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Series GSE138902 Query DataSets for GSE138902
Status Public on Oct 16, 2019
Title Single-cell RNA seq reveals the transcriptional landscape and heterogeneity of macrophages in murine gut tissues
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary CD11b+ cell populations, especially macrophages are highly heterogeneous tissue resident immune cells in both mice and human. Exact subsets and their phenotype remain unknown. We here analyzed gut CD11b+ cell populations using scRNA-seq in normal, inflamed and Nlrc4 deficient mice. There existed twelve CD11b+ cell populations and subsets in SPF mice. These CD11b+ subsets were changeable dependent on inflammation and gut environment. We found consistent high expression of Ly6C, Cd62L, previously undescribed Trem1 and Ccr7 in Ly6Chigh macrophages and Cd206 and Cx3cr1 in Ly6Clow/neg cell population in different mice. However, signature genes showed that resident macrophages but not inflammatory macrophages were highly conserved in normal and inflamed mice. Gut microbiota play a role in accumulation and differentiation of gut macrophages. Both Ly6Chigh and Ly6Clow macrophages in intestine and colon tissues are similar. These uncover the transcriptional landscape and phenotypic heterogeneity of CD11b+ cells, especially macrophages in gut tissues.
Overall design 10X Genomics scRNA-seq was performed to better assess immune cell heterogeneity in gut lamina propria (LP).
Contributor(s) Wei M, Chen W, Yang Y, Wei J, Qi H, Zhang Y, Yang R
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Submission date Oct 15, 2019
Last update date Oct 19, 2019
Contact name Ming Wei
Organization name Nankai University
Department Department of Immunology, Nankai University School of Medicine
Lab Rongcun Yang Lab
Street address 94 Weijin road
City Tianjin
ZIP/Postal code 300071
Country China
Platforms (1)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (9)
GSM4121441 scRNA-Seq_WTC /Colon (1)
GSM4121442 scRNA-Seq_WTC /Colon (2)
GSM4121443 scRNA-Seq_WTDSS/Colon
BioProject PRJNA577708
SRA SRP225788

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Supplementary file Size Download File type/resource
GSE138902_RAW.tar 203.7 Mb (http)(custom) TAR (of MTX, TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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