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| Status |
Public on Mar 10, 2021 |
| Title |
Lnc453774.1 mediated gene expression in human HK-2 cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Long noncoding RNAs (lncRNAs) have been proposed to be engaged in the pathogenesis of renal fibrosis. The current study aims to determine the role of lnc453774.1 in the development of renal fibrosis and its underlying mechanism.Transforming growth factor-β1 (TGF-β1)-induced cell model of renal fibrosis was constructed. RNA sequencing was performed to identify DEGs targeted by lnc453774.1 in TGF-β1-induced renal fibrosis. Dataset GSE23338 was adopted to identify DEGs in 48 h TGF-β1-stimuated human kidney epithelial cells, and these DEGs were interested with genes in the key module using a WGCNA to generate key genes associated with renal fibrosis. Miranda software was adopted to predict miRs that have targeting relationship with keys genes and lnc453774.1, and key genes that have targeting relationship with these miRs were regarded as important genes. A PPI network among lnc453774.1, important genes and reported genes related to autophagy, oxidative stress, and cell adhesion was constructed to select key target genes by lnc453774.1. Twenty key genes regulated by lnc453774.1 was yielded by intersecting genes in key module (turquoise) and dataset GSE23338. Fourteen miRs have targeting relationship with lnc453774.1 and key genes, and 8 important genes targeted by these 14 miRs were identified. FBN1, IGF1R and KLF7 were identified to be associated with autophagy, oxidative stress, and cell adhesion and were upregulated in the lnc453774.1-overexpressing in TGF-β1-induced cells. These results show FBN1, IGF1R and KLF7 serve as downstream targets of lnc453774.1 and protect against renal fibrosis by regulating autophagy, oxidative stress, and cell adhesion.
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| Overall design |
Human renal proximal tubular epithelial cells (HK-2 cells) were cultured in dulbecco's modified eagle medium (DMEM)/F12 supplemented with 10% fetal bovine serum (FBS) at 37°C, 5% CO2, and passaged upon 70-80% confluence. TGF-β1 at a concentration of 5ng/ml for 24 h was adopted to stimulate HK-2 cells to prepare a cell model of renal fibrosis. Lentiviral vector containing (LV)-lnc453774.1 and short hairpin RNA (shRNA)-lnc453774.1 plasmids were prepared, and infected into HK-2 cells of renal fibrosis using liposome 2000 [the overexpressed (OE) group and the knockdown (KD) group]. TGF-β1-stimulated HK-2 cells with no-load vector was used as the control group. The total RNA was extracted from the 3 control, 3 OE group and 3 KD groups for sequencing library construction.
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| Contributor(s) |
Yuan X, Tang W, Peng L, Chen Y, Tang S, Ge H, Wang X, Xiao X |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Mar 09, 2021 |
| Last update date |
Apr 20, 2022 |
| Contact name |
Xiangcheng Xiao |
| Organization name |
Xiangya Hospital, Central South University
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| Department |
Department of Nephrology
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| Street address |
No. 87, Xiangya Road, Kaifu District
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| City |
Changsha |
| State/province |
Hunan |
| ZIP/Postal code |
410008 |
| Country |
China |
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| Platforms (1) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA708293 |
| SRA |
SRP309978 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE168559_Raw_gene_counts_matrix.txt.gz |
343.5 Kb |
(ftp)(http) |
TXT |
| Raw data are available in SRA |
| Processed data are available on Series record |
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