Search results for the GEO ID: GSE7669  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM183695 | GPL8300 |
|
fibroblasts_RA_patient88
|
Synovial fibroblasts, rheumatoid arthritis patient 88.
|
female, 62 yrs, treatment with NSAIDs.
|
see publication for details
|
| Sample_geo_accession | GSM183695
| | Sample_status | Public on Aug 30 2007
| | Sample_submission_date | Apr 24 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Clinic of Orthopedics, FSU Jena, Waldkrankenhaus “Rudolf Elle”, Eisenberg, Germany
| | Sample_treatment_protocol_ch1 = Synovial tissue was obtained from open joint replacement surgery or arthroscopic synovectomy at the Clinic of Orthopedics, Waldkrankenhaus “Rudolf Elle” (Eisenberg, Germany). Patients with RA or OA (n | 6 each for gene expression analysis and further patients for validation experiments) were classified according to the ACR criteria.
| | Sample_growth_protocol_ch1 | The tissue samples were minced, digested with trypsin/collagenase P, and the resulting single cell suspension cultured for 7 days. Non-adherent cells were removed by medium exchange. SFB were then negatively purified using Dynabeads® M-450 CD14 and subsequently cultured over 2 passages in DMEM containing 100 μg/ml gentamycin, 100 μg/ml penicillin/streptomycin, 20 mM HEPES and 10% fetal calf serum (FCS, all from PAA Laboratories, Cölbe, Germany).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the end of the 2nd passage, the SFB were starved with medium containing 1% fetal calf serum (FCS) for 72 h, to minimize stimulating effects by serum components. After washing with PBS, the cells were lysed with RLT buffer (Qiagen, Hilden, Germany) and frozen at -70°C. Total RNA was isolated using the RNeasy Kit (Qiagen) according to the supplier’s recommendation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA probes were labeled according to the supplier’s instructions (Affymetrix, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips was performed according to the supplier’s instructions (http://www.affymetrix.com).
| | Sample_scan_protocol | Microarrays were analyzed by laser scanning (Hewlett-Packard Gene Scanner).
| | Sample_data_processing | Background-corrected signal intensities were determined using the MAS 5.0 software (Affymetrix).
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Andreas,,Beyer
| | Sample_contact_email | mail@a-beyer.de
| | Sample_contact_institute | BIOTEC
| | Sample_contact_address | Tatzberg. 47/49
| | Sample_contact_city | Dresden
| | Sample_contact_zip/postal_code | 01277
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM183nnn/GSM183695/suppl/GSM183695.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM183nnn/GSM183695/suppl/GSM183695.CHP.gz
| | Sample_series_id | GSE7669
| | Sample_data_row_count | 12625
| | |
|
GSM185526 | GPL8300 |
|
fibroblasts_RA_patient96
|
Synovial fibroblasts, rheumatoid arthritis patient 96.
|
male, 67 yrs, treatment with NSAIDs.
|
see publication for details
|
| Sample_geo_accession | GSM185526
| | Sample_status | Public on Aug 30 2007
| | Sample_submission_date | Apr 30 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Clinic of Orthopedics, FSU Jena, Waldkrankenhaus “Rudolf Elle”, Eisenberg, Germany
| | Sample_treatment_protocol_ch1 = Synovial tissue was obtained from open joint replacement surgery or arthroscopic synovectomy at the Clinic of Orthopedics, Waldkrankenhaus “Rudolf Elle” (Eisenberg, Germany). Patients with RA or OA (n | 6 each for gene expression analysis and further patients for validation experiments) were classified according to the ACR criteria.
