Search results for the GEO ID: GSE12860 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM322609 | GPL96 |
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RASF stimulated chondrocytes rep 1 GSM253283
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Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 1, RASF stimulated
|
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 supernatant of RASF cultured in the same medium
|
Gene expression data of human chondrocytes stimulated with supernatant of RASF
|
Sample_geo_accession | GSM322609
| Sample_status | Public on Sep 20 2008
| Sample_submission_date | Sep 19 2008
| Sample_last_update_date | Sep 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | 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 NDSF, RASF or treated RASF
| Sample_growth_protocol_ch1 | 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, NDSF, or treated RASF
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)
| Sample_hyb_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.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| Sample_data_processing = Data were processed with GCOS 1.4 (TGT | 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)
| Sample_platform_id | GPL96
| Sample_contact_name | Thomas,,Häupl
| Sample_contact_email | thomas.haeupl@charite.de
| Sample_contact_phone | +49(0)30 450513293
| Sample_contact_fax | +49(0)30 450513957
| Sample_contact_department | Rheumatology
| Sample_contact_institute | Charité
| Sample_contact_address | Tucholskystr. 2
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322609/suppl/GSM322609.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322609/suppl/GSM322609.EXP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322609/suppl/GSM322609_MAS5_data.txt.gz
| Sample_relation | Reanalysis of: GSM253283
| Sample_series_id | GSE12860
| Sample_data_row_count | 22283
| |
|
GSM322610 | GPL96 |
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RASF stimulated chondrocytes rep 2 GSM253284
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Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 2, RASF stimulated
|
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 supernatant of RASF cultured in the same medium
|
Gene expression data of human chondrocytes stimulated with supernatant of RASF
|
Sample_geo_accession | GSM322610
| Sample_status | Public on Sep 20 2008
| Sample_submission_date | Sep 19 2008
| Sample_last_update_date | Sep 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | 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 NDSF, RASF or treated RASF
| Sample_growth_protocol_ch1 | 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, NDSF, or treated RASF
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)
| Sample_hyb_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.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| Sample_data_processing = Data were processed with GCOS 1.4 (TGT | 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)
| Sample_platform_id | GPL96
| Sample_contact_name | Thomas,,Häupl
| Sample_contact_email | thomas.haeupl@charite.de
| Sample_contact_phone | +49(0)30 450513293
| Sample_contact_fax | +49(0)30 450513957
| Sample_contact_department | Rheumatology
| Sample_contact_institute | Charité
| Sample_contact_address | Tucholskystr. 2
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322610/suppl/GSM322610.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322610/suppl/GSM322610.EXP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322610/suppl/GSM322610_MAS5_data.txt.gz
| Sample_relation | Reanalysis of: GSM253284
| Sample_series_id | GSE12860
| Sample_data_row_count | 22283
| |
|
GSM322611 | GPL96 |
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NDSF stimulated chondrocytes rep 1 GSM253285
|
Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 1, NDSF stimulated
|
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 supernatant of NDSF cultured in the same medium
|
Gene expression data of human chondrocytes stimulated with supernatant of NDSF
|
Sample_geo_accession | GSM322611
| Sample_status | Public on Sep 20 2008
| Sample_submission_date | Sep 19 2008
| Sample_last_update_date | Sep 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | 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 NDSF, RASF or treated RASF
| Sample_growth_protocol_ch1 | 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, NDSF, or treated RASF
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)
| Sample_hyb_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.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| Sample_data_processing = Data were processed with GCOS 1.4 (TGT | 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)
| Sample_platform_id | GPL96
| Sample_contact_name | Thomas,,Häupl
| Sample_contact_email | thomas.haeupl@charite.de
| Sample_contact_phone | +49(0)30 450513293
| Sample_contact_fax | +49(0)30 450513957
| Sample_contact_department | Rheumatology
| Sample_contact_institute | Charité
| Sample_contact_address | Tucholskystr. 2
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322611/suppl/GSM322611.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322611/suppl/GSM322611.EXP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322611/suppl/GSM322611_MAS5_data.txt.gz
