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Sample GSM729766 Query DataSets for GSM729766
Status Public on May 24, 2011
Title Empty vector A549 stable transfectants, culture 2
Sample type RNA
 
Source name A549/vec cells
Organism Homo sapiens
Characteristics cell line: A549 lung cancer cells
disease: Lung adenocarcinoma
transfection: Empty pLemiR plasmid
Treatment protocol Adherent cells on a 10 cm culture dish were rinsed with phosphate-buffered saline, and treated at 37 ºC for 5 minutes with 0.75 ml of 0.05% trypsin with 0.25 mM ethylene-diamine-tetraacetic acid. Phosphate-buffered saline (10 ml) was used to collect the detached cells which were then spun down at 500 g for 10 minutes at room temperature. The cell pellet was used to isolate RNA.
Growth protocol Cells were cultured to 80%-95% confluence in 10 cm tissue culture plates in +DMEM medium containing 10% fetal bovine serum and 2 µg/ml puromycin, at 37 ºC with 5% carbon dioxide and 90% humidity.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Purelink™ RNA isolation kit (Invitrogen®) as per the manufacturer's recommended protocol. RNA quantity and quality was assessed on a Bioanalyzer™ 2100 instrument (Agilent®). The RNA preparations had 260 nm/280 nm absorbance ratios in the 1.9-2.0 range, 260 nm/230 nm absorbance ratios >1.8, and RNA integrity numbers >7.
Label Biotin
Label protocol Illumina® TotalPrep RNA Amplification kit (Ambion®) was used to convert 500 ng of RNA to cDNA which was then transcribed in vitro to generate biotin-labeled RNA.
 
Hybridization protocol Hybridization reagents were mixed with 750 ng of labeled RNA, and the mixture was hybridized overnight at 58 ºC to HumanRef-8 v3.0 Expression BeadChips™ array (Illumina®).
Scan protocol Following washing and staining with Cy3 dye-labeled streptavidin, BeadChips™ (Illumina®) were imaged using the BeadArray Reader (Illumina®)
Description A0-3
Biological replicate 2
Data processing Data was acquired with GenomeStudio™ software (version 2010.1, Illumina®), and then processed for background-correction, variance-stabilizing transformation, and then robust splines-normalization between arrays using the lumi Bioconductor package (version 1.14) for R language (version 2.11.1) with default settings.
 
Submission date May 24, 2011
Last update date May 24, 2011
Contact name Santosh Kumar Patnaik
Phone 716-8458364
Organization name Roswell Park Comprehensive Cancer Center
Department Thoracic Surgery
Street address Elm and Carlton Streets
City Buffalo
State/province NY
ZIP/Postal code 14263
Country USA
 
Platform ID GPL6883
Series (1)
GSE29496 Overexpression of the lung cancer-prognostic miR-146b microRNAs has a minimal and negative effect on the malignant phenotype of A549 lung cancer cells

Data table header descriptions
ID_REF
VALUE Robust splines-normalized signal
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1762337 70.06232698 0.14887
ILMN_2055271 70.23133724 0.14563
ILMN_2383229 67.5050253 0.27184
ILMN_1806310 73.08442087 0.06472
ILMN_1779670 65.07191021 0.47573
ILMN_2321282 63.30681897 0.6699
ILMN_1772582 68.70403852 0.19417
ILMN_1717783 59.81730467 0.92557
ILMN_1814316 61.79216429 0.81553
ILMN_2359168 64.89633052 0.49191
ILMN_1731507 64.36827939 0.55016
ILMN_1787689 68.44797711 0.20388
ILMN_1745607 59.00588725 0.95469
ILMN_2136495 62.41725472 0.76375
ILMN_1668111 63.39552056 0.66667
ILMN_2295559 66.98777832 0.31068
ILMN_1735045 113.5043674 0.00647
ILMN_1680754 69.21476867 0.16828
ILMN_2375184 64.4564577 0.53722
ILMN_1659452 66.81485552 0.32039

Total number of rows: 24526

Table truncated, full table size 734 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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