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| Status |
Public on Dec 31, 2020 |
| Title |
Setd1a and Setd1b loss-of-function in murine macrophages |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Setd1bKO primary murine bone marrow-derived macrophages (BMDMs) were treated with lipopolysaccharide (LPS) or dexamethasone and LPS (Dex+LPS) and gene expression differences in response to treatment analysed by PolyA RNA-Sequencing. No Dex-treatment dependent gene expression differences were identified. Setd1aDel/+ Raw264.7 cells with reduced Setd1a expression were analyzed with regards to their reponse to Dex when inflammatorily challenged with LPS by mRNA-Seq. We observed reduced GR-dependent gene acivation in Setd1a hypermorphic Raw264.7 cells. Wild type and Setd1aDel/+ Raw264.7 cells were treated with LPS or LPS and interferon beta (IFNB1) to show the IFNB1-dependent loss of gene expression in LPS-stimulated Setd1aDel/+ cells.
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| Overall design |
We profiled mRNA expression by RNA-Seq in form wild-type or Setd1bKO BMDMs treated with either vehicle (0.1% EtOH) for 16h, 6h LPS (0.1% EtOH, 100ng/ml LPS) or 16h Dex+6h LPS (1 uM Dex, 100ng/ml LPS) in order to study the function of Setd1b as GR?s nuclear interaction parner. For the analysis of Setd1a-dependent gene expression, we performed mRNA-Seq from wild-type or Setd1aDel/+ Raw264.7 cells. Raw264.7 cells were treated with Dex for either 16h (vehicle: 16h 0.1% EtOH; LPS: 6h 100 ng/ul LPS, Dex+LPS: 16h 1 uM Dex, 6h 100 ng/ul LPS) or 6h (vehicle: 6h 0.1% EtOH; LPS: 6h 100 ng/ul LPS, Dex+LPS: 6h 1 uM Dex, 6h 100 ng/ul LPS; Dex: 6h 1 uM Dex). Furthermore, we profiled wild type and Setd1aDel/+ RAW264.7 cells after 6h of LPS stimulation (100 ng/ml) and compared the effect of Setd1a deletion on gene expression to LPS+IFNB1 (6h 100ng/ml LPS + 10 ng/ml IFNB1) stimulated cells of both genotypes. Three biological replicates were sequenced per treatment and genotype.
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| Contributor(s) |
Greulich F, Uhlenhaut NH |
| Citation(s) |
33567280 |
| Submission date |
Sep 24, 2019 |
| Last update date |
Feb 22, 2021 |
| Contact name |
Franziska Greulich |
| E-mail(s) |
franziska.greulich@tum.de
|
| Organization name |
TU München
|
| Department |
Metabolic Programming
|
| Lab |
AG Uhlenhaut
|
| Street address |
Gregor-Mendel-Str. 2
|
| City |
Freising |
| ZIP/Postal code |
85354 |
| Country |
Germany |
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| Platforms (2) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (72)
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| Relations |
| BioProject |
PRJNA573920 |
| SRA |
SRP223111 |
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