| Sample_relation | Reanalysis of: GSM253285
| Sample_series_id | GSE12860
| Sample_data_row_count | 22283
| |
|
GSM322612 | GPL96 |
|
NDSF stimulated chondrocytes rep 2 GSM253286
|
Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 2, NDSF stimulated
|
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 supernatant of NDSF cultured in the same medium
|
Gene expression data of human chondrocytes stimulated with supernatant of NDSF
|
Sample_geo_accession | GSM322612
| Sample_status | Public on Sep 20 2008
| Sample_submission_date | Sep 19 2008
| Sample_last_update_date | Sep 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | 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 NDSF, RASF or treated RASF
| Sample_growth_protocol_ch1 | 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, NDSF, or treated RASF
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)
| Sample_hyb_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.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| Sample_data_processing = Data were processed with GCOS 1.4 (TGT | 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)
| Sample_platform_id | GPL96
| Sample_contact_name | Thomas,,Häupl
| Sample_contact_email | thomas.haeupl@charite.de
| Sample_contact_phone | +49(0)30 450513293
| Sample_contact_fax | +49(0)30 450513957
| Sample_contact_department | Rheumatology
| Sample_contact_institute | Charité
| Sample_contact_address | Tucholskystr. 2
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322612/suppl/GSM322612.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322612/suppl/GSM322612.EXP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322612/suppl/GSM322612_MAS5_data.txt.gz
| Sample_relation | Reanalysis of: GSM253286
| Sample_series_id | GSE12860
| Sample_data_row_count | 22283
| |
|
GSM322613 | GPL96 |
|
Chondrocytes stimulated with diclofenac treated RASF rep 1
|
Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 4, stimulated with supernatant from diclofenac treated RASF
|
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 supernatant of RASF cultured in the same medium and treated with diclofenac for 48h
|
Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with diclofenac
|
Sample_geo_accession | GSM322613
| Sample_status | Public on Sep 20 2008
| Sample_submission_date | Sep 19 2008
| Sample_last_update_date | Sep 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | 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 NDSF, RASF or treated RASF
| Sample_growth_protocol_ch1 | 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, NDSF, or treated RASF
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)
| Sample_hyb_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.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| Sample_data_processing = Data were processed with GCOS 1.4 (TGT | 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)
| Sample_platform_id | GPL96
| Sample_contact_name | Thomas,,Häupl
| Sample_contact_email | thomas.haeupl@charite.de
| Sample_contact_phone | +49(0)30 450513293
| Sample_contact_fax | +49(0)30 450513957
| Sample_contact_department | Rheumatology
| Sample_contact_institute | Charité
| Sample_contact_address | Tucholskystr. 2
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322613/suppl/GSM322613.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322613/suppl/GSM322613.EXP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322613/suppl/GSM322613_MAS5_data.txt.gz
| Sample_series_id | GSE12860
| Sample_data_row_count | 22283
| |
|
GSM322614 | GPL96 |
|
Chondrocytes stimulated with diclofenac treated RASF rep 2
|
Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 5, stimulated with supernatant from diclofenac treated RASF
|
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 supernatant of RASF cultured in the same medium and treated with diclofenac for 48h
|
Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with diclofenac
|
Sample_geo_accession | GSM322614
| Sample_status | Public on Sep 20 2008
| Sample_submission_date | Sep 19 2008
| Sample_last_update_date | Sep 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | 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 NDSF, RASF or treated RASF
| Sample_growth_protocol_ch1 | 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, NDSF, or treated RASF
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)
| Sample_hyb_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.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| Sample_data_processing = Data were processed with GCOS 1.4 (TGT | 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)
| Sample_platform_id | GPL96
| Sample_contact_name | Thomas,,Häupl
| Sample_contact_email | thomas.haeupl@charite.de
| Sample_contact_phone | +49(0)30 450513293
| Sample_contact_fax | +49(0)30 450513957
| Sample_contact_department | Rheumatology
| Sample_contact_institute | Charité
| Sample_contact_address | Tucholskystr. 2
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322614/suppl/GSM322614.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322614/suppl/GSM322614.EXP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322614/suppl/GSM322614_MAS5_data.txt.gz
