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Sample GSM554783 Query DataSets for GSM554783
Status Public on Sep 01, 2012
Title Cyclopamin, 12h, rep2
Sample type RNA
 
Source name Coculture of 92% hMSCs and 8% huvEC, treated with cyclopamin, after 12 hours
Organism Homo sapiens
Characteristics cell type: co-culture of hMSC (92%) and hUVEC (8%)
treatment: Cyclopamine
Treatment protocol coculture of 92% hMSCs and 8% huvEC (150,000 cells in total) in Deepwell 96 well-plates (adapted hanging-drop method) supplemented or not in cyclopamine, for 12 days. Medium was changed every third day by transferring the spherical aggregate to a new plate.
Growth protocol Co-culture of hMSC (92%) and hUVEC (8%) were obtained by resuspending a total of 150,000 cell per spherical aggregate in 2 ml of differentiation medium and then seeded in a well of a Deepwell 96 well-plate (Nunc).
Extracted molecule total RNA
Extraction protocol RNA was isolated by using an RNeasy mini kit (Qiagen)
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
 
Hybridization protocol Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.
Scan protocol Affymetrix GeneArray Scanner3000
Description The effect of Cyclopamine on expression of Hedgehog, angiogenesis and axon guidance marker genes was analyzed by seeding a coculture of 92% hMSCs and 8% huvEC (150,000 cells in total) in Deepwell 96 well-plates (adapted hanging-drop method) supplemented or not in cyclopamine, for 12 days.
Data processing The data were analyzed with a commercial software called JMP Genomics, version 3.2, from SAS. Gene expression profiling was performed using arrays of HG133 Plus2 -type from Affymetrix. A Custom CDF Version 12 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.
 
Submission date Jun 10, 2010
Last update date Sep 01, 2012
Contact name Carsten Sticht
Organization name University Heidelberg
Department ZMF
Street address Theodor-Kutzer-Ufer
City Mannheim
ZIP/Postal code 68169
Country Germany
 
Platform ID GPL10526
Series (1)
GSE22293 Engineering endochondral ossification using Sonic Hedgehog for bone regeneration

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
1_at 7.63098145
10_at 7.32972301
100_at 8.71240234
1000_at 8.9089741
10000_at 7.73132324
10001_at 8.79286595
10002_at 7.29951172
10003_at 6.9712358
10004_at 8.34133185
100048912_at 7.08830181
100049716_at 8.4037642
10005_at 8.87293837
10006_at 10.952474
10007_at 11.6276634
10008_at 7.63754272
10009_at 9.03873698
100093630_at 10.7283203
1001_at 8.62970526
10010_at 9.60286458
100101467_at 8.7437221

Total number of rows: 17726

Table truncated, full table size 341 Kbytes.




Supplementary file Size Download File type/resource
GSM554783.CEL.gz 8.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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