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Sample GSM669431 Query DataSets for GSM669431
Status Public on Dec 31, 2015
Title HK-2 cells, CsA, t48h, control sample, biological rep 1, lab 3
Sample type RNA
 
Source name Human renal proximal tubular epithelial cells, control for CsA, t48h
Organism Homo sapiens
Characteristics cell line: HK-2
cell type: immortalized human renal proximal tubular epithelial cells
treatment: control
treatment duration: 48 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 CsA-t48h_ctrl-rep-1_lab_3
Data processing Data was normalized using the gcrma library (version 2.8.1) of Bioconductor.
 
Submission date Feb 05, 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)
GSE27095 Expression data in HK-2 cells following exposure to CsA
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 9.57266891
1053_at 9.163099505
117_at 2.853282778
121_at 9.866190412
1255_g_at 2.257052902
1294_at 3.033227296
1316_at 2.949382745
1320_at 2.784221201
1405_i_at 2.784368283
1431_at 2.71801872
1438_at 2.028712051
1487_at 7.158955081
1494_f_at 2.337525336
1552256_a_at 8.161358119
1552257_a_at 7.741316467
1552258_at 2.351726793
1552261_at 2.835017338
1552263_at 5.739394832
1552264_a_at 8.467225385
1552266_at 2.911164607

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM669431_ba_48h_ctrl_a_nc07.cel.gz 8.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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