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| 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
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| 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.
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| 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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| Web link |
https://www.biorxiv.org/content/10.1101/2024.04.23.590767v1
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| Contributor(s) |
Ver Heul AM, Zamidar L, Yang T, Kim BS |
| Citation(s) |
38712036 |
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| Submission date |
Dec 24, 2021 |
| Last update date |
Aug 03, 2024 |
| Contact name |
Aaron Ver Heul |
| E-mail(s) |
averheul@wustl.edu
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| Organization name |
Washington University School of Medicine
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| Department |
Medicine
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| Lab |
Ver Heul Lab
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| Street address |
660 S Euclid Ave.
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| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA792191 |
| 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) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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