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Accession: PRJNA784108 ID: 784108

Smad4 modulates expression of chemokine receptor Ccr6 in mouse colon stroma (house mouse)

See Genome Information for Mus musculus
Purpose: To understand how loss of epithelial Smad4 alters gene expression in mouse colon stroma Methods: To understand the extent of Smad-mediated gene regulation in the colon, we isolated colon epithelium from three Smad4ΔLrig1 and from three SMAD4+ control mice (either mice lacking a CreERT allele and treated with tamoxifen, or mice bearing a CreERT allele but treated with vehicle only) and analyzed the colonic stroma by RNAseq. Results: A comparison of gene expression within the sub-epithelial stroma of Smad4Lrig1 mice relative to SMAD4+ control mice demonstrated a marked increase in inflammatory gene signaling. Of the 95 genes that were upregulated by at least 2.5-fold (≥1.32 Log2 Fold Change) and a false discovery rate <0.05, 51 genes are known to be expressed on immune cells or have immune-related functions, including Ccr6. Conclusions: SMAD4 modulates inflammatory signaling in colonic stroma to repress colitis-associated tumor formation Overall design: Three Smad4Lrig1 and three SMAD4+ control mice were dissected 1 month after administration of tamoxifen. Colon crypts were chelated using Ethylenediaminetetraacetic acid (EDTA). Following crypt chelation, the sub-epithelial stroma was removed from the underlying muscle layer by scraping. RNA was then made from the sub-epithelial stroma using RNeasy kit (Qiagen, Germantown, MD) and RNA-seq performed by the Vanderbilt Technologies for Advanced Genomics (VANTAGE) core facility. 32–37 million 51–base pair, single-end reads were generated per sample. Reads were mapped to the mouse genome mm10 using TopHat-2.1.0, uniquely mapping 86%–95% single-end reads to the genome, depending on the study. The number of reads that fell into annotated genes were counted using samtools-1.3.1 and HTSeq-0.5.4p5. Count-based differential expression analysis was performed using edgeR_3.4.2.
AccessionPRJNA784108; GEO: GSE189667
Data TypeTranscriptome or Gene expression
ScopeMultiisolate
OrganismMus musculus[Taxonomy ID: 10090]
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus; Mus musculus
SubmissionRegistration date: 27-Nov-2021
Vanderbilt University Medical Center
RelevanceModel Organism
Project Data:
Resource NameNumber
of Links
Sequence data
SRA Experiments6
Other datasets
BioSample6
GEO DataSets1
GEO Data Details
ParameterValue
Data volume, Supplementary Mbytes2
SRA Data Details
ParameterValue
Data volume, Gbases9
Data volume, Mbytes5965

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