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Sample GSM746015 Query DataSets for GSM746015
Status Public on Jun 22, 2011
Title Fibroblasts - Fibronectin vs. Plastic
Sample type protein
 
Channel 1
Source name dermal fibroblasts, plastic
Organism Mus musculus
Characteristics background strain: C57BL/6
tissue: skin (dermis)
cell type: primary fibroblasts
growth condition: plastic
sample type: control
Growth protocol Cells were seeded at 35,000 cells per 10 cm2 on plastic or fibronectin and harvested after 48 hours.
Extracted molecule protein
Extraction protocol Cells were rinsed with cold PBS and detached with trypsin. Cell pellets were collected by centrifugation and rinsed with cold PBS. Cells were lysed in lysis buffer and sonicated to rupture cells and shear nuclear DNA. Homogenate was centrifuged, and the supernatant fraction was collected and assayed for protein concentration.
Label fluorescent dye (maximum excitation wavelength at 550 nm)
Label protocol Control and treatment lysate samples are labeled with the same dye; they are analyzed separately, but on the same chip (www.kinexus.ca).
 
Channel 2
Source name dermal fibroblasts, fibronectin
Organism Mus musculus
Characteristics background strain: C57BL/6
tissue: skin (dermis)
cell type: primary fibroblasts
growth condition: fibronectin
sample type: treated
Treatment protocol Concentration of fibronectin on fibronectin-coated plates was 2 μg/cm2.
Growth protocol Cells were seeded at 35,000 cells per 10 cm2 on plastic or fibronectin and harvested after 48 hours.
Extracted molecule protein
Extraction protocol Cells were rinsed with cold PBS and detached with trypsin. Cell pellets were collected by centrifugation and rinsed with cold PBS. Cells were lysed in lysis buffer and sonicated to rupture cells and shear nuclear DNA. Homogenate was centrifuged, and the supernatant fraction was collected and assayed for protein concentration.
Label fluorescent dye (maximum excitation wavelength at 550 nm)
Label protocol Control and treatment lysate samples are labeled with the same dye; they are analyzed separately, but on the same chip (www.kinexus.ca).
 
 
Hybridization protocol Kinexus Bioinformatics Corp. (Vancouver, BC) (www.kinexus.ca).
Scan protocol Kinexus Bioinformatics Corp. (Vancouver, BC) (www.kinexus.ca).
Description Tissue from TCF Reporter Mice (Cheon et al. 2002 PNAS 99:6973-6978 (PMID 11983872)).
Data processing The analysis for each target includes the following parameters: Flag (indication of spot's quality), Signal Median (measurement of spot intensity), Background median, signal/noise ratio, net signal median, Normalized Net Signal Median, Control average, Control % range, Treated Average, Treated % Range, Treated Average/Control (Fold change), % CFC, Log2(Treated Average/Control Average), confidence. (References Kinexus Bioinformatics Literature: Customer Information Package Version 8JN18 and Kinex Reference page). Data processing/analysis was performed by Kinexus Bioinformatics Corp.
 
Submission date Jun 21, 2011
Last update date Aug 29, 2011
Contact name Benjamin Alman
Organization name Hospital for Sick Children
Department Developmental and Stem Cell Biology
Lab Alman Lab
Street address TMDT, 101 College Street
City Toronto
State/province Ontario
ZIP/Postal code M5G 1L7
Country Canada
 
Platform ID GPL13757
Series (1)
GSE30135 Protein expression in primary murine dermal fibroblasts grown on fibronectin vs. plastic

Data table header descriptions
ID_REF
VALUE Log2 (treated average/control average) ratio

Data table
ID_REF VALUE
1 -2.376235371
2 -0.175650495
3 -2.387342469
4 -1.260814041
5 -1.51035697
6 -0.500140956
7 -1.007082885
8 -1.596014935
9 -0.571606398
10 -3.241142382
11 -2.336255688
12 -1.6016131
13 -1.432705269
14 0.395346208
15 -0.68501437
16 -1.404852418
17 -1.511569972
18 -4.708354205
19 -1.916589681
20 -0.589137702

Total number of rows: 800

Table truncated, full table size 12 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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