| Sample_series_id | GSE12860
| Sample_data_row_count | 22283
| |
|
GSM322615 | GPL96 |
|
Chondrocytes stimulated with prioxicam treated RASF rep 1
|
Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 4, stimulated with supernatant from prioxicam treated RASF
|
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 supernatant of RASF cultured in the same medium and treated with piroxicam for 48h
|
Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with piroxicam
|
Sample_geo_accession | GSM322615
| Sample_status | Public on Sep 20 2008
| Sample_submission_date | Sep 19 2008
| Sample_last_update_date | Sep 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | 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 NDSF, RASF or treated RASF
| Sample_growth_protocol_ch1 | 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, NDSF, or treated RASF
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)
| Sample_hyb_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.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| Sample_data_processing = Data were processed with GCOS 1.4 (TGT | 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)
| Sample_platform_id | GPL96
| Sample_contact_name | Thomas,,Häupl
| Sample_contact_email | thomas.haeupl@charite.de
| Sample_contact_phone | +49(0)30 450513293
| Sample_contact_fax | +49(0)30 450513957
| Sample_contact_department | Rheumatology
| Sample_contact_institute | Charité
| Sample_contact_address | Tucholskystr. 2
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322615/suppl/GSM322615.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322615/suppl/GSM322615.EXP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322615/suppl/GSM322615_MAS5_data.txt.gz
| Sample_series_id | GSE12860
| Sample_data_row_count | 22283
| |
|
GSM322616 | GPL96 |
|
Chondrocytes stimulated with prioxicam treated RASF rep 2
|
Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 5, stimulated with supernatant from prioxicam treated RASF
|
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 supernatant of RASF cultured in the same medium and treated with piroxicam for 48h
|
Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with piroxicam
|
Sample_geo_accession | GSM322616
| Sample_status | Public on Sep 20 2008
| Sample_submission_date | Sep 19 2008
| Sample_last_update_date | Sep 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | 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 NDSF, RASF or treated RASF
| Sample_growth_protocol_ch1 | 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, NDSF, or treated RASF
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)
| Sample_hyb_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.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| Sample_data_processing = Data were processed with GCOS 1.4 (TGT | 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)
| Sample_platform_id | GPL96
| Sample_contact_name | Thomas,,Häupl
| Sample_contact_email | thomas.haeupl@charite.de
| Sample_contact_phone | +49(0)30 450513293
| Sample_contact_fax | +49(0)30 450513957
| Sample_contact_department | Rheumatology
| Sample_contact_institute | Charité
| Sample_contact_address | Tucholskystr. 2
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322616/suppl/GSM322616.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322616/suppl/GSM322616.EXP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322616/suppl/GSM322616_MAS5_data.txt.gz
| Sample_series_id | GSE12860
| Sample_data_row_count | 22283
| |
|
GSM322617 | GPL96 |
|
Chondrocytes stimulated with chloroquine phosphate (resochin) treated RASF rep 1
|
Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 4, stimulated with supernatant from chloroquine phosphate (resochin) treated RASF
|
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 supernatant of RASF cultured in the same medium and treated with chloroquine phosphate (resochin) for 48h
|
Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with chloroquine phosphate (resochin)
|
Sample_geo_accession | GSM322617
| Sample_status | Public on Sep 20 2008
| Sample_submission_date | Sep 19 2008
| Sample_last_update_date | Sep 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | 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 NDSF, RASF or treated RASF
| Sample_growth_protocol_ch1 | 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, NDSF, or treated RASF
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)
| Sample_hyb_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.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| Sample_data_processing = Data were processed with GCOS 1.4 (TGT | 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)
| Sample_platform_id | GPL96
| Sample_contact_name | Thomas,,Häupl
| Sample_contact_email | thomas.haeupl@charite.de
| Sample_contact_phone | +49(0)30 450513293
| Sample_contact_fax | +49(0)30 450513957
| Sample_contact_department | Rheumatology
| Sample_contact_institute | Charité
| Sample_contact_address | Tucholskystr. 2
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322617/suppl/GSM322617.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322617/suppl/GSM322617.EXP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322617/suppl/GSM322617_MAS5_data.txt.gz
