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Sample GSM672096 Query DataSets for GSM672096
Status Public on Dec 31, 2015
Title HK-2 cells, Fk and Ra, t12h, control sample, biological rep 3, Tox1
Sample type RNA
 
Source name Human renal proximal tubular epithelial cells, control for Fk and Ra, t12h
Organism Homo sapiens
Characteristics cell line: HK-2
cell type: immortalized human renal proximal tubular epithelial cells
treatment: control
treatment duration: 12 hrs
Treatment protocol Cells were seeded 24 hours before treatment on Greiner 6-well plates at a density of 7x10^5 cells per well with 2mls of medium per well. Cells were treated at ~90% confluency with the required doses for the required timepoints. Control cells were exposed to an appropriate concentration of the control vehicle.
Growth protocol HK-2 cells were maintained in a 1-1 mixture of DMEM and Ham'sF12 containing 5 mM glucose supplemented with 10 ng/ml human recombinant EGF, 36 ng/ml hydrocortisone, 5 µg/ml bovine insulin, 5 µg/ml human transferrin, 5 ng/ml sodium selenite, 2 mM Glutamax (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the Qiagen RNeasy mini kit.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
 
Hybridization protocol 15 ug fragmented labelled cRNA was hybridized for 16 hours at 45oC to Affymetrix HGU133_Plus 2.0 GeneChips, which were then stained and washed on an Affymetrix Fluidics Station 400.
Scan protocol Fluorescence was read with an Affymetrix 3000 Scanner.
Description Fk_and_Ra-t12h_ctrl-rep-3
Data processing Data was normalized using the gcrma library (version 2.8.1) of Bioconductor.
 
Submission date Feb 09, 2011
Last update date Dec 31, 2015
Contact name Peadar O'Gaora
Organization name UCD
Street address Belfield
City Dublin
ZIP/Postal code Dublin 4
Country Ireland
 
Platform ID GPL570
Series (2)
GSE27202 Expression data in HK-2 cells following exposure to Tox 1 compounds: CsA, Fk, Nnm and Ra
GSE27211 Gene expression changes in HK-2 cells following exposure to nephrotoxic compounds

Data table header descriptions
ID_REF
VALUE Log2 gcrma signal

Data table
ID_REF VALUE
1007_s_at 9.221051424
1053_at 9.531564707
117_at 3.683070407
121_at 10.58815378
1255_g_at 2.216599007
1294_at 2.954849862
1316_at 2.787178855
1320_at 3.114423355
1405_i_at 2.792105734
1431_at 2.654106894
1438_at 2.044236402
1487_at 7.267445046
1494_f_at 2.160755512
1552256_a_at 9.22002363
1552257_a_at 9.21725166
1552258_at 2.420553365
1552261_at 2.820772003
1552263_at 6.044284091
1552264_a_at 9.337167929
1552266_at 3.066742292

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM672096_du_12h_ctl_C.CEL.gz 5.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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