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Sample GSM253288 Query DataSets for GSM253288
Status Public on Jan 04, 2008
Title unstimulated chondrocytes rep 2
Sample type RNA
 
Source name unstimulated chondrocytes
Organism Homo sapiens
Characteristics human chondrocytes cultured in RPMI 1640 medium supplemented with 10% human serum, 100ng/ml amphotericin B, 100U/ml penicillin and 100µg/ml streptomycin for 2 passages, 3D cultured for 14 days in alginate beads in presence of 170µM L-ascorbic acid 2-phosphate and subsequently stimulated for 48h with medium control
Treatment protocol Human chondrocytes were isolated by enzymatic digestion (1 U collagenase P, 333 U collagenase II and 33 U hyaluronidase), passage 2 chondrocytes were encapsulated in alginate beads (20 Mio cells/ml in 1,5% (w/v) alginate) and stimulated with conditioned medium of RASF and NDSF.
Growth protocol Human chondrocytes obtained from lateral condyle of femur bones of 6 donors post mortem were amplified by cultivation in RPMI 1640 medium supplemented with 10% human serum, 100ng/ml amphotericin B, 100U/ml penicillin and 100µg/ml streptomycin for 2 passages, subsequently 3D cultured in alginate beads for 14 days in presence of 170µM L-ascorbic acid 2-phosphate and finally stimulated with conditioned medium of RASF and NDSF, respectively, or remaining unstimulated as control.
Extracted molecule total RNA
Extraction protocol Prior to RNA extraction, alginate beads were solubilized on ice in 55mM sodium citrate, 30mM EDTA and 150mM NaCl and cells were centrifuged at 800g for 5min (4°C). Total RNA isolation was proceeded according to the manufacturer’s protocol. Additionally, a proteinase K and DNase I digestion were performed. Isolation of total RNA was done for the six different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding two different experimental groups of NDSF and RASF stimulated chondrocytes and of unstimulated chondrocytes, respectively.
Label biotin
Label protocol 2.5µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix).
 
Hybridization protocol 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v4 protocol.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
Description human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 2, unstimulated
Data processing Data were processed with GCOS 1.4 (TGT = 150) and subsequently imported and further analyzed in the online database SiPaGene (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA).
 
Submission date Dec 26, 2007
Last update date Jan 03, 2008
Contact name Thomas Häupl
E-mail(s) thomas.haeupl@charite.de
Phone +49 30 450513293
Organization name Charité
Department Rheumatology
Street address Charitéplatz 1
City Berlin
ZIP/Postal code 10117
Country Germany
 
Platform ID GPL96
Series (1)
GSE10024 Key Regulatory Molecules of Cartilage Destruction in Rheumatoid Arthritis: An in vitro Study

Data table header descriptions
ID_REF
VALUE MAS 5.0 signal value
ABS_CALL detection call
DETECTION P-VALUE p-value
VALUE_RMA RMA signal value

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE VALUE_RMA
AFFX-BioB-5_at 107.8 P 0.001102 6.750845567
AFFX-BioB-M_at 182.8 P 0.00007 7.2605409
AFFX-BioB-3_at 104.7 P 0.000147 6.119448017
AFFX-BioC-5_at 351 P 0.000081 7.968963817
AFFX-BioC-3_at 335.4 P 0.00006 8.072042585
AFFX-BioDn-5_at 784.7 P 0.000044 9.15540977
AFFX-BioDn-3_at 1610.5 P 0.000169 10.77683283
AFFX-CreX-5_at 3878.9 P 0.000044 11.85414327
AFFX-CreX-3_at 6931.1 P 0.000044 12.70159695
AFFX-DapX-5_at 65 P 0.000258 5.006750019
AFFX-DapX-M_at 139.9 P 0.001593 5.866715923
AFFX-DapX-3_at 176.8 P 0.000225 6.674257255
AFFX-LysX-5_at 15.8 A 0.156732 4.358777735
AFFX-LysX-M_at 29.5 A 0.095667 5.165759109
AFFX-LysX-3_at 32.4 P 0.00762 4.664585868
AFFX-PheX-5_at 16 A 0.216504 4.56725419
AFFX-PheX-M_at 8.3 A 0.300606 4.631279385
AFFX-PheX-3_at 32.7 A 0.102165 5.495294038
AFFX-ThrX-5_at 23.7 P 0.010317 5.120068243
AFFX-ThrX-M_at 42.2 P 0.030976 4.73992767

Total number of rows: 22283

Table truncated, full table size 840 Kbytes.




Supplementary file Size Download File type/resource
GSM253288.CEL.gz 2.1 Mb (ftp)(http) CEL
GSM253288.EXP.gz 509 b (ftp)(http) EXP
Processed data included within Sample table

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