| Sample_series_id | GSE12860
| Sample_data_row_count | 22283
| |
|
GSM322618 | GPL96 |
|
Chondrocytes stimulated with chloroquine phosphate (resochin) treated RASF rep 2
|
Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 5, stimulated with supernatant from chloroquine phosphate (resochin) treated RASF
|
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 supernatant of RASF cultured in the same medium and treated with chloroquine phosphate (resochin) for 48h
|
Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with chloroquine phosphate (resochin)
|
Sample_geo_accession | GSM322618
| Sample_status | Public on Sep 20 2008
| Sample_submission_date | Sep 19 2008
| Sample_last_update_date | Sep 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | 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 NDSF, RASF or treated RASF
| Sample_growth_protocol_ch1 | 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, NDSF, or treated RASF
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)
| Sample_hyb_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.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| Sample_data_processing = Data were processed with GCOS 1.4 (TGT | 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)
| Sample_platform_id | GPL96
| Sample_contact_name | Thomas,,Häupl
| Sample_contact_email | thomas.haeupl@charite.de
| Sample_contact_phone | +49(0)30 450513293
| Sample_contact_fax | +49(0)30 450513957
| Sample_contact_department | Rheumatology
| Sample_contact_institute | Charité
| Sample_contact_address | Tucholskystr. 2
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322618/suppl/GSM322618.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322618/suppl/GSM322618.EXP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322618/suppl/GSM322618_MAS5_data.txt.gz
| Sample_series_id | GSE12860
| Sample_data_row_count | 22283
| |
|
GSM322619 | GPL96 |
|
Chondrocytes stimulated with sodium aurothiomalate (tauredon) treated RASF rep 1
|
Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 4, stimulated with supernatant from sodium aurothiomalate (tauredon) treated RASF
|
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 supernatant of RASF cultured in the same medium and treated with sodium aurothiomalate (tauredon) for 48h
|
Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with sodium aurothiomalate (tauredon)
|
Sample_geo_accession | GSM322619
| Sample_status | Public on Sep 20 2008
| Sample_submission_date | Sep 19 2008
| Sample_last_update_date | Sep 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | 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 NDSF, RASF or treated RASF
| Sample_growth_protocol_ch1 | 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, NDSF, or treated RASF
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)
| Sample_hyb_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.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| Sample_data_processing = Data were processed with GCOS 1.4 (TGT | 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)
| Sample_platform_id | GPL96
| Sample_contact_name | Thomas,,Häupl
| Sample_contact_email | thomas.haeupl@charite.de
| Sample_contact_phone | +49(0)30 450513293
| Sample_contact_fax | +49(0)30 450513957
| Sample_contact_department | Rheumatology
| Sample_contact_institute | Charité
| Sample_contact_address | Tucholskystr. 2
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322619/suppl/GSM322619.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322619/suppl/GSM322619.EXP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322619/suppl/GSM322619_MAS5_data.txt.gz
| Sample_series_id | GSE12860
| Sample_data_row_count | 22283
| |
|
GSM322620 | GPL96 |
|
Chondrocytes stimulated with sodium aurothiomalate (tauredon) treated RASF rep 2
|
Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 5, stimulated with supernatant from sodium aurothiomalate (tauredon) treated RASF
|
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 supernatant of RASF cultured in the same medium and treated with sodium aurothiomalate (tauredon) for 48h
|
Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with sodium aurothiomalate (tauredon)
|
Sample_geo_accession | GSM322620
| Sample_status | Public on Sep 20 2008
| Sample_submission_date | Sep 19 2008
| Sample_last_update_date | Sep 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | 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 NDSF, RASF or treated RASF
| Sample_growth_protocol_ch1 | 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, NDSF, or treated RASF
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)
| Sample_hyb_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.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| Sample_data_processing = Data were processed with GCOS 1.4 (TGT | 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)
| Sample_platform_id | GPL96
| Sample_contact_name | Thomas,,Häupl
| Sample_contact_email | thomas.haeupl@charite.de
| Sample_contact_phone | +49(0)30 450513293
| Sample_contact_fax | +49(0)30 450513957
