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Sample GSM1954223 Query DataSets for GSM1954223
Status Public on Nov 25, 2015
Title myoblasts treated with palmitate (0.1 mmol/l)- rep4
Sample type RNA
 
Channel 1
Source name C2C12 myoblasts- 48-h exposure to palmitate (final concentration 0.1 mmol/l) added to 5%FBS/DMEM
Organism Mus musculus
Characteristics cell line: C2C12
age: 3th day of proliferation
tissue: myoblasts
tratment: palmitate (0.1 mmol/l)- treated
Treatment protocol After reaching ~40% confluence, the proliferating myoblasts were subjected to 48-h exposure to palmitate (final concentration 0.1 mmol/l) added to 5%FBS/DMEM, according to experimental protocol described previously (Lee et al. 2009). The control cultures were maintained in 5% FBS/DMEM, containing the same amounts of ethanol and FFA-free bovine serum albumin as the experimental medium. To preserve the characteristics of C2C12 cell line, the cells were split up to a maximum of 7 times.
Growth protocol Research work was carried out on the murine myogenic C2C12 cell line (satellite cells from thigh muscle), purchased from the European Collection of Animal Cell Culture (ECACC). This cell line undergoes proliferation and differentiation in response to growth factors present in the extracellular environment, thus, it is a useful model to study the mechanisms controlling myogenesis (Yaffe and Saxel 1977). Mouse C2C12 myoblasts were maintained free of contamination at the exponential phase of growth in DMEM supplemented with 10% FBS (Foetal Bovine Serum) and an antibiotic-antimycotic mixture (Life Technologies), in controlled humidified air supplemented with 5% CO2, at 37oC. The growing medium was changed every other day.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted and purified from C2C12 cells using the Total RNA kit (A&A Biotechnology, Poland) according to the manufacturer’s protocol. The isolated RNA samples were dissolved in RNase-free water. The quantity of the isolated RNA was measured using Nano-Drop (NanoDrop Technologies, USA). The RNA samples were treated with DNase I to eliminate DNA contamination and subsequently purified using the RNeasy MiniElute Cleanup Kit (Qiagen, Germany). Subsequently, the RNA samples were analyzed on a BioAnalyzer (Agilent, USA) to measure the final RNA quality and integrity.
Label Cy5
Label protocol The total RNA (1 μg) was extracted, amplified and labeled in accordance with the protocol for Agilent Gene Expression oligo microarrays
 
Channel 2
Source name C2C12 myoblasts- 3th day of proliferation in [10%HS/24h/3d]
Organism Mus musculus
Characteristics cell line: C2C12
age: 3th day of proliferation
tissue: myoblasts
treatment: CTRL- untreated
Treatment protocol After reaching ~40% confluence, the proliferating myoblasts were subjected to 48-h exposure to palmitate (final concentration 0.1 mmol/l) added to 5%FBS/DMEM, according to experimental protocol described previously (Lee et al. 2009). The control cultures were maintained in 5% FBS/DMEM, containing the same amounts of ethanol and FFA-free bovine serum albumin as the experimental medium. To preserve the characteristics of C2C12 cell line, the cells were split up to a maximum of 7 times.
Growth protocol Research work was carried out on the murine myogenic C2C12 cell line (satellite cells from thigh muscle), purchased from the European Collection of Animal Cell Culture (ECACC). This cell line undergoes proliferation and differentiation in response to growth factors present in the extracellular environment, thus, it is a useful model to study the mechanisms controlling myogenesis (Yaffe and Saxel 1977). Mouse C2C12 myoblasts were maintained free of contamination at the exponential phase of growth in DMEM supplemented with 10% FBS (Foetal Bovine Serum) and an antibiotic-antimycotic mixture (Life Technologies), in controlled humidified air supplemented with 5% CO2, at 37oC. The growing medium was changed every other day.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted and purified from C2C12 cells using the Total RNA kit (A&A Biotechnology, Poland) according to the manufacturer’s protocol. The isolated RNA samples were dissolved in RNase-free water. The quantity of the isolated RNA was measured using Nano-Drop (NanoDrop Technologies, USA). The RNA samples were treated with DNase I to eliminate DNA contamination and subsequently purified using the RNeasy MiniElute Cleanup Kit (Qiagen, Germany). Subsequently, the RNA samples were analyzed on a BioAnalyzer (Agilent, USA) to measure the final RNA quality and integrity.
Label Cy3
Label protocol The total RNA (1 μg) was extracted, amplified and labeled in accordance with the protocol for Agilent Gene Expression oligo microarrays
 
 
Hybridization protocol The cRNA was fragmented and hybridized to Agilent whole mouse genome oligonucleotide microarray (4 × 44K slide format) at 37 ºC for 17 hours (protocol Version 5.7, March 2008).
Scan protocol After washing the slides were scanned with a DNA microarray Agilent Technologies Scanner G2505C US10353831.
Description Biological replicate 4 of 4. Control: myoblasts cells, untreated, harvested after 3 day of proliferation.
Data processing The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE2_107_Sep09 and Grid: 026655_D_F_20100123) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw data were processed using GeneSpring 12GX (Agilent). Total detected entities were filtered by flags (present, marginal) and coeffi. In statistical analysis of differential gene expression unpaired t-test testing the null hypothesis of no differential expression between the control and experimental group was used. The statistical significance was set at P≤0.05. Moreover, the Benjamini-Hochberg FDR (False discovery rate) test with the significance level p≤0.05 was employed. Absolute fold change cut-off for ontological analyses was 1.6. For interaction network analysis were used all entities with significant changes in expression.
 
Submission date Nov 24, 2015
Last update date Nov 25, 2015
Contact name Zofia Wicik
E-mail(s) zofiawicik@gmail.com
Organization name Mossakowski Medical Research Center
Department Department of Human Epigenetics
Street address Pawinskiego 5
City Warsaw
State/province mazovia
ZIP/Postal code 02-106
Country Poland
 
Platform ID GPL11202
Series (1)
GSE75378 The effect of palmitate on gene expression profile in proliferating myoblasts

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (palmitate treated vs untreated myoblasts)

Data table
ID_REF VALUE
GE_BrightCorner -2.4334936
DarkCorner -0.48634827
A_55_P1989846 -0.49074244
A_55_P1991598 -0.4911544
A_55_P2022211 0.3793297
A_55_P1980764 0.4323767
A_55_P1964375 0.09664632
A_51_P128876 -0.9435711
A_55_P2121042 -0.49256185
A_52_P219230 -0.4928098
A_51_P207591 3.757332E-4
A_55_P2131920 -0.02963734
A_55_P2404223 0.030841887
A_55_P2101944 -0.027923655
A_52_P358860 -0.5133782
A_51_P119031 -0.341363
A_51_P309854 -0.4659706
A_51_P343900 0.11385819
A_51_P234359 0.004573844
A_51_P487813 -0.107172064

Total number of rows: 39485

Table truncated, full table size 959 Kbytes.




Supplementary file Size Download File type/resource
GSM1954223_US10353831_252665511038_S01_GE2_107_Sep09_1_4.txt.gz 4.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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