| | Sample_growth_protocol_ch1 | The tissue samples were minced, digested with trypsin/collagenase P, and the resulting single cell suspension cultured for 7 days. Non-adherent cells were removed by medium exchange. SFB were then negatively purified using Dynabeads® M-450 CD14 and subsequently cultured over 2 passages in DMEM containing 100 μg/ml gentamycin, 100 μg/ml penicillin/streptomycin, 20 mM HEPES and 10% fetal calf serum (FCS, all from PAA Laboratories, Cölbe, Germany).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the end of the 2nd passage, the SFB were starved with medium containing 1% fetal calf serum (FCS) for 72 h, to minimize stimulating effects by serum components. After washing with PBS, the cells were lysed with RLT buffer (Qiagen, Hilden, Germany) and frozen at -70°C. Total RNA was isolated using the RNeasy Kit (Qiagen) according to the supplier’s recommendation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA probes were labeled according to the supplier’s instructions (Affymetrix, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips was performed according to the supplier’s instructions (http://www.affymetrix.com).
| | Sample_scan_protocol | Microarrays were analyzed by laser scanning (Hewlett-Packard Gene Scanner).
| | Sample_data_processing | Background-corrected signal intensities were determined using the MAS 5.0 software (Affymetrix).
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Andreas,,Beyer
| | Sample_contact_email | mail@a-beyer.de
| | Sample_contact_institute | BIOTEC
| | Sample_contact_address | Tatzberg. 47/49
| | Sample_contact_city | Dresden
| | Sample_contact_zip/postal_code | 01277
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185526/suppl/GSM185526.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185526/suppl/GSM185526.CHP.gz
| | Sample_series_id | GSE7669
| | Sample_data_row_count | 12625
| | |
|
GSM185527 | GPL8300 |
|
fibroblasts_RA_patient73
|
Synovial fibroblasts, rheumatoid arthritis patient no. 73.
|
male, 68 yrs, treatment with MTX.
|
see publication for details
|
| Sample_geo_accession | GSM185527
| | Sample_status | Public on Aug 30 2007
| | Sample_submission_date | Apr 30 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Clinic of Orthopedics, FSU Jena, Waldkrankenhaus “Rudolf Elle”, Eisenberg, Germany
| | Sample_treatment_protocol_ch1 = Synovial tissue was obtained from open joint replacement surgery or arthroscopic synovectomy at the Clinic of Orthopedics, Waldkrankenhaus “Rudolf Elle” (Eisenberg, Germany). Patients with RA or OA (n | 6 each for gene expression analysis and further patients for validation experiments) were classified according to the ACR criteria.
| | Sample_growth_protocol_ch1 | The tissue samples were minced, digested with trypsin/collagenase P, and the resulting single cell suspension cultured for 7 days. Non-adherent cells were removed by medium exchange. SFB were then negatively purified using Dynabeads® M-450 CD14 and subsequently cultured over 2 passages in DMEM containing 100 μg/ml gentamycin, 100 μg/ml penicillin/streptomycin, 20 mM HEPES and 10% fetal calf serum (FCS, all from PAA Laboratories, Cölbe, Germany).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the end of the 2nd passage, the SFB were starved with medium containing 1% fetal calf serum (FCS) for 72 h, to minimize stimulating effects by serum components. After washing with PBS, the cells were lysed with RLT buffer (Qiagen, Hilden, Germany) and frozen at -70°C. Total RNA was isolated using the RNeasy Kit (Qiagen) according to the supplier’s recommendation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA probes were labeled according to the supplier’s instructions (Affymetrix, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips was performed according to the supplier’s instructions (http://www.affymetrix.com).
| | Sample_scan_protocol | Microarrays were analyzed by laser scanning (Hewlett-Packard Gene Scanner).
| | Sample_data_processing | Background-corrected signal intensities were determined using the MAS 5.0 software (Affymetrix).