| Sample_contact_department | Rheumatology
| Sample_contact_institute | Charité
| Sample_contact_address | Tucholskystr. 2
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322620/suppl/GSM322620.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322620/suppl/GSM322620.EXP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322620/suppl/GSM322620_MAS5_data.txt.gz
| Sample_series_id | GSE12860
| Sample_data_row_count | 22283
| |
|
GSM322621 | GPL96 |
|
Chondrocytes stimulated with azathioprine (imurek) treated RASF rep 1
|
Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 4, stimulated with supernatant from azathioprine (imurek) treated RASF
|
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 supernatant of RASF cultured in the same medium and treated with azathioprine (imurek) for 48h
|
Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with azathioprine (imurek)
|
Sample_geo_accession | GSM322621
| Sample_status | Public on Sep 20 2008
| Sample_submission_date | Sep 19 2008
| Sample_last_update_date | Sep 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | 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 NDSF, RASF or treated RASF
| Sample_growth_protocol_ch1 | 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, NDSF, or treated RASF
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)
| Sample_hyb_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.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| Sample_data_processing = Data were processed with GCOS 1.4 (TGT | 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)
| Sample_platform_id | GPL96
| Sample_contact_name | Thomas,,Häupl
| Sample_contact_email | thomas.haeupl@charite.de
| Sample_contact_phone | +49(0)30 450513293
| Sample_contact_fax | +49(0)30 450513957
| Sample_contact_department | Rheumatology
| Sample_contact_institute | Charité
| Sample_contact_address | Tucholskystr. 2
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322621/suppl/GSM322621.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322621/suppl/GSM322621.EXP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322621/suppl/GSM322621_MAS5_data.txt.gz
| Sample_series_id | GSE12860
| Sample_data_row_count | 22283
| |
|
GSM322622 | GPL96 |
|
Chondrocytes stimulated with azathioprine (imurek) treated RASF rep 2
|
Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 5, stimulated with supernatant from azathioprine (imurek) treated RASF
|
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 supernatant of RASF cultured in the same medium and treated with azathioprine (imurek) for 48h
|
Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with azathioprine (imurek)
|
Sample_geo_accession | GSM322622
| Sample_status | Public on Sep 20 2008
| Sample_submission_date | Sep 19 2008
| Sample_last_update_date | Sep 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | 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 NDSF, RASF or treated RASF
| Sample_growth_protocol_ch1 | 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, NDSF, or treated RASF
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)
| Sample_hyb_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.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| Sample_data_processing = Data were processed with GCOS 1.4 (TGT | 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)
| Sample_platform_id | GPL96
| Sample_contact_name | Thomas,,Häupl
| Sample_contact_email | thomas.haeupl@charite.de
| Sample_contact_phone | +49(0)30 450513293
| Sample_contact_fax | +49(0)30 450513957
| Sample_contact_department | Rheumatology
| Sample_contact_institute | Charité
| Sample_contact_address | Tucholskystr. 2
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322622/suppl/GSM322622.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322622/suppl/GSM322622.EXP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322622/suppl/GSM322622_MAS5_data.txt.gz
| Sample_series_id | GSE12860
| Sample_data_row_count | 22283
| |
|
GSM322623 | GPL96 |
|
Chondrocytes stimulated with methotrexate treated RASF rep 1
|
Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 10, stimulated with supernatant from methotrexate treated RASF
|
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 supernatant of RASF cultured in the same medium and treated with methotrexate for 48h
|
Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with methotrexate
|
Sample_geo_accession | GSM322623
| Sample_status | Public on Sep 20 2008
| Sample_submission_date | Sep 19 2008
| Sample_last_update_date | Sep 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | 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 NDSF, RASF or treated RASF
| Sample_growth_protocol_ch1 | 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, NDSF, or treated RASF
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)
| Sample_hyb_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.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| Sample_data_processing = Data were processed with GCOS 1.4 (TGT | 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)
| Sample_platform_id | GPL96
| Sample_contact_name | Thomas,,Häupl
| Sample_contact_email | thomas.haeupl@charite.de
| Sample_contact_phone | +49(0)30 450513293
