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Sample GSM416697 Query DataSets for GSM416697
Status Public on Jan 28, 2010
Title negative control inhibitor_17-8
Sample type RNA
 
Source name ES2 ovarian cancer cell line
Organism Homo sapiens
Characteristics protocol: control
Treatment protocol Transfection conditions for each clear cell ovarian cancer cell line were optimized for maximum efficiency in preliminary experiments using Dy547-labeled miRIDIAN hairpin inhibitor and mimic transfection controls (Dharmacon). ES-2 cells were transfected in 6-well plates (2.5 x 105 cells/well) using 10 μl X-tremeGENE siRNA Transfection Reagent (Roche) and 2 μg hsa-mir-182 hairpin inhibitor (50 nM final concentration) (Dharmacon). Control groups were cells treated with transfection reagent alone (mock transfection), and cells transfected with miRIDIAN hairpin inhibitor negative control #1 or mimic negative control #2, which are based on C. elegans miRNAs that have minimal sequence identity to human miRNAs (Dharmacon).
Growth protocol ES-2 cells were cultured in DMEM/F12 (Invitrogen), with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin solution (Invitrogen).
Extracted molecule total RNA
Extraction protocol Cells were harvested 48 hours after transfection. Total RNA was extracted using the mirVana miRNA Isolation Kit (ABI). RNA quality were inspected on a 2100 Bioanalyzer (Agilent).
Label biotin
Label protocol According to Illumina protocol.
 
Hybridization protocol According to Illumina protocol.
Scan protocol According to Illumina protocol.
Description negative control inhibitor (mir-182 knockdown control), biological rep3
Data processing The image data were compiled into a project using Beadstudio software gene expression module version 3.2.7. No normalization was used. The data was exported as txt files using the build-in function of export to GeneSpring GX format. The option of sample probe profile was chosen. Data were subsequently quantile normalized for the analysis.
 
Submission date Jun 12, 2009
Last update date Jan 28, 2010
Contact name Chad Creighton
E-mail(s) creighto@bcm.tmc.edu
Organization name Baylor College of Medicine
Department Biostatistics, Ducan Cancer Center
Street address One Baylor Plaza, Mail Stop: BCM305
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL6947
Series (2)
GSE16572 Gene expression analyses of mir-182 knockdown in ovarian clear cell cancer cell line
GSE16574 Gene expression analyses of putative miRNA targets in ovarian clear cell cancer cell lines

Data table header descriptions
ID_REF
VALUE quantile-normalized signal intensity

Data table
ID_REF VALUE
ILMN_1802380 671.0085
ILMN_1893287 40.8
ILMN_1736104 43.9
ILMN_1792389 38.9
ILMN_1854015 62
ILMN_1904757 64.9
ILMN_1740305 40.8
ILMN_1665168 39.4
ILMN_2375156 65.1
ILMN_1705423 45.9
ILMN_1716072 45.2
ILMN_1697642 741.0206
ILMN_1788184 54.75
ILMN_1681845 484.4848
ILMN_1823296 44.2
ILMN_1889845 38.9
ILMN_1746923 42.3
ILMN_1690979 57.8692
ILMN_1811114 41.8
ILMN_1660729 42.4

Total number of rows: 48803

Table truncated, full table size 924 Kbytes.




Supplementary file Size Download File type/resource
GSM416697.txt.gz 711.4 Kb (ftp)(http) TXT
Processed data included within Sample table

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