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Sample GSM1246636 Query DataSets for GSM1246636
Status Public on Oct 22, 2013
Title Lung Cancer Cell Line RVH6849
Sample type RNA
 
Source name Total RNA from RVH6849 cells
Organism Homo sapiens
Characteristics cell line: RVH6849
Treatment protocol Not Applicable
Growth protocol Cells were cultured in RPMI-1640, supplemented with 10% FBS and 1X Penicillin/Streptomycin. Xenografts were grown by subcutaneous injection of two million trypsin-dissociated tumor cells into non-obese diabetic/severe combinted immunodeficient mice.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from confluent cell lines or fresh-frozen xenograft tissues using Trizol reagent (Life Technologies, Carlsbad, CA, USA) according to the manufacturer's instructions, followed by DNase I treatment (Life Technologies) and purification using the Qiagen RNeasy kit (Qiagen, Venlo, Netherlands). RNA quantity and quality was assessed using the Qubit Fluorometer (Life Technologies), NanoDrop 1000 (Nanodrop Technologies, Wilmington, DE, USA), and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Label FAM
Label protocol cDNA for each miRNA of interest was synthesized from an input of five nanograms total RNA using the TaqMan® microRNA Reverse Transcription Reagents and specific reverse transcription primers (Life Technologies, Carlsbad, CA, USA). Real-time PCR with TaqMan® probes was performed on a Life Technologies ViiA™ 7 Real-Time PCR System (Life Technologies, Carlsbad, CA, USA) using the following conditions: 10 min at 95°C, followed by 40 cycles of 95°C for 30 sec and 60°C for 1 min. All assays were performed in triplicates.
 
Hybridization protocol n/a
Scan protocol n/a
Data processing CT values were determined using the SDS software (Life Technologies, Carlsbad, CA, USA) with automatic baseline and threshold settings. The data was loaded into the R statistical environment (v2.14.0) and pre-processed. Triplicate CT values were averaged and normalized to the geometric mean of hsa-let-7g, hsa-miR-191 and hsa-miR-335-3p, which were selected as endogenous controls. CT values greater than 36 were considered to be below the limit of detection. Fold changes were calculated as Xenograft-Cell Line. Matrix non-normalized contains the mean of triplicate raw CT values. Matrix normalized contains log2|2^-ΔCT| values; where ΔCT = CT_target - CT_endogenous_controls. Fold Change contains CT values of xenografts compared to CT values of cell lines (ΔCT_xenograft - ΔCT_cell_line).
 
Submission date Oct 21, 2013
Last update date Oct 22, 2013
Contact name Shirley Tam
E-mail(s) shirley.tam@mail.utoronto.ca
Organization name Ontario Institute for Cancer Research
Department Genome Technologies
Street address 661 University Avenue, Suite 510, MaRS Building, West Tower
City Toronto
State/province Ontario
ZIP/Postal code M5G 0A3
Country Canada
 
Platform ID GPL17808
Series (2)
GSE51503 Comparison of microRNA Profiling Platforms (RT-PCR)
GSE51508 Comparison of microRNA Profiling Platforms

Data table header descriptions
ID_REF
VALUE log2|2^-ΔCT| where ΔCT represent CT values normalized to the endogenous controls

Data table
ID_REF VALUE
hsa-let-7a 1.558089727
hsa-let-7c -5.172310273
hsa-let-7e 3.829883683
hsa-miR-1 -9.220610273
hsa-miR-107 -3.162610273
hsa-miR-10b -5.656610273
hsa-miR-1178
hsa-miR-1201 -3.265310273
hsa-miR-1247 -9.388416317
hsa-miR-1248 -9.388416317
hsa-miR-1259 -1.444610273
hsa-miR-126 -7.457610273
hsa-miR-1260 -1.582910273
hsa-miR-127-3p -9.220610273
hsa-miR-1274b 6.122089727
hsa-miR-1275 -9.220610273
hsa-miR-1280 4.356089727
hsa-miR-1296 -3.747416317
hsa-miR-1299 -7.586310273
hsa-miR-1305 -9.220610273

Total number of rows: 89

Table truncated, full table size 2 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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