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Andreas,,Beyer
| | Sample_contact_email | mail@a-beyer.de
| | Sample_contact_institute | BIOTEC
| | Sample_contact_address | Tatzberg. 47/49
| | Sample_contact_city | Dresden
| | Sample_contact_zip/postal_code | 01277
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185527/suppl/GSM185527.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185527/suppl/GSM185527.CHP.gz
| | Sample_series_id | GSE7669
| | Sample_data_row_count | 12625
| | |
|
GSM185528 | GPL8300 |
|
fibroblasts_RA_patient74
|
Synovial fibroblasts, rheumatoid arthritis patient no. 74.
|
female, 71 yrs, treatment with NSAIDs.
|
see publication for details
|
| Sample_geo_accession | GSM185528
| | Sample_status | Public on Aug 30 2007
| | Sample_submission_date | Apr 30 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Clinic of Orthopedics, FSU Jena, Waldkrankenhaus “Rudolf Elle”, Eisenberg, Germany
| | Sample_treatment_protocol_ch1 = Synovial tissue was obtained from open joint replacement surgery or arthroscopic synovectomy at the Clinic of Orthopedics, Waldkrankenhaus “Rudolf Elle” (Eisenberg, Germany). Patients with RA or OA (n | 6 each for gene expression analysis and further patients for validation experiments) were classified according to the ACR criteria.
| | Sample_growth_protocol_ch1 | The tissue samples were minced, digested with trypsin/collagenase P, and the resulting single cell suspension cultured for 7 days. Non-adherent cells were removed by medium exchange. SFB were then negatively purified using Dynabeads® M-450 CD14 and subsequently cultured over 2 passages in DMEM containing 100 μg/ml gentamycin, 100 μg/ml penicillin/streptomycin, 20 mM HEPES and 10% fetal calf serum (FCS, all from PAA Laboratories, Cölbe, Germany).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the end of the 2nd passage, the SFB were starved with medium containing 1% fetal calf serum (FCS) for 72 h, to minimize stimulating effects by serum components. After washing with PBS, the cells were lysed with RLT buffer (Qiagen, Hilden, Germany) and frozen at -70°C. Total RNA was isolated using the RNeasy Kit (Qiagen) according to the supplier’s recommendation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA probes were labeled according to the supplier’s instructions (Affymetrix, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips was performed according to the supplier’s instructions (http://www.affymetrix.com).
| | Sample_scan_protocol | Microarrays were analyzed by laser scanning (Hewlett-Packard Gene Scanner).
| | Sample_data_processing | Background-corrected signal intensities were determined using the MAS 5.0 software (Affymetrix).
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Andreas,,Beyer
| | Sample_contact_email | mail@a-beyer.de
| | Sample_contact_institute | BIOTEC
| | Sample_contact_address | Tatzberg. 47/49
| | Sample_contact_city | Dresden
| | Sample_contact_zip/postal_code | 01277
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185528/suppl/GSM185528.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185528/suppl/GSM185528.CHP.gz
| | Sample_series_id | GSE7669
| | Sample_data_row_count | 12625
| | |
|
GSM185529 | GPL8300 |
|
fibroblasts_RA_patient87
|
Synovial fibroblasts, rheumatoid arthritis patient no. 87
|
female, 65 yrs, treatment with NSAIDs.
|
see publication for details
|
| Sample_geo_accession | GSM185529
| | Sample_status | Public on Aug 30 2007
| | Sample_submission_date | Apr 30 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Clinic of Orthopedics, FSU Jena, Waldkrankenhaus “Rudolf Elle”, Eisenberg, Germany
| | Sample_treatment_protocol_ch1 = Synovial tissue was obtained from open joint replacement surgery or arthroscopic synovectomy at the Clinic of Orthopedics, Waldkrankenhaus “Rudolf Elle” (Eisenberg, Germany). Patients with RA or OA (n | 6 each for gene expression analysis and further patients for validation experiments) were classified according to the ACR criteria.
