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Sample GSM498597 Query DataSets for GSM498597
Status Public on Dec 31, 2010
Title PT1
Sample type RNA
 
Source name PT adherent bone cell
Organism Rattus norvegicus
Characteristics cell type: prothrombin adherent cells from long bone
strain: Sprague Dawley
Treatment protocol Rat bone cells from 2-5 day old Sprague Dawley rats were extracted, as described by Hu et al. Exp Cell Res. 2008; 314: 638-50, in α-Minimum Essential Medium Eagle (α-MEM, Sigma-Aldrich, USA) supplemented with 1 mg/ml BSA and 100 mM HEPES, pH 7.4 (Invitrogen, USA). After the extraction were bone cells adhered to 96-well Nunc MaxiSorp plates (Nunc, Germany), coated with bovine milk OPN or mouse PT.
Growth protocol Prothrombin (PT) and osteopontin (OPN) promotes adhesion of different TRAP-positive multinucleated cells isolated from rat long bone (Hu et al. Exp Cell Res. 2008; 314: 638-50).
Extracted molecule total RNA
Extraction protocol RNA was extracted with the RNeasy plus mini kit (Qiagen, USA)
Label biotin
Label protocol GeneChip Whole Transcript (WT) sense target labeling assay manual (Affymetrix, USA), version 4 - starting with 300 ng RNA and following the Total RNA labeling protocol to prepare targets for GeneChip gene 1.0 ST Arrays (omitting RiboMinus procedure).
 
Hybridization protocol GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix, USA).
Scan protocol Arrays were scanned on a GeneChip scanner 3000 7G using default scanner settings. Affymetrix GeneChip® Command Console® (AGCC) was used to process all Affymetrix arrays through fluidics and scanning, and the generation of CEL-files.
Description Gene expression data from PT adherent bone cells
Data processing Probe set signal values were calculated using GeneChip® Expression Console software using the following methods; Summarization: PLIER, Background Correction: PM-GCBG, Normalization: Global Median.
 
Submission date Jan 19, 2010
Last update date Dec 31, 2010
Contact name Erik Karlström
E-mail(s) erik.karlstrom@ki.se
Organization name Karolinska Institutet
Department Department of Laboratory Medicine
Street address Division of Pathology
City Stockholm
ZIP/Postal code SE-141 86
Country Sweden
 
Platform ID GPL6247
Series (1)
GSE19950 Multinucleated Tartrate Resistant Acid Phosphatase Positive Cells with Macrophage and Osteoclast Phenotypes in Bone

Data table header descriptions
ID_REF
VALUE Quantification

Data table
ID_REF VALUE
10700001 8090.1
10700002 357.746
10700003 2831.25
10700004 360.247
10700005 1700.06
10700006 10.5272
10700007 12.7071
10700008 0.359098
10700009 780.031
10700010 23.6677
10700011 50.4103
10700012 50.8125
10700013 4775.85
10700014 2839.36
10700015 969.01
10700016 8.14566
10700017 184.473
10700018 4.10517
10700019 8.963
10700020 7953.66

Total number of rows: 29215

Table truncated, full table size 481 Kbytes.




Supplementary file Size Download File type/resource
GSM498597.CEL.gz 4.1 Mb (ftp)(http) CEL
GSM498597.chp.gz 234.1 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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