| Sample_contact_fax | +49(0)30 450513957
| Sample_contact_department | Rheumatology
| Sample_contact_institute | Charité
| Sample_contact_address | Tucholskystr. 2
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322623/suppl/GSM322623.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322623/suppl/GSM322623.EXP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322623/suppl/GSM322623_MAS5_data.txt.gz
| Sample_series_id | GSE12860
| Sample_data_row_count | 22283
| |
|
GSM322624 | GPL96 |
|
Chondrocytes stimulated with methotrexate treated RASF rep 2
|
Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 11, stimulated with supernatant from methotrexate treated RASF
|
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 supernatant of RASF cultured in the same medium and treated with methotrexate for 48h
|
Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with methotrexate
|
Sample_geo_accession | GSM322624
| Sample_status | Public on Sep 20 2008
| Sample_submission_date | Sep 19 2008
| Sample_last_update_date | Sep 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | 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 NDSF, RASF or treated RASF
| Sample_growth_protocol_ch1 | 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, NDSF, or treated RASF
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)
| Sample_hyb_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.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| Sample_data_processing = Data were processed with GCOS 1.4 (TGT | 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)
| Sample_platform_id | GPL96
| Sample_contact_name | Thomas,,Häupl
| Sample_contact_email | thomas.haeupl@charite.de
| Sample_contact_phone | +49(0)30 450513293
| Sample_contact_fax | +49(0)30 450513957
| Sample_contact_department | Rheumatology
| Sample_contact_institute | Charité
| Sample_contact_address | Tucholskystr. 2
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322624/suppl/GSM322624.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322624/suppl/GSM322624.EXP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322624/suppl/GSM322624_MAS5_data.txt.gz
| Sample_series_id | GSE12860
| Sample_data_row_count | 22283
| |
|
GSM322625 | GPL96 |
|
Chondrocytes stimulated with prednisolone (solu-decortin) treated RASF rep 1
|
Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 8, stimulated with supernatant from prednisolone (solu-decortin) treated RASF
|
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 supernatant of RASF cultured in the same medium and treated with prednisolone (solu-decortin) for 48h
|
Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with prednisolone (solu-decortin)
|
Sample_geo_accession | GSM322625
| Sample_status | Public on Sep 20 2008
| Sample_submission_date | Sep 19 2008
| Sample_last_update_date | Sep 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | 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 NDSF, RASF or treated RASF
| Sample_growth_protocol_ch1 | 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, NDSF, or treated RASF
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)
| Sample_hyb_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.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| Sample_data_processing = Data were processed with GCOS 1.4 (TGT | 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)
| Sample_platform_id | GPL96
| Sample_contact_name | Thomas,,Häupl
| Sample_contact_email | thomas.haeupl@charite.de
| Sample_contact_phone | +49(0)30 450513293
| Sample_contact_fax | +49(0)30 450513957
| Sample_contact_department | Rheumatology
| Sample_contact_institute | Charité
| Sample_contact_address | Tucholskystr. 2
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322625/suppl/GSM322625.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322625/suppl/GSM322625.EXP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322625/suppl/GSM322625_MAS5_data.txt.gz
| Sample_series_id | GSE12860
| Sample_data_row_count | 22283
| |
|
GSM322626 | GPL96 |
|
Chondrocytes stimulated with prednisolone (solu-decortin) treated RASF rep 2
|
Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 9, stimulated with supernatant from prednisolone (solu-decortin) treated RASF
|
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 supernatant of RASF cultured in the same medium and treated with prednisolone (solu-decortin) for 48h
|
Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with prednisolone (solu-decortin)
|
Sample_geo_accession | GSM322626
| Sample_status | Public on Sep 20 2008
| Sample_submission_date | Sep 19 2008
| Sample_last_update_date | Sep 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | 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 NDSF, RASF or treated RASF
| Sample_growth_protocol_ch1 | 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, NDSF, or treated RASF
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)
| Sample_hyb_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.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| Sample_data_processing = Data were processed with GCOS 1.4 (TGT | 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)
| Sample_platform_id | GPL96