| | Sample_growth_protocol_ch1 | The tissue samples were minced, digested with trypsin/collagenase P, and the resulting single cell suspension cultured for 7 days. Non-adherent cells were removed by medium exchange. SFB were then negatively purified using Dynabeads® M-450 CD14 and subsequently cultured over 2 passages in DMEM containing 100 μg/ml gentamycin, 100 μg/ml penicillin/streptomycin, 20 mM HEPES and 10% fetal calf serum (FCS, all from PAA Laboratories, Cölbe, Germany).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the end of the 2nd passage, the SFB were starved with medium containing 1% fetal calf serum (FCS) for 72 h, to minimize stimulating effects by serum components. After washing with PBS, the cells were lysed with RLT buffer (Qiagen, Hilden, Germany) and frozen at -70°C. Total RNA was isolated using the RNeasy Kit (Qiagen) according to the supplier’s recommendation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA probes were labeled according to the supplier’s instructions (Affymetrix, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips was performed according to the supplier’s instructions (http://www.affymetrix.com).
| | Sample_scan_protocol | Microarrays were analyzed by laser scanning (Hewlett-Packard Gene Scanner).
| | Sample_data_processing | Background-corrected signal intensities were determined using the MAS 5.0 software (Affymetrix).
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Andreas,,Beyer
| | Sample_contact_email | mail@a-beyer.de
| | Sample_contact_institute | BIOTEC
| | Sample_contact_address | Tatzberg. 47/49
| | Sample_contact_city | Dresden
| | Sample_contact_zip/postal_code | 01277
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185529/suppl/GSM185529.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185529/suppl/GSM185529.CHP.gz
| | Sample_series_id | GSE7669
| | Sample_data_row_count | 12625
| | |
|
GSM185530 | GPL8300 |
|
fibroblasts_RA_patient108
|
Synovial fibroblasts, rheumatoid arthritis patient no 108.
|
female, 72 yrs, treatment with NSAIDs & steroids.
|
see publication for details
|
| Sample_geo_accession | GSM185530
| | Sample_status | Public on Aug 30 2007
| | Sample_submission_date | Apr 30 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Clinic of Orthopedics, FSU Jena, Waldkrankenhaus “Rudolf Elle”, Eisenberg, Germany
| | Sample_treatment_protocol_ch1 = Synovial tissue was obtained from open joint replacement surgery or arthroscopic synovectomy at the Clinic of Orthopedics, Waldkrankenhaus “Rudolf Elle” (Eisenberg, Germany). Patients with RA or OA (n | 6 each for gene expression analysis and further patients for validation experiments) were classified according to the ACR criteria.
| | Sample_growth_protocol_ch1 | The tissue samples were minced, digested with trypsin/collagenase P, and the resulting single cell suspension cultured for 7 days. Non-adherent cells were removed by medium exchange. SFB were then negatively purified using Dynabeads® M-450 CD14 and subsequently cultured over 2 passages in DMEM containing 100 μg/ml gentamycin, 100 μg/ml penicillin/streptomycin, 20 mM HEPES and 10% fetal calf serum (FCS, all from PAA Laboratories, Cölbe, Germany).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the end of the 2nd passage, the SFB were starved with medium containing 1% fetal calf serum (FCS) for 72 h, to minimize stimulating effects by serum components. After washing with PBS, the cells were lysed with RLT buffer (Qiagen, Hilden, Germany) and frozen at -70°C. Total RNA was isolated using the RNeasy Kit (Qiagen) according to the supplier’s recommendation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA probes were labeled according to the supplier’s instructions (Affymetrix, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips was performed according to the supplier’s instructions (http://www.affymetrix.com).
| | Sample_scan_protocol | Microarrays were analyzed by laser scanning (Hewlett-Packard Gene Scanner).
| | Sample_data_processing | Background-corrected signal intensities were determined using the MAS 5.0 software (Affymetrix).
