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| Status |
Public on Mar 27, 2023 |
| Title |
Identification of a Broadly Fibrogenic Macrophage Subset Induced by Type 3 Inflammation |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Cross-sectional single cell RNA sequencing (scRNAseq) of hepatic cells enzymatically isolated from murine models of toxin- (CCl4) or diet-induced (Gubra Amlyn Nash or GAN) liver fibrosis to identify macrophage populations associated with fibrosis.
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| Overall design |
Cells were enzymatically isolated from murine livers at the peak of fibrosis (see paper for details), FACS sorted to remove dead cells and fixed in methanol before analysis using 10x Genomics scRNAseq platform. For samples labeled MMPNeg or MMPPos, cells were additionally FACS sorted based on signal from the MMPsense dye which distinguishes active intracellular matrix metalloproteases (MMPs).
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| Web link |
https://doi.org/10.1126/sciimmunol.add8945
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| Contributor(s) |
Barron AM, Christensen SM, Wadsworth II MH, Chen X, Wang C, Kravarik KM, Wynn TA, Dower K |
| Citation(s) |
37027478 |
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| Submission date |
Mar 26, 2023 |
| Last update date |
May 06, 2023 |
| Contact name |
Ken Dower |
| E-mail(s) |
ken.dower@pfizer.com
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| Organization name |
Pfizer, Inc.
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| Department |
Inflammation and Immunology Research Unit
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| Lab |
Fibrosis discovery group
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| Street address |
1 Portland St.
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (22)
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| GSM7117461 |
CCl4, biol rep 1, MMPsense negative, scRNAseq |
| GSM7117462 |
CCl4, biol rep 1, MMPsense positive, scRNAseq |
| GSM7117463 |
Olive oil, biol rep 1, MMPsense negative, scRNAseq |
| GSM7117464 |
Olive oil, biol rep 1, MMPsense positive, scRNAseq |
| GSM7117465 |
Chow, biol reps 1-3, isotype, scRNAseq |
| GSM7117466 |
GAN, biol reps 1-3, isotype, scRNAseq |
| GSM7117467 |
GAN, biol reps 1-3, anti-TGFβ, scRNAseq |
| GSM7265554 |
Chow, biol rep 4, scRNAseq |
| GSM7265555 |
Chow, biol rep 5, scRNAseq |
| GSM7265556 |
Chow, biol rep 6, scRNAseq |
| GSM7265557 |
GAN, biol rep 4, scRNAseq |
| GSM7265558 |
GAN, biol rep 5, scRNAseq |
| GSM7265559 |
GAN, biol rep 6, scRNAseq |
| GSM7265560 |
GAN, biol rep 7, isotype, scRNAseq |
| GSM7265561 |
GAN, biol rep 8, isotype, scRNAseq |
| GSM7265562 |
GAN, biol rep 9, isotype, scRNAseq |
| GSM7265563 |
GAN, biol rep 4, anti-TGFβ, scRNAseq |
| GSM7265564 |
GAN, biol rep 5, anti-TGFβ, scRNAseq |
| GSM7265565 |
GAN, biol rep 6, anti-TGFβ, scRNAseq |
| GSM7265566 |
Chow, biol rep 7, isotype, scRNAseq |
| GSM7265567 |
Chow, biol rep 8, isotype, scRNAseq |
| GSM7265568 |
Chow, biol rep 9, isotype, scRNAseq |
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| Relations |
| BioProject |
PRJNA948863 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE228232_RAW.tar |
1.1 Gb |
(http)(custom) |
TAR (of LOOM, MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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