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Sample GSM1556696 Query DataSets for GSM1556696
Status Public on Jan 11, 2015
Title AdiposeDerivedStemCells6_osteo_rep1
Sample type RNA
 
Source name Adipose-derived stem cells, donor 6, passage 3, osteogenic differentiation
Organism Homo sapiens
Characteristics differentiation status: osteogenic differentiation
original cell type: Adipose-derived stem cells
Treatment protocol Cells were treated with osteogenic-induction medium, prepared from DMEM-high glucose plus osteogenic stimulatory supplement, dexamethasone (final concentration 10^-8 M) and ascorbic acid (50 μg/ml). When formation of cell multilayers became evident, β-glycerophosphate was added to the osteogenic-induction medium (10^-6 M) and differentiation was performed for another 2 weeks. Control cells were simultaneously cultured in the complete proliferation medium.
Growth protocol Sections of adipose tissue were digested with 0.2% collagenase type I in DMEM at 37°C and filtered through 100 μm filter. Cells were grown in DMEM, supplemented with 10% FCS and antibiotics, in a humidified atmosphere with 5% CO2 at 37°C and passaged when reached subconfluence of 75-90%.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from 2 mln. cells on average with mirVana miRNA Isolation Kit according to manufacturer’s protocol (Life Technologies). Extracted RNA was quantified using NanoDrop-2000 spectrophotometer (Thermo Fisher Scientific) and quality was monitored with Agilent 2100 Bioanalyzer (Agilent Technologies).
Label Cy3
Label protocol Cyanine-3 labeled cRNA was prepared from 200 ng of purified RNA using Low Input Quick Amp Labeling Kit, One Color and RNA Spike-In Kit, One Color acording to manufacturer's protocol (Agilent Technologies), followed by purification with RNeasy Mini Kit (Qiagen). Dye incorporation and cRNA yield was measured with NanoDrop 2000.
 
Hybridization protocol All amount of labeled cRNA was prepared for hybridization using Gene Expression Hybridization Kit following manufacturer's protocol (Agilent technologies). Samples were hybridized onto Human Gene Expression (v2) 8×60K microarrays for 17 hours at 65°C in a rotating hybridization oven (Agilent Technologies).
Scan protocol Microarrays were scanned immediately after washing using SureScan microarray scanner (Agilent Technologies).
Description Gene expression in osteogenically differentiated ADSCs from donor 6
Data processing Scanned images were analyzed with Feature Extraction software v10.7 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09, grid 039494_D_F_20120628 for ADSC4 and 039494_D_F_20140228 for ADSC6 and ADSC7). Background subtracted and spatially detrended signals were obtained.
 
Submission date Dec 01, 2014
Last update date Jan 11, 2015
Contact name Kristina Daniunaite
Organization name Vilnius University
Department Institute of Biosciences
Lab Human Genome Research Centre
Street address Sauletekio Ave. 7
City Vilnius
ZIP/Postal code LT-10257
Country Lithuania
 
Platform ID GPL17077
Series (1)
GSE63754 Gene expression profile of osteogenically differentiated human adipose-derived stem cells

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner 7.7089357
DarkCorner -4.88592
A_23_P117082 4.8222046
A_33_P3246448 1.7744427
A_33_P3318220 -3.7013931
A_33_P3236322 -4.263418
A_33_P3319925 -4.777306
A_21_P0000509 6.2645063
A_21_P0000744 1.1743355
A_24_P215804 0.30080128
A_23_P110167 3.119403
A_33_P3211513 -0.6015358
A_23_P103349 -5.246261
A_32_P61480 -4.577955
A_33_P3788124 -4.856856
A_33_P3414202 -1.7024412
A_33_P3316686 -1.7523375
A_33_P3300975 2.6794071
A_33_P3263061 4.579276
A_33_P3261373 -4.238656

Total number of rows: 50688

Table truncated, full table size 1187 Kbytes.




Supplementary file Size Download File type/resource
GSM1556696_ADSC6_osteo.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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