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Andreas,,Beyer
| | Sample_contact_email | mail@a-beyer.de
| | Sample_contact_institute | BIOTEC
| | Sample_contact_address | Tatzberg. 47/49
| | Sample_contact_city | Dresden
| | Sample_contact_zip/postal_code | 01277
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185530/suppl/GSM185530.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185530/suppl/GSM185530.CHP.gz
| | Sample_series_id | GSE7669
| | Sample_data_row_count | 12625
| | |
|
GSM185531 | GPL8300 |
|
fibroblasts_OA_patient77
|
Synovial fibroblasts, osteoarthritis patient no. 77.
|
female, 66 yrs, no concurrent treatment.
|
see publication for details
|
| Sample_geo_accession | GSM185531
| | Sample_status | Public on Aug 30 2007
| | Sample_submission_date | Apr 30 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Clinic of Orthopedics, FSU Jena, Waldkrankenhaus “Rudolf Elle”, Eisenberg, Germany
| | Sample_treatment_protocol_ch1 = Synovial tissue was obtained from open joint replacement surgery or arthroscopic synovectomy at the Clinic of Orthopedics, Waldkrankenhaus “Rudolf Elle” (Eisenberg, Germany). Patients with RA or OA (n | 6 each for gene expression analysis and further patients for validation experiments) were classified according to the ACR criteria.
| | Sample_growth_protocol_ch1 | The tissue samples were minced, digested with trypsin/collagenase P, and the resulting single cell suspension cultured for 7 days. Non-adherent cells were removed by medium exchange. SFB were then negatively purified using Dynabeads® M-450 CD14 and subsequently cultured over 2 passages in DMEM containing 100 μg/ml gentamycin, 100 μg/ml penicillin/streptomycin, 20 mM HEPES and 10% fetal calf serum (FCS, all from PAA Laboratories, Cölbe, Germany).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the end of the 2nd passage, the SFB were starved with medium containing 1% fetal calf serum (FCS) for 72 h, to minimize stimulating effects by serum components. After washing with PBS, the cells were lysed with RLT buffer (Qiagen, Hilden, Germany) and frozen at -70°C. Total RNA was isolated using the RNeasy Kit (Qiagen) according to the supplier’s recommendation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA probes were labeled according to the supplier’s instructions (Affymetrix, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips was performed according to the supplier’s instructions (http://www.affymetrix.com).
| | Sample_scan_protocol | Microarrays were analyzed by laser scanning (Hewlett-Packard Gene Scanner).
| | Sample_data_processing | Background-corrected signal intensities were determined using the MAS 5.0 software (Affymetrix).
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Andreas,,Beyer
| | Sample_contact_email | mail@a-beyer.de
| | Sample_contact_institute | BIOTEC
| | Sample_contact_address | Tatzberg. 47/49
| | Sample_contact_city | Dresden
| | Sample_contact_zip/postal_code | 01277
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185531/suppl/GSM185531.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185531/suppl/GSM185531.CHP.gz
| | Sample_series_id | GSE7669
| | Sample_data_row_count | 12625
| | |
|
GSM185532 | GPL8300 |
|
fibroblasts_OA_patient81
|
Synovial fibroblasts, osteoarthritis patient no. 81.
|
female, 56 yrs, no concurrent treatment.
|
see publication for details
|
| Sample_geo_accession | GSM185532
| | Sample_status | Public on Aug 30 2007
| | Sample_submission_date | Apr 30 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Clinic of Orthopedics, FSU Jena, Waldkrankenhaus “Rudolf Elle”, Eisenberg, Germany
| | Sample_treatment_protocol_ch1 = Synovial tissue was obtained from open joint replacement surgery or arthroscopic synovectomy at the Clinic of Orthopedics, Waldkrankenhaus “Rudolf Elle” (Eisenberg, Germany). Patients with RA or OA (n | 6 each for gene expression analysis and further patients for validation experiments) were classified according to the ACR criteria.
| | Sample_growth_protocol_ch1 | The tissue samples were minced, digested with trypsin/collagenase P, and the resulting single cell suspension cultured for 7 days. Non-adherent cells were removed by medium exchange. SFB were then negatively purified using Dynabeads® M-450 CD14 and subsequently cultured over 2 passages in DMEM containing 100 μg/ml gentamycin, 100 μg/ml penicillin/streptomycin, 20 mM HEPES and 10% fetal calf serum (FCS, all from PAA Laboratories, Cölbe, Germany).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the end of the 2nd passage, the SFB were starved with medium containing 1% fetal calf serum (FCS) for 72 h, to minimize stimulating effects by serum components. After washing with PBS, the cells were lysed with RLT buffer (Qiagen, Hilden, Germany) and frozen at -70°C. Total RNA was isolated using the RNeasy Kit (Qiagen) according to the supplier’s recommendation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA probes were labeled according to the supplier’s instructions (Affymetrix, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips was performed according to the supplier’s instructions (http://www.affymetrix.com).
