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| Status |
Public on Dec 16, 2013 |
| Title |
HG stimulated mesangial cells |
| Sample type |
SRA |
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| Source name |
mesangial cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: mesangial cells
treatment: high glucose
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| Treatment protocol |
The cells were stimulated with 30 mM glucose (Wako, Tokyo) for 24 hours for hyperglycemic stimulation. For osmotic control, the cells were cultured with 30 mM mannitol (Wako) for 24 hours.
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| Growth protocol |
Normal human mesangial cells (Lonza, Basel, Switzerland) were cultured in mesangial culture kit (Lonza). Human immortalized TECs, HK-2 (ATCC, Manassas, VA) was cultured in 10% FBS DMEM (Life technologies, Tokyo) with 100 µg/ml streptomycin and 100 U/ml penicillin. All the cells were grown in a humidified atmosphere (5% CO2/95% air) at 37°C and were seeded onto six-well cell culture cluster (Corning Incorporated, Corning, NY).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using mRNA Isolation kit (Sigma-Aldolich, St louis, MO)
Gene expression analysis was performed by SAGE method and NGS. NGS data from the PGMTM was generated from 1μg of total RNA isolated from cell line. SAGE libraries were constructed using the SOLiD SAGETM kit from Life Technologies (Life Technologies) according to manufacturer’s protocol. DNA was recovered from the agarose gel using PureLink Gel Extraction kit (Life Technologies).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
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| Description |
Sample 1
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| Data processing |
For each of the samples, the PGMTM raw reads were aligned against the human refseq genes (http://www.ncbi.nlm.nih.gov/refseq/ Nov. 2012) using BWA 0.6.2 which uses the 25_1 mapping parameter.
We generated unique gene counts by excluding reads that mapped to contigs of more than one gene.
Reads mapping to several contigs within an isogroup were only counted once.
Genome_build: RefSeq Release 56
Supplementary_files_format_and_content: The processed data was normalized transcripts per million. Text file includes normalized numbers of read tags for each group (mesangium cell and HK-II, HG and mannitol) and gene identifiers.
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| Submission date |
Nov 26, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Yasunori Iwata |
| Organization name |
Kanazawa University
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| Street address |
13-1
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| City |
Kanazawa |
| State/province |
Ishikawa |
| ZIP/Postal code |
920-0934 |
| Country |
Japan |
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| Platform ID |
GPL17301 |
| Series (1) |
| GSE52734 |
Gene expression analysis of high-glucose stimulated human mesangial cells and tubular epithelial cells |
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| Relations |
| BioSample |
SAMN02420635 |
| SRA |
SRX383893 |
| 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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