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Series GSE192597 Query DataSets for GSE192597
Status Public on Apr 28, 2024
Title Single nuclei RNA sequencing of skin draining lymph nodes in the setting of skin inflammation and RAG1 fate mapping
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Type 2 inflammation contributes to the pathology of skin diseases such as atopic dermatitis (AD) and urticaria. We previously found that AD-like inflammation induced by calcipotriol in mice is critically mediated by group 2 innate lymphoid cells (ILC2s), while T cells and B cells are dispensable given development of robust AD-like disease in RAG knockout mice. Indeed, we found that in RAG knockout mice AD-like inflammation was worse, with a proportion of ILC2s displaying increased markers of activation. The goal of this study was to characterize transcriptional and epigenomic changes in ILC populations with a history, or not, of expressing RAG1 in the setting of AD-like skin inflammation.
Overall design Mice expressing a Cre-inducible dimeric dimeric red fluorescent protein (tdRFP) were crossed to mice expressing transgenic Cre under the control of the Rag1 promoter, allowing labeling of any cells that expressed RAG1. These mice were treated with topical calcipotriol to induce atopic-dermatitis-like inflammation and cells from lymph nodes draining the affected skin were collected for sequencing. Since our focus was on ILCs, we used magnetic-activated cell sorting to deplete T cells, B cells and granulocytes. Using a custom reference library including the sequence for tdRFP, we were able to determine which of the cells we sequenced had a history, or not, of expressing RAG1 to enable analysis of any transcriptional or epigenomic differences RAG1 expression might confer on ILCs.
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Contributor(s) Ver Heul AM, Zamidar L, Yang T, Kim BS
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Submission date Dec 24, 2021
Last update date Apr 29, 2024
Contact name Aaron Ver Heul
Organization name Washington University School of Medicine
Department Medicine
Lab Ver Heul Lab
Street address 660 S Euclid Ave.
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (4)
GSM5752979 LN-1, GEX
GSM5752980 LN-2, GEX
GSM5752981 LN-1, ATAC
BioProject PRJNA792191

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Supplementary file Size Download File type/resource
GSE192597_Cell_Ranger_ARC_outs_aggr.tar.gz 4.2 Gb (ftp)(http) TAR
GSE192597_RAW.tar 3.2 Gb (http)(custom) TAR (of H5, TBI, TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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