| | Sample_scan_protocol | Microarrays were analyzed by laser scanning (Hewlett-Packard Gene Scanner).
| | Sample_data_processing | Background-corrected signal intensities were determined using the MAS 5.0 software (Affymetrix).
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Andreas,,Beyer
| | Sample_contact_email | mail@a-beyer.de
| | Sample_contact_institute | BIOTEC
| | Sample_contact_address | Tatzberg. 47/49
| | Sample_contact_city | Dresden
| | Sample_contact_zip/postal_code | 01277
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185532/suppl/GSM185532.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185532/suppl/GSM185532.CHP.gz
| | Sample_series_id | GSE7669
| | Sample_data_row_count | 12625
| | |
|
GSM185533 | GPL8300 |
|
fibroblasts_OA_patient90
|
Synovial fibroblasts, osteoarthritis patient no. 90.
|
female, 61 yrs, no concurrent treatment.
|
see publication for details
|
| Sample_geo_accession | GSM185533
| | Sample_status | Public on Aug 30 2007
| | Sample_submission_date | Apr 30 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Clinic of Orthopedics, FSU Jena, Waldkrankenhaus “Rudolf Elle”, Eisenberg, Germany
| | Sample_treatment_protocol_ch1 = Synovial tissue was obtained from open joint replacement surgery or arthroscopic synovectomy at the Clinic of Orthopedics, Waldkrankenhaus “Rudolf Elle” (Eisenberg, Germany). Patients with RA or OA (n | 6 each for gene expression analysis and further patients for validation experiments) were classified according to the ACR criteria.
| | Sample_growth_protocol_ch1 | The tissue samples were minced, digested with trypsin/collagenase P, and the resulting single cell suspension cultured for 7 days. Non-adherent cells were removed by medium exchange. SFB were then negatively purified using Dynabeads® M-450 CD14 and subsequently cultured over 2 passages in DMEM containing 100 μg/ml gentamycin, 100 μg/ml penicillin/streptomycin, 20 mM HEPES and 10% fetal calf serum (FCS, all from PAA Laboratories, Cölbe, Germany).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the end of the 2nd passage, the SFB were starved with medium containing 1% fetal calf serum (FCS) for 72 h, to minimize stimulating effects by serum components. After washing with PBS, the cells were lysed with RLT buffer (Qiagen, Hilden, Germany) and frozen at -70°C. Total RNA was isolated using the RNeasy Kit (Qiagen) according to the supplier’s recommendation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA probes were labeled according to the supplier’s instructions (Affymetrix, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips was performed according to the supplier’s instructions (http://www.affymetrix.com).
| | Sample_scan_protocol | Microarrays were analyzed by laser scanning (Hewlett-Packard Gene Scanner).
| | Sample_data_processing | Background-corrected signal intensities were determined using the MAS 5.0 software (Affymetrix).
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Andreas,,Beyer
| | Sample_contact_email | mail@a-beyer.de
| | Sample_contact_institute | BIOTEC
| | Sample_contact_address | Tatzberg. 47/49
| | Sample_contact_city | Dresden
| | Sample_contact_zip/postal_code | 01277
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185533/suppl/GSM185533.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185533/suppl/GSM185533.CHP.gz
| | Sample_series_id | GSE7669
| | Sample_data_row_count | 12625
| | |
|
GSM185534 | GPL8300 |
|
fibroblasts_OA_patient102
|
Synovial fibroblasts, osteoarthritis patient no. 102.