| Sample_contact_name | Thomas,,Häupl
| Sample_contact_email | thomas.haeupl@charite.de
| Sample_contact_phone | +49(0)30 450513293
| Sample_contact_fax | +49(0)30 450513957
| Sample_contact_department | Rheumatology
| Sample_contact_institute | Charité
| Sample_contact_address | Tucholskystr. 2
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322626/suppl/GSM322626.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322626/suppl/GSM322626.EXP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322626/suppl/GSM322626_MAS5_data.txt.gz
| Sample_series_id | GSE12860
| Sample_data_row_count | 22283
| |
|
GSM322627 | GPL96 |
|
Chondrocytes stimulated with methylprednisolone (urbason) treated RASF rep 1
|
Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 6, stimulated with supernatant from methylprednisolone (urbason) treated RASF
|
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 supernatant of RASF cultured in the same medium and treated with methylprednisolone (urbason) for 48h
|
Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with methylprednisolone (urbason)
|
Sample_geo_accession | GSM322627
| Sample_status | Public on Sep 20 2008
| Sample_submission_date | Sep 19 2008
| Sample_last_update_date | Sep 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | 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 NDSF, RASF or treated RASF
| Sample_growth_protocol_ch1 | 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, NDSF, or treated RASF
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)
| Sample_hyb_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.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| Sample_data_processing = Data were processed with GCOS 1.4 (TGT | 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)
| Sample_platform_id | GPL96
| Sample_contact_name | Thomas,,Häupl
| Sample_contact_email | thomas.haeupl@charite.de
| Sample_contact_phone | +49(0)30 450513293
| Sample_contact_fax | +49(0)30 450513957
| Sample_contact_department | Rheumatology
| Sample_contact_institute | Charité
| Sample_contact_address | Tucholskystr. 2
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322627/suppl/GSM322627.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322627/suppl/GSM322627.EXP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322627/suppl/GSM322627_MAS5_data.txt.gz
| Sample_series_id | GSE12860
| Sample_data_row_count | 22283
| |
|
GSM322628 | GPL96 |
|
Chondrocytes stimulated with methylprednisolone (urbason) treated RASF rep 2
|
Human chondrocytes isolated from lateral condyle of femur bone in culture from donor pool 7, stimulated with supernatant from methylprednisolone (urbason) treated RASF
|
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 supernatant of RASF cultured in the same medium and treated with methylprednisolone (urbason) for 48h
|
Gene expression data of human chondrocytes stimulated with supernatant of RASF treated for 48h with methylprednisolone (urbason)
|
Sample_geo_accession | GSM322628
| Sample_status | Public on Sep 20 2008
| Sample_submission_date | Sep 19 2008
| Sample_last_update_date | Sep 19 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | 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 NDSF, RASF or treated RASF
| Sample_growth_protocol_ch1 | 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, NDSF, or treated RASF
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | 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 different stimulated donor chondrocytes separately. Afterwards, equal amounts of total RNA from three stimulated donor chondrocytes were pooled, yielding different experimental groups of chondrocytes stimulated with supernatant of NDSF, RASF or treated RASF
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | 2.5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents (Affymetrix)
| Sample_hyb_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.
| Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
| Sample_data_processing = Data were processed with GCOS 1.4 (TGT | 150) and subsequently imported and further analyzed in the BioRetis online database (www.bioretis.de). Additionally, expression data was processed with Robust Multi-Array Analysis version 0.4a7 (RMA)
| Sample_platform_id | GPL96
| Sample_contact_name | Thomas,,Häupl
| Sample_contact_email | thomas.haeupl@charite.de
| Sample_contact_phone | +49(0)30 450513293
| Sample_contact_fax | +49(0)30 450513957
| Sample_contact_department | Rheumatology
| Sample_contact_institute | Charité
| Sample_contact_address | Tucholskystr. 2
| Sample_contact_city | Berlin
| Sample_contact_zip/postal_code | 10117
| Sample_contact_country | Germany
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322628/suppl/GSM322628.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322628/suppl/GSM322628.EXP.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM322nnn/GSM322628/suppl/GSM322628_MAS5_data.txt.gz
| Sample_series_id | GSE12860
| Sample_data_row_count | 22283
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Make groups for comparisons |
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Select GSMs and click on "Add groups" |
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