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Sample GSM1015375 Query DataSets for GSM1015375
Status Public on Nov 19, 2013
Title SGBS_12h_1
Sample type RNA
 
Source name SGBS cell line undergoing differentiation
Organism Homo sapiens
Characteristics cell line: SGBS
time: 12 h
Treatment protocol See growth protocol for induction of differentiation.
Growth protocol SGBS cells were cultured in Dulbecco's modified Eagle's medium (DMEM)/Nutrient Mix F12 (Gibco) containing 8 mg/l biotin, 4 mg/l pantothenate, 0.1 mg/mg streptomycin and 100 U/ml penicillin (OF medium) supplemented with 10% FBS in a humidified 95%air/5%CO2 incubator. The cells were seeded into culture medium flasks or plates, which were coated with a solution of 10 microL/ml fibronectin and 0.05% gelatine in phosphate-buffered saline. Confluent cells were cultured in serum-free OF medium for 2 days followed by stimulation to differentiate with OF media supplemented with 0.01 mg/ml human transferrin, 200 nM T3, 100 nM cortisol, 20 nM insulin, 500 microM IBMX and 100 nM rosiglitazone (Cayman Chemicals). After day 4, the differentiating cells were kept in OF media supplemented with 0.01 mg/ml human transferrin, 100 nM cortisol and 20 nM insulin.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TriSure (Bioline). 1 mL of TriSure was added per a confluent 6-well to lyse the cells. RNA extracted with 200 uL chloroform and precipitated from the aqueous phase with 400 uL isopropanol by incubating at -20C overnight.
Label Cy3
Label protocol Labelled as recommended by manufacturer
 
Hybridization protocol Hybridized as recommended by manufacturer
Scan protocol Scanned as recommended by manufacturer
Description SGBS preadipocyte cells originate from male patient with SGB syndrome and are cultured 2 days in serum-free OF medium prior to differentiation. Subsequently QuickDiff medium is added for the first 4 days of differentiation and then changed for 3FC medium. Please see Wabitsch M. et al. Int J Obes Relat Metab Disord. 2001 for more details
Data processing R/Bioconductor lumi package with vst transformation and rsn normalization. (control probe values in separate table, subtracted prior to vst transformation using lumiB method bgAdjust)
 
Submission date Oct 04, 2012
Last update date Nov 19, 2013
Contact name Merja Heinäniemi
Organization name university of eastern finland
Street address Yliopistonranta 1
City Kuopio
ZIP/Postal code 70210
Country Finland
 
Platform ID GPL6947
Series (2)
GSE41352 Integrated analysis of transcript level regulation of metabolism during human adipocyte differentiation [time course]
GSE41578 Integrated analysis of transcript level regulation of metabolism during human adipocyte differentiation

Data table header descriptions
ID_REF
VALUE Log2 signal from vst transformed and rsn normalized data values (control probe data in separate file, used lumiB method bgAdjust using control probe data prior to vst transformation)
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1762337 7.50602066863731 0.4321476
ILMN_2055271 7.65313488949126 0.02503294
ILMN_1736007 7.51275832909289 0.3623188
ILMN_2383229 7.49512233103817 0.5401844
ILMN_1806310 7.48562764774984 0.6205534
ILMN_1779670 7.47374053713312 0.7167326
ILMN_2321282 7.51807457350823 0.3254282
ILMN_1671474 7.53184910381545 0.2648221
ILMN_1772582 7.48072170243613 0.6600791
ILMN_1735698 7.47665771276953 0.6877471
ILMN_1653355 7.57903751158528 0.1001318
ILMN_1717783 7.47459407547531 0.7101449
ILMN_1705025 7.51951710561254 0.3214756
ILMN_1814316 7.38795611058228 0.9960474
ILMN_2359168 7.49109723497769 0.5744401
ILMN_1731507 7.43791906935729 0.9183136
ILMN_1787689 7.52038406331091 0.3175231
ILMN_1745607 7.46967996143955 0.7444005
ILMN_2136495 7.47079560046098 0.7404479
ILMN_1668111 7.45475156188755 0.828722

Total number of rows: 48802

Table truncated, full table size 1839 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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