|
female, 73 yrs, treatment with NSAIDs.
|
see publication for details
|
| Sample_geo_accession | GSM185534
| | Sample_status | Public on Aug 30 2007
| | Sample_submission_date | Apr 30 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Clinic of Orthopedics, FSU Jena, Waldkrankenhaus “Rudolf Elle”, Eisenberg, Germany
| | Sample_treatment_protocol_ch1 = Synovial tissue was obtained from open joint replacement surgery or arthroscopic synovectomy at the Clinic of Orthopedics, Waldkrankenhaus “Rudolf Elle” (Eisenberg, Germany). Patients with RA or OA (n | 6 each for gene expression analysis and further patients for validation experiments) were classified according to the ACR criteria.
| | Sample_growth_protocol_ch1 | The tissue samples were minced, digested with trypsin/collagenase P, and the resulting single cell suspension cultured for 7 days. Non-adherent cells were removed by medium exchange. SFB were then negatively purified using Dynabeads® M-450 CD14 and subsequently cultured over 2 passages in DMEM containing 100 μg/ml gentamycin, 100 μg/ml penicillin/streptomycin, 20 mM HEPES and 10% fetal calf serum (FCS, all from PAA Laboratories, Cölbe, Germany).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the end of the 2nd passage, the SFB were starved with medium containing 1% fetal calf serum (FCS) for 72 h, to minimize stimulating effects by serum components. After washing with PBS, the cells were lysed with RLT buffer (Qiagen, Hilden, Germany) and frozen at -70°C. Total RNA was isolated using the RNeasy Kit (Qiagen) according to the supplier’s recommendation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA probes were labeled according to the supplier’s instructions (Affymetrix, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips was performed according to the supplier’s instructions (http://www.affymetrix.com).
| | Sample_scan_protocol | Microarrays were analyzed by laser scanning (Hewlett-Packard Gene Scanner).
| | Sample_data_processing | Background-corrected signal intensities were determined using the MAS 5.0 software (Affymetrix).
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Andreas,,Beyer
| | Sample_contact_email | mail@a-beyer.de
| | Sample_contact_institute | BIOTEC
| | Sample_contact_address | Tatzberg. 47/49
| | Sample_contact_city | Dresden
| | Sample_contact_zip/postal_code | 01277
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185534/suppl/GSM185534.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185534/suppl/GSM185534.CHP.gz
| | Sample_series_id | GSE7669
| | Sample_data_row_count | 12625
| | |
|
GSM185535 | GPL8300 |
|
fibroblasts_OA_patient115
|
Synovial fibroblasts, osteoarthritis patient no. 115.
|
female, 56 yrs, treatment with NSAIDs.
|
see publication for details
|
| Sample_geo_accession | GSM185535
| | Sample_status | Public on Aug 30 2007
| | Sample_submission_date | Apr 30 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Clinic of Orthopedics, FSU Jena, Waldkrankenhaus “Rudolf Elle”, Eisenberg, Germany
| | Sample_treatment_protocol_ch1 = Synovial tissue was obtained from open joint replacement surgery or arthroscopic synovectomy at the Clinic of Orthopedics, Waldkrankenhaus “Rudolf Elle” (Eisenberg, Germany). Patients with RA or OA (n | 6 each for gene expression analysis and further patients for validation experiments) were classified according to the ACR criteria.
| | Sample_growth_protocol_ch1 | The tissue samples were minced, digested with trypsin/collagenase P, and the resulting single cell suspension cultured for 7 days. Non-adherent cells were removed by medium exchange. SFB were then negatively purified using Dynabeads® M-450 CD14 and subsequently cultured over 2 passages in DMEM containing 100 μg/ml gentamycin, 100 μg/ml penicillin/streptomycin, 20 mM HEPES and 10% fetal calf serum (FCS, all from PAA Laboratories, Cölbe, Germany).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the end of the 2nd passage, the SFB were starved with medium containing 1% fetal calf serum (FCS) for 72 h, to minimize stimulating effects by serum components. After washing with PBS, the cells were lysed with RLT buffer (Qiagen, Hilden, Germany) and frozen at -70°C. Total RNA was isolated using the RNeasy Kit (Qiagen) according to the supplier’s recommendation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA probes were labeled according to the supplier’s instructions (Affymetrix, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips was performed according to the supplier’s instructions (http://www.affymetrix.com).
