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Series GSE137944 Query DataSets for GSE137944
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
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.
 
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.
 
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 M√ľnchen
Department Metabolic Programming
Lab AG Uhlenhaut
Street address Gregor-Mendel-Str. 2
City Freising
ZIP/Postal code 85354
Country Germany
 
Platforms (2)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (72)
GSM4094735 Raw_wt_16hveh_rep1
GSM4094736 Raw_wt_16hveh_rep2
GSM4094737 Raw_wt_16hveh_rep3
Relations
BioProject PRJNA573920
SRA SRP223111

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE137944_Raw264_Setd1aDelSetvsWt_mRNA_DexLPSoverLPS_6h16hmerged_TPMs.txt.gz 2.4 Mb (ftp)(http) TXT
GSE137944_Raw264_wtDel_Ifnb1LPSoverLPS_unfiltered_GEO.txt.gz 804.0 Kb (ftp)(http) TXT
GSE137944_macro_wtAndSetd1bKO_DexLPSoverLPS_TPMs.txt.gz 1.2 Mb (ftp)(http) TXT
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Processed data are available on Series record

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