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Sample GSM2149150 Query DataSets for GSM2149150
Status Public on May 11, 2016
Title COS conditions rep 1
Sample type RNA
 
Channel 1
Source name C2C12
Organism Mus musculus
Characteristics cell type: Myotubes
treatment: COS culture conditions day 5-8 post differentiation: 4% O2, low-frequency (1Hz/0.1Hz for 18h/6h respectively) biphasic 5ms square-wave electrical stimulation, and daily TNF-α (20 pg/ml; R&D systems) and IL-6 (100 pg/ml; R&D systems)
Treatment protocol All treatments started day 5 post differentiation including transfer to new culture conditions (COS) and/or treatment with additional soluble agents. All media and treatments were changed every 24hrs prior to harvesting cells (D5-D7).
Growth protocol C2C12 myoblasts (ATCC) less than 10 passages grown in high-glucose DMEM (Gibco) with 10% FBS (invitrogen) seeded on 0.15% gelatin-coated 6-well plates at at 2.2 x 10^6 cells per well, grown to 80% confluence and differentiated in medium containing 10% horse serum. All initial cultures were performed in standard tissue culture conditions (21% O2, 5% CO2, humidified incubator at 37C)
Extracted molecule total RNA
Extraction protocol RNA was extracted using the miRNeasy mini protocol (Qiagen) as per the manufacturer's instructions
Label Hy3
Label protocol 2µg total RNA from each experimental sample was covalently 3’-labeled with a single Hy3 (test) or Hy5 (reference) fluorophore per molecule using the Hi-Power Labeling kit (Exiqon, Woburn MA)
 
Channel 2
Source name C2C12
Organism Mus musculus
Characteristics cell type: Myotubes
treatment: STD culture conditions: 21% O2
Treatment protocol All treatments started day 5 post differentiation including transfer to new culture conditions (COS) and/or treatment with additional soluble agents. All media and treatments were changed every 24hrs prior to harvesting cells (D5-D7).
Growth protocol C2C12 myoblasts (ATCC) less than 10 passages grown in high-glucose DMEM (Gibco) with 10% FBS (invitrogen) seeded on 0.15% gelatin-coated 6-well plates at at 2.2 x 10^6 cells per well, grown to 80% confluence and differentiated in medium containing 10% horse serum. All initial cultures were performed in standard tissue culture conditions (21% O2, 5% CO2, humidified incubator at 37C)
Extracted molecule total RNA
Extraction protocol RNA was extracted using the miRNeasy mini protocol (Qiagen) as per the manufacturer's instructions
Label Hy5
Label protocol 2µg total RNA from each experimental sample was covalently 3’-labeled with a single Hy3 (test) or Hy5 (reference) fluorophore per molecule using the Hi-Power Labeling kit (Exiqon, Woburn MA)
 
 
Hybridization protocol Performed on fully-automated enclosed hybridisation station (Tecan HS400Pro). Samples were injected manually then co-hybridised (56 degrees C x 16 hrs) then washed and dried automatically prior to scanning
Scan protocol Scanned on an Agilent G2505B scanner.
Description Biological replicate: 1 of 6: COS culture conditions vs STD
Data processing Two-colour images were analysed using Spot software (CSIRO, 2007) and mean signal intensity for each spot was determined after background correction and Loess print-tip (within-array) normalisation of the log2 ratio (FlexArray, Genome Quebec, McGill University).
Normalized log2 ratio (Hy3/Hy5)
 
Submission date May 10, 2016
Last update date May 11, 2016
Contact name R. Thomas Jagoe
E-mail(s) thomas.jagoe@mcgill.ca
Phone 15143408222
Organization name McGill University
Department Medicine
Street address Jewish General Hospital, 3755 Cote Ste Catherine
City Montreal
State/province Quebec
ZIP/Postal code H3T 1E2
Country Canada
 
Platform ID GPL21849
Series (1)
GSE81138 miRNA profiling of mature C2C12 myotubes using modified (COS) vs standard (STD) tissue culture conditions

Supplementary file Size Download File type/resource
GSM2149150_003MOD58_v11_003.spot.gz 1.4 Mb (ftp)(http) SPOT
Processed data are available on Series record

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