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Sample GSM507421 Query DataSets for GSM507421
Status Public on Feb 11, 2010
Title TGF-beta_48hrs_rep2
Sample type RNA
 
Source name HK-2 cells
Organism Homo sapiens
Characteristics cell line: HK-2
Treatment protocol For microarray analyses, cells were cultured in 5mM-DMEM/F12 without supplements (control) or with 5nM C-peptide for either 18h or 48h. Alternatively, cells were treated with 2ng/ml TGF-b1 either alone or in combination with C-peptide for 48h. All treatments were performed in triplicate to yield 18 flasks, and RNA from each flask hybridized to a separate chip to give an n of 3 for each of 6 treatments. Flasks were subjected to identical media changes and cells cultured for identical periods in media without supplements. In all experiments, cells were serum-starved overnight before agonist addition. Treatments were initiated such that 18h and 48h incubation periods ended coincidentally and all RNA was prepared at this point.
Growth protocol HK-2 cells (passages 18-30) were maintained in DMEM/Hams F12 (DMEM/F12) (17.5mM glucose), supplemented with 10% fetal calf serum (FCS), glutamine (2mM), penicillin (100 IU/ml) and streptomycin (100ng/ml). Cells were cultured at 37oC in a humidified atmosphere of 5% CO2 in air. Prior to treatment, cells were cultured in DMEM/F12 low glucose (5mM) (5mM-DMEM/F12) for 48h.
Extracted molecule total RNA
Extraction protocol RNA was prepared by acid-guanidinium extraction using a Genelute mammalian total RNA miniprep kit (Sigma-Aldrich, Poole, UK) following the manufacturer’s instructions.
Label biotin
Label protocol Standard Illumina hybridization protocol performed by Geneservice (Cambridge, UK)
 
Hybridization protocol Standard Illumina hybridization protocol performed by Geneservice (Cambridge, UK)
Scan protocol Standard Illumina scanning protocol performed by Geneservice (Cambridge, UK)
Description HK-2 cells cultured 48h with 2ng/ml TGF-b2
Data processing The array intensity data were analysed using Illumina GenomeStudio Gene Expression Module (v1.1.1) (Illumina Cambridge, UK) for visualisation and normalisation. The quantile normalisation method was used for all analyses and average background correction performed within the Beadstudio software.
 
Submission date Feb 09, 2010
Last update date Feb 12, 2010
Contact name Nigel John Brunskill
E-mail(s) [email protected]
Phone +44 116 2588043
Organization name University of Leicester
Department Infection Immunity and Inflammation
Street address University Road
City Leicester
State/province Leics
ZIP/Postal code LE1 9HN
Country United Kingdom
 
Platform ID GPL6884
Series (1)
GSE20247 C-peptide and/or transforming growth factor beta 1 effect on human proximal tubular cell line

Data table header descriptions
ID_REF
VALUE quantile normalized AVG_signal
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1809034 195.3 1
ILMN_1660305 131.6 1
ILMN_1792173 267.8 1
ILMN_1762337 -3.2 0.28327
ILMN_2055271 7.4 0.92885
ILMN_1736007 -1.7 0.4058
ILMN_1814316 -7 0.0448
ILMN_2359168 -1.1 0.47036
ILMN_1731507 -0.9 0.4809
ILMN_1787689 -3.4 0.2556
ILMN_1745607 1.1 0.65349
ILMN_2136495 -3.2 0.28063
ILMN_1668111 -6.3 0.06588
ILMN_2295559 2.2 0.74308
ILMN_1735045 177.7 1
ILMN_1680754 4.6 0.85903
ILMN_2375184 1.1 0.65217
ILMN_1659452 6.6 0.91436
ILMN_1767388 9.6 0.95389
ILMN_1675204 -10.3 0.00659

Total number of rows: 48803

Table truncated, full table size 1155 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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