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| Status |
Public on Jun 07, 2023 |
| Title |
Single Cell Transcriptomics of Bone Marrow Derived Macrophages reveal Ccl5 as a marker of Direct IFNAR-independent Responses to DNA Sensing |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Bone marrow derived macrophages (BMDMs) are a common model for macrophage type 1 interferon responses. We used single cell RNA-seq (scRNA-seq) to identify direct responders for dsDNA sensing.
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| Overall design |
Bone marrow cells were isolated from C57BL/6J wild-type and IFNAR -/- mice. The cells were treated with macrophage colony-stimulating factor (M-CSF) and then stimulated with control vehicle, dsDNA, or dsDNA and IFNAR antibody for analysis with scRNA-seq.
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| Contributor(s) |
King KR, McCarty E, Yu J, Ninh VK, Calcagno DM, Lee J |
| Citation(s) |
37275883 |
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| Submission date |
Apr 10, 2023 |
| Last update date |
Jun 08, 2023 |
| Contact name |
Kevin Robert King |
| E-mail(s) |
krking@health.ucsd.edu, krking@ucsd.edu
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| Phone |
4805595759
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| Organization name |
University of California San Diego
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| Department |
Bioengineering; Medicine
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| Street address |
9500 Gilman Dr
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (8)
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| GSM7158692 |
IFNAR 1 - Wt Control Macrophages, 2 biol replicates (cell culture), scRNA-seq |
| GSM7158693 |
IFNAR 2 - Wt Macrophages dsDNA, 2 biol replicates (cell culture), scRNA-seq |
| GSM7158694 |
IFNAR 3 - Wt Macrophages, dsDNA+IFNARab, 2 biol replicates (cell culture), scRNA-seq |
| GSM7158695 |
WT Isotype Control, 3 biol replicates (cell culture), scRNA-seq |
| GSM7158696 |
WT dsDNA, 4 biol replicates (cell culture), scRNA-seq |
| GSM7158697 |
WT dsDNA+anti-IFNARab, 4 biol replicates (cell culture), scRNA-seq |
| GSM7158698 |
IFNAR KO Control, 3 biol replicates (cell culture), scRNA-seq |
| GSM7158699 |
IFNAR KO dsDNA, 5 biol replicates (cell culture), scRNA-seq |
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| Relations |
| BioProject |
PRJNA953992 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE229311_RAW.tar |
389.9 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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