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| Status |
Public on Aug 29, 2022 |
| Title |
HGTEPP-3 |
| Sample type |
SRA |
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| Source name |
Human renal proximal tubular epithelial cell line
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Kidney
treatment: Case group (TEPP-46)
cell line: HK-2 cells
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| Treatment protocol |
Three replicates of cells exposed to HG were treated with (case group) or without (control group) 10-μM TEPP-46 for 1 day, separately.
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| Growth protocol |
The cultured HK-2 cells were obtained from Beijing Beina Chuanglian Biotechnology Research Institute, where they were cultured in Dulbecco’s modified eagle medium (DMEM) with the low glucose (Sigma-Aldrich Inc, St. Louis, USA) supplemented with 10% fetal bovine serum (Sigma-Aldrich, St. Louis, USA), 10 units/ml penicillin and 10 mg/ml streptomycin, and maintained in the continuous culture at 37°C in a humidified atmosphere (5% CO2) in an incubator. Growth medium was shifted every 2 or 3 day and cells were sub-cultured until further measurements at 80% colony confluency.
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| Extracted molecule |
total RNA |
| Extraction protocol |
2 μg RNA per cell replicate sample were extracted for RNA sample preparation
Libraries were prepared according to Illumina's instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Quality control of raw data was done based on three criteria: the contaminated reads for adapters (> 5 bp adapter sequences), low quality reads (Phred quality value ≤ 19 more than 15%) and reads with Ns (Ns > 5%). The filtered clean reads were then aligned to the human reference genome GRCh38.p13 (Genome Reference Consortium Human Build 38) using HISAT2 software (version 2.1.0). Afterwards, the fragments per kilobase million mapped reads (FPKM) (Supplementary file 1) were calculated based on the read counts derived for each gene using HTSeq software (version 0.6.0).
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample
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| Submission date |
Jun 08, 2022 |
| Last update date |
Aug 29, 2022 |
| Contact name |
Xiao Wang |
| E-mail(s) |
xiao@kongelarsen.dk
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| Organization name |
Konge Larsen Aps
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| Street address |
Bagsværdvej 103, ST
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| City |
Kongens Lyngby |
| ZIP/Postal code |
2800 |
| Country |
Denmark |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE205674 |
Transcriptomic signatures responding to PKM2 activator TEPP-46 in the hyperglycemic human renal proximal epithelial tubular cells |
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| Relations |
| BioSample |
SAMN28920856 |
| SRA |
SRX15631119 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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