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| Status |
Public on Oct 01, 2022 |
| Title |
Large-scale multiplexed profiling of mouse kidney fibrogenesis with sci-RNA-seq3 |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We employed single-cell combinatorial indexing RNA-seq (sci-RNA-seq), a scRNA-seq technology with high throughput, high sample multiplexing capacity and low costs, to decipher the molecular events involved in mouse kidney fibrogenesis. With the hypothesis that different types of kidney insults may lead to distinct cellular injury responses, we leveraged sci-RNA-seq to profile mouse kidneys collected from two mouse kidney fibrogenesis models, unilateral ischemia-reperfusion injury (uni-IRI) and unilateral ureteral obstruction (UUO), at multiple stages. We described an atlas of kidney fibrogenesis (available at http://humphreyslab.com/SingleCell/) with a total of 309,666 cells profiled from 11 biological conditions and 24 samples in one experiment. We discovered that uni-IRI and UUO produced two types of early-stage injured PT cells with different transcriptomic signature. Further investigation on the two cell states highlighted their distinct mechanisms of metabolic regulation. Analysis of other structures of TECs revealed a common cellular response to injury and repair. In addition, we described the heterogeneity within kidney stroma and the dynamics of cell-cell communications in kidney fibrogenesis.
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| Overall design |
We induced uni-IRI and UUO surgeries on wild-type adult male mice, which were euthanized at multiple timepoints as the disease progresses (0, 6 hours and 2, 7, 14, 28 days post uni-IRI or 0, 2, 4, 6, 10, 14 days post UUO; n = 2 for each timepoint). For each sample mentioned above, nuclei were extracted from the kidney tissue, fixed and snap-frozen. We generated a sci-RNA-seq3 (current version of sci-RNA-seq) library based on a previously demonstrated protocol, including nuclei permeabilization, three-level combinatorial indexing composed of reverse transcription (RT), hairpin ligation and indexed PCR, and library purification. In this experiment, we also introduced a species-mixing control by spiking a nuclei mixture collected from human HEK-293T and mouse C3H/10T1/2 cultured cells.
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| Contributor(s) |
Humphreys BD, Li H |
| Citation(s) |
36265491 |
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| Submission date |
Dec 14, 2021 |
| Last update date |
Oct 21, 2022 |
| Contact name |
Benjamin Humphreys |
| Organization name |
Washington University School of Medicine
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| Street address |
660 S Euclid Ave
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| City |
Saint 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 (1) |
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| Relations |
| BioProject |
PRJNA788883 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE190887_RAW.tar |
874.3 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE190887_cell_annotate.txt.gz |
3.3 Mb |
(ftp)(http) |
TXT |
| GSE190887_gene_name_annotate.txt.gz |
1.0 Mb |
(ftp)(http) |
TXT |
| GSE190887_meta_cell_type_sample.csv.gz |
2.3 Mb |
(ftp)(http) |
CSV |
| GSE190887_report.MM.txt.gz |
14.6 Mb |
(ftp)(http) |
TXT |
| GSE190887_report_annotate.txt.gz |
167 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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