| | Sample_scan_protocol | Microarrays were analyzed by laser scanning (Hewlett-Packard Gene Scanner).
| | Sample_data_processing | Background-corrected signal intensities were determined using the MAS 5.0 software (Affymetrix).
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Andreas,,Beyer
| | Sample_contact_email | mail@a-beyer.de
| | Sample_contact_institute | BIOTEC
| | Sample_contact_address | Tatzberg. 47/49
| | Sample_contact_city | Dresden
| | Sample_contact_zip/postal_code | 01277
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185535/suppl/GSM185535.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185535/suppl/GSM185535.CHP.gz
| | Sample_series_id | GSE7669
| | Sample_data_row_count | 12625
| | |
|
GSM185536 | GPL8300 |
|
fibroblasts_OA_patient118
|
Synovial fibroblasts, osteoarthritis patient no. 118.
|
male, 72 yrs, treatment with NSAIDs.
|
see publication for details
|
| Sample_geo_accession | GSM185536
| | Sample_status | Public on Aug 30 2007
| | Sample_submission_date | Apr 30 2007
| | Sample_last_update_date | Mar 16 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Clinic of Orthopedics, FSU Jena, Waldkrankenhaus “Rudolf Elle”, Eisenberg, Germany
| | Sample_treatment_protocol_ch1 = Synovial tissue was obtained from open joint replacement surgery or arthroscopic synovectomy at the Clinic of Orthopedics, Waldkrankenhaus “Rudolf Elle” (Eisenberg, Germany). Patients with RA or OA (n | 6 each for gene expression analysis and further patients for validation experiments) were classified according to the ACR criteria.
| | Sample_growth_protocol_ch1 | The tissue samples were minced, digested with trypsin/collagenase P, and the resulting single cell suspension cultured for 7 days. Non-adherent cells were removed by medium exchange. SFB were then negatively purified using Dynabeads® M-450 CD14 and subsequently cultured over 2 passages in DMEM containing 100 μg/ml gentamycin, 100 μg/ml penicillin/streptomycin, 20 mM HEPES and 10% fetal calf serum (FCS, all from PAA Laboratories, Cölbe, Germany).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | At the end of the 2nd passage, the SFB were starved with medium containing 1% fetal calf serum (FCS) for 72 h, to minimize stimulating effects by serum components. After washing with PBS, the cells were lysed with RLT buffer (Qiagen, Hilden, Germany) and frozen at -70°C. Total RNA was isolated using the RNeasy Kit (Qiagen) according to the supplier’s recommendation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA probes were labeled according to the supplier’s instructions (Affymetrix, Santa Clara, CA, USA).
| | Sample_hyb_protocol | Hybridization and washing of gene chips was performed according to the supplier’s instructions (http://www.affymetrix.com).
| | Sample_scan_protocol | Microarrays were analyzed by laser scanning (Hewlett-Packard Gene Scanner).
| | Sample_data_processing | Background-corrected signal intensities were determined using the MAS 5.0 software (Affymetrix).
| | Sample_platform_id | GPL8300
| | Sample_contact_name | Andreas,,Beyer
| | Sample_contact_email | mail@a-beyer.de
| | Sample_contact_institute | BIOTEC
| | Sample_contact_address | Tatzberg. 47/49
| | Sample_contact_city | Dresden
| | Sample_contact_zip/postal_code | 01277
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185536/suppl/GSM185536.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM185nnn/GSM185536/suppl/GSM185536.CHP.gz
| | Sample_series_id | GSE7669
| | Sample_data_row_count | 12625
| | |
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