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| Status |
Public on Dec 01, 2023 |
| Title |
KO-2, FA model (14 days), scRNAseq |
| Sample type |
SRA |
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| Source name |
kidney
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| Organism |
Mus musculus |
| Characteristics |
tissue: kidney
genotype: Aoah-/-
age: 6-8 weeks old
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| Extracted molecule |
total RNA |
| Extraction protocol |
The kidney tissues were harvested after cardiac perfusion with cold PBS, then weighed, minced and incubated with 1 mg/ml type IV collagenase and 10μg/ml DNase I (both from Sigma, USA) for 40 minutes at 37℃ shaker. The digested tissue suspensions were then passed through a 40μm cell strainer and washed in PBS with 1% FBS. Erythrocytes were lysed and single cell suspension was acquired. Cells were stained with 0.4% trypan blue solution (Thermo Fisher, USA), and cell viability was was examined by Countess®II Automated Cell Counter (Thermo Fisher, USA).
Single-cell RNA sequencing libraries were prepared using the Chromium Single Cell 3′ v2 Reagent Kit (10x Genomics) according to the manufacture’s protocol. Briefly, single cells were encapsulated in oil beads with a unique molecular identifier (UMI) barcode to generate single-cellGelBeads-in-Emulsion(GEMs). Then cells were lysed and the released RNA was barcoded through reverse transcription in individual GEMs. After the reverse transcription step, cDNAs were amplified, fragmented and used for 3’ gene expression library construction.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics
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| Data processing |
Sequencing of the libraries was performed on a NovaSeq6000 (Illumina) using paired-end 2×150 bp sequencing. Raw sequencing data were processed following the Chromium's Cell Ranger 3.1.0 pipeline with default parameters. The raw sequencing data (FASTQs files) were aligned to the mouse genome using STAR algorithm. Then gene-barcode matrices containing the barcoded cells and gene expression counts were generated and imported into the Seurat (version 4.2.0) R toolkit for quality control and subsequent analysis. Unless specified, the default parameters were used for all functions. For quality control, cells with detected genes between 200 to 5000, mitochondrial gene percentages less than 30%, unique gene counts between 200 to 20000 were kept. In the remaining cells, gene expression matrices were log normalized for each cell by the total expression and multiplied this by a scale factor (10000 by default). Principal component analysis (PCA) for dimensional reduction was performed based on the highly variable genes (top 2000). Clusters were then visualized using the Uniform Manifold Approximation and Projection (UMAP) (ArXive-prints1802.03426,2018). Cell type identification were performed based on the expression of known cell markers.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Jun 05, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Zhenkai Wu |
| E-mail(s) |
wtwzk110@sjtu.edu.cn
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| Organization name |
Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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| Street address |
No. 639, Zhizaoju Road, Huangpu District, Shanghai, China.
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| City |
Shanghai |
| ZIP/Postal code |
200001 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE234090 |
Acyloxyacyl Hydrolase Protects against Kidney Injury via Inhibition of Tubular CD74-Macrophage Crosstalk |
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| Relations |
| BioSample |
SAMN35620586 |
| SRA |
SRX20592096 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7445528_KO-2_barcodes.tsv.gz |
118.8 Kb |
(ftp)(http) |
TSV |
| GSM7445528_KO-2_features.tsv.gz |
245.2 Kb |
(ftp)(http) |
TSV |
| GSM7445528_KO-2_matrix.mtx.gz |
143.2 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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