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Sample GSM1282554 Query DataSets for GSM1282554
Status Public on Dec 01, 2015
Title Oleate rep 1 vs. Palmitate rep 4
Sample type RNA
 
Channel 1
Source name LHCN-M2 mytoubes
Organism Homo sapiens
Characteristics treatment: 0.5 mM Oleate
cell line: LHCN-M2
differentiation: 10 days post-differentiation induction
tissue: skeletal muscle
Treatment protocol Sodium salts of palmitic and oleic acids were prepared in deionized water containing 1.2 equivalents of NaOH at 70ºC, until an optically clear dispersion was obtained. The fatty acid salt solution was added to cell culture media containing fatty acid-free bovine serum albumin (BSA) with continuous agitation. The fatty acid: BSA molar ratio were 5:1.
Growth protocol Myoblasts were grown in DMEM/MEM199 (4:1) added with 15% fetal bovine serum (FBS), 16 mM Hepes, 0.03 μg/ml zinc sulfate, 1.4 μg/ml vitamin B12, 0.055 µg/ml dexamethasone , 0.025 μg/ml human hepatocyte growth factor and 2.5 ng/ml fibroblast growth factor. In confluent cultures, myoblast fusion was stimulated by incubating cells in the DMEM/MEM199 media supplemented with 0.005% FBS, 20 mM Hepes, 10 µg/ml insulin, 0.1 mg/ml apotransferrin and 0.055 µg/ml dexamethasone during 2 days. To further induce cell differentiation, media was then switched to DMEM/MEM199 supplemented with 0.005% FBS, 20 mM Hepes and 0.055 µg/ml dexamethasone, and the culture was continued for 8 additional days.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cultured LHCN-M2 myotubes with RNeasy kit (Qiagen, Valencia, CA, USA), with the same DNase treatment than in the RNeasy fibrous tissue kit, and homogenized with a Polytron.
Label Cy5
Label protocol Low Input Quick Amp Labeling Protocol v 6.5 (Agilent)
 
Channel 2
Source name LHCN-M2 mytoubes
Organism Homo sapiens
Characteristics treatment: 0.5 mM Palmitate
cell line: LHCN-M2
differentiation: 10 days post-differentiation induction
tissue: skeletal muscle
Treatment protocol Sodium salts of palmitic and oleic acids were prepared in deionized water containing 1.2 equivalents of NaOH at 70ºC, until an optically clear dispersion was obtained. The fatty acid salt solution was added to cell culture media containing fatty acid-free bovine serum albumin (BSA) with continuous agitation. The fatty acid: BSA molar ratio were 5:1.
Growth protocol Myoblasts were grown in DMEM/MEM199 (4:1) added with 15% fetal bovine serum (FBS), 16 mM Hepes, 0.03 μg/ml zinc sulfate, 1.4 μg/ml vitamin B12, 0.055 µg/ml dexamethasone , 0.025 μg/ml human hepatocyte growth factor and 2.5 ng/ml fibroblast growth factor. In confluent cultures, myoblast fusion was stimulated by incubating cells in the DMEM/MEM199 media supplemented with 0.005% FBS, 20 mM Hepes, 10 µg/ml insulin, 0.1 mg/ml apotransferrin and 0.055 µg/ml dexamethasone during 2 days. To further induce cell differentiation, media was then switched to DMEM/MEM199 supplemented with 0.005% FBS, 20 mM Hepes and 0.055 µg/ml dexamethasone, and the culture was continued for 8 additional days.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cultured LHCN-M2 myotubes with RNeasy kit (Qiagen, Valencia, CA, USA), with the same DNase treatment than in the RNeasy fibrous tissue kit, and homogenized with a Polytron.
Label Cy3
Label protocol Low Input Quick Amp Labeling Protocol v 6.5 (Agilent)
 
 
Hybridization protocol Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
Scan protocol Scanned on an Agilent G2505C scanner.
Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).
Description Zhu, C. H et al. 2007. Cellular senescence in human myoblasts is overcome by human telomerase reverse transcriptase and cyclin-dependent kinase 4: consequences in aging muscle and therapeutic strategies for muscular dystrophies. Aging Cell 6: 515-523.
Data processing Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.
 
Submission date Dec 09, 2013
Last update date Dec 01, 2015
Contact name Anna Maria Gómez Foix
E-mail(s) agomezfoix@ub.edu
Phone 34-93-4039283
Organization name Universitat de Barcelona
Department Bioquímica i Biologia Molecular
Lab Enginyeria Cel.lular i Teràpia Gènica
Street address Diagonal 643
City Barcelona
ZIP/Postal code 08028
Country Spain
 
Platform ID GPL13607
Series (1)
GSE53116 GENE TARGETS OF PALMITATE, OLEATE AND THEIR MIXTURE IN CULTURED LHCN-M2 MYOTUBES

Data table header descriptions
ID_REF
VALUE normalized log2 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 -0.177132998
2 0.059961513
3 -0.370643567
4 -0.785702945
5 0.51919988
6 -0.486327724
7 -0.588010333
8 0.003479287
9 -0.457146472
10 0.241127894
11 -0.29318052
12 0.745233988
13 1.899016945
14 0.19976783
15 0.999066842
16 -0.316766658
17 -0.360206349
18 0.164095225
19 -0.003904066
20 0.82609409

Total number of rows: 62976

Table truncated, full table size 1120 Kbytes.




Supplementary file Size Download File type/resource
GSM1282554_D.txt.gz 6.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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