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Sample GSM440899 Query DataSets for GSM440899
Status Public on Sep 20, 2009
Title GN5, Control, Rep2
Sample type RNA
 
Source name GN5 cells, Vehicle Control
Organism Rattus norvegicus
Characteristics rapamycin response: Intermediate
doubling time: 21.6h
tumorigenic: Yes
Treatment protocol 10^6 cells were plated on 100mm plates and allowed to attach overnight. Cells were treated with DMSO vehicle or 50nM rapamycin for 24 hours.
Growth protocol GN5 cells were cultured in DMEM/F12 containing 10% fetal bovine serum, 2mM L-glutamine and 0.1% antibiotic-antimycotic solution. H5D cells were cultured in Waymouth MB 752/1 containing 10% fetal bovine serum and 0.1% antibiotic-antimycotic solution. All cells were grown at 37°C with 5.0% carbon dioxide.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was further purified using the RNeasy kit (Qiagen). RNA quality was evaluated using the Agilent Bioanalyzer.
Label Biotin
Label protocol Biotinylated cRNA was prepared from 500ng of total RNA using the TotalPrep RNA Amplification kit (Applied Biosystems) according to the manufacturer's directions.
 
Hybridization protocol cRNA (750ng) was hybridized at 58°C for 16 hours on a RatRef-12 Expression BeadChips. BeadChips were washed and stained as outlined in the Illumina protocol.
Scan protocol BeadChips were scanned using the Illumina Iscan.
Description Derived from WB-F344 cell line using NNN
Data processing Scanned files were quantile normalized using BeadStudio software (Illumina). The data was further analyzed using Partek software, version 6.3 (Partek). For gene expression comparisons, genes with detection p-values >0.01 from BeadStudio or fold-change less than 1.2 were excluded from further analyses. A two-sample t-test using p-value cutoff of 0.05 with multiple test correction (Bejamini and Hochberg false discovery rate) was applied for each gene to determine if the gene was differentially expressed in the pairwise comparison. Triplicate control and rapamycin samples from each cell line were used in these comparisons.
 
Submission date Aug 14, 2009
Last update date Sep 14, 2009
Contact name Jennifer Ann Sanders
E-mail(s) Jennifer_Sanders@brown.edu
Organization name Rhode Island Hospital
Department Pediatric Endocrinology
Street address 593 Eddy Street
City Providence
State/province RI
ZIP/Postal code 02903
Country USA
 
Platform ID GPL6101
Series (2)
GSE17662 Modulation of gene expression by rapamycin in hepatic cell lines, H5D and GN5
GSE17677 Modulation of gene expression by rapamycin in hepatic cell lines

Data table header descriptions
ID_REF
VALUE Quantile normalized
GN5 V2.Detection Pval

Data table
ID_REF VALUE GN5 V2.Detection Pval
ILMN_1369537 96.78575 0
ILMN_1358051 104.5917 0
ILMN_1361746 73.2711 0.3034826
ILMN_1352975 170.6083 0
ILMN_1368384 77.43336 0.1604478
ILMN_1355285 91.0407 0.001243781
ILMN_1376898 81.58969 0.07462686
ILMN_1368325 189.219 0
ILMN_1353563 299.4992 0
ILMN_1348794 61.82168 0.8718905
ILMN_1364273 107.5414 0
ILMN_1369433 77.41195 0.1616915
ILMN_1349007 202.7655 0
ILMN_1374156 89.18969 0.004975124
ILMN_1360232 58.01749 0.9539801
ILMN_1355155 2884.588 0
ILMN_1362563 76.5224 0.1965174
ILMN_1355815 79.83799 0.1007463
ILMN_1373215 90.99903 0.001243781
ILMN_1374139 1000.942 0

Total number of rows: 22523

Table truncated, full table size 635 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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