assets.researchsquare.com/files/rs-337351/v1_stamped.pdf
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| |
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| Contributor(s) |
Mosler T, Voigt A, Beli P, Kreim N |
| Citation(s) |
34916496 |
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https://doi.org/10.21203/rs.3.rs-337351/v1
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| |
| Submission date |
Mar 03, 2021 |
| Last update date |
Jan 11, 2022 |
| Contact name |
Petra Beli |
| E-mail(s) |
p.beli@imb-mainz.de
|
| Organization name |
Institute of Molecular Biology (IMB)
|
| Street address |
Ackermannweg 4
|
| City |
Mainz |
| ZIP/Postal code |
55128 |
| Country |
Germany |
| |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (10)
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| This SubSeries is part of SuperSeries: |
| GSE168173 |
MapR in U2OS and HCT116 cells and RNA-seq in U2OS |
|
| Relations |
| BioProject |
PRJNA706394 |
| SRA |
SRP309134 |
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