Search results for the GEO ID: GSE15602  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM390153 | GPL570 |
|
RA Synovial biopsy T12 post-adalimumab therapy, Moderate Responder 1
|
Synovial biopsy, RA patient, 12 weeks after adalimumab therapy, moderate responder
|
tissue: synovial tissue from knee
disease: rheumatoid arthritis
|
Patient has rheumatoid arthritis (RA), according to the American College of rheumatology criteria for the diagnosis of RA. All patients included in this study had active disease at the time of initiation of adalimumab therapy and were resistant to conventional therapy. They all had erosive changes imaged on conventional x-rays of the hands and/or feet. All patients were treated with disease-modifying antirheumatic drugs (DMARD’s), 23 with methotrexate (median dose 15 mg/week, range 7.5 – 20 mg/week), and 2 with leflunomide (20 mg/day); 18 of them were treated with low-dose steroids (prednisolone ≤ 7.5 mg/day). Six patients had been included in double-blind clinical trials before inclusion in the present study (1 in a Golimumab versus placebo trial, 3 in a MapKinase inhibitor versus placebo trial and 2 in a TACE-inhibitor versus placebo trial). These trials were stopped at least 3 months prior to initiation of TNF-blocking therapy. All drug dosages were stable from at least 3 months prior to initiation of TNF blocking therapy until completion of the study. No steroid injections were allowed during the duration of the study.
|
| Sample_geo_accession | GSM390153
| | Sample_status | Public on Apr 15 2009
| | Sample_submission_date | Apr 08 2009
| | Sample_last_update_date | Apr 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Adalimumab therapy was initiated at a dosage of 40 mg subcutaneously every other week. Disease activity at baseline and 12 weeks after initiation of therapy (T12) was evaluated using DAS(28)-CRP (3- and 4-variables) scores, and response to therapy was assessed according to the EULAR response criteria that categorize patients in responders (good- or moderate-) and non- (or poor-) responders based on changes in DAS activity between T0 and T12 and absolute DAS values at T12.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | Synovial biopsies were obtained by needle-arthroscopy of knee of the patients at T12. For each procedure, 4 to 8 synovial samples were snap-frozen in liquid nitrogen and stored at –80°C for later RNA extraction. The same amount of tissue was kept at -80°C for immunostaining experiments on frozen sections. The remaining material was fixed in 10% formalin and paraffin embedded for conventional optical evaluation and immunostaining of selected markers. All the experiments (RNA extraction, histology, immunohistochemistry) were performed on at least 4 biopsies harvested during every procedure in order to correct for variations related to the potential heterogeneous distribution of synovial inflammation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from the synovial biopsies using the Nucleospin® RNA II extraction kit (Macherey-Nagel), including DNase treatment of the samples. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent Technologies Inc). All samples had a 28s/18s ratio > 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling of RNA (cRNA synthesis) was performed according to a standard Affymetrix® procedure (One-Cycle Target Labeling kit, Affymetrix UK Ltd., High Wycombe, UK); briefly total RNA was first reverse transcribed into single-stranded cDNA using a T7-Oligo(dT) Promoter Primer and Superscript II reverse transcriptase. Next, RNase H was added together with E. Coli DNA polymerase I and E. Coli DNA ligase, followed by a short incubation with T4 DNA polymerase in order to achieve synthesis of the second-strand cDNA. The purified double-stranded cDNA served as the template for the in vitro transcription reaction, which was carried out overnight in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. At the end of this procedure, the biotinylated complementary RNA (cRNA) was cleaned, and fragmented by a 35-minute incubation at 95°c.
| | Sample_hyb_protocol | GeneChip® Human genome U133 Plus 2.0 Arrays (spotted with 1,300,000 oligonucleotides informative for 47,000 transcripts originated from 39,000 genes, Affymetrix UK Ltd, High Wycombe, UK) were hybridized overnight at 45°c in monoplicates with 10 μg cRNA. The slides were then washed and stained using the EukGE-WS2v5 Fluidics protocol on the Genechip® Fluidics Station (Affymetrix) before being scanned on a Genechip® Scanner 3000.
| | Sample_scan_protocol | The slides were scanned on a Genechip® Scanner 3000.
| | Sample_data_processing | For the initial normalization and analysis steps, data were retrieved on Affymetrix GCOS software. The frequency of positive genes (genes with a flag present) was between 45 and 55% on each slide. After scaling of all probe sets to a value of 100, the amplification scale was reported inferior to 3.0 for all slides. The signals yielded by the poly-A RNA, hybridization and housekeeping controls (GAPDH 3’/5’ ratio < 2) were indicative of the good quality of the amplification and hybridization procedures.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernard,Robert,Lauwerys
| | Sample_contact_email | Bernard.Lauwerys@ruma.ucl.ac.be
| | Sample_contact_phone | +32.2.764.53.91
| | Sample_contact_fax | +32.2.764.53.74
| | Sample_contact_laboratory | Rheumatology Unit
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Université catholique de Louvain
| | Sample_contact_address | Avenue Hippocrate 10
| | Sample_contact_city | Brussels
| | Sample_contact_zip/postal_code | 1200
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM390nnn/GSM390153/suppl/GSM390153.CEL.gz
| | Sample_series_id | GSE15602
| | Sample_data_row_count | 54675
| | |
|
GSM390154 | GPL570 |
|
RA Synovial biopsy T12 post-adalimumab therapy, Moderate Responder 2
|
Synovial biopsy, RA patient, 12 weeks after adalimumab therapy, moderate responder
|
tissue: synovial tissue from knee
disease: rheumatoid arthritis
|
Patient has rheumatoid arthritis (RA), according to the American College of rheumatology criteria for the diagnosis of RA. All patients included in this study had active disease at the time of initiation of adalimumab therapy and were resistant to conventional therapy. They all had erosive changes imaged on conventional x-rays of the hands and/or feet. All patients were treated with disease-modifying antirheumatic drugs (DMARD’s), 23 with methotrexate (median dose 15 mg/week, range 7.5 – 20 mg/week), and 2 with leflunomide (20 mg/day); 18 of them were treated with low-dose steroids (prednisolone ≤ 7.5 mg/day). Six patients had been included in double-blind clinical trials before inclusion in the present study (1 in a Golimumab versus placebo trial, 3 in a MapKinase inhibitor versus placebo trial and 2 in a TACE-inhibitor versus placebo trial). These trials were stopped at least 3 months prior to initiation of TNF-blocking therapy. All drug dosages were stable from at least 3 months prior to initiation of TNF blocking therapy until completion of the study. No steroid injections were allowed during the duration of the study.
|
| Sample_geo_accession | GSM390154
| | Sample_status | Public on Apr 15 2009
| | Sample_submission_date | Apr 08 2009
| | Sample_last_update_date | Apr 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Adalimumab therapy was initiated at a dosage of 40 mg subcutaneously every other week. Disease activity at baseline and 12 weeks after initiation of therapy (T12) was evaluated using DAS(28)-CRP (3- and 4-variables) scores, and response to therapy was assessed according to the EULAR response criteria that categorize patients in responders (good- or moderate-) and non- (or poor-) responders based on changes in DAS activity between T0 and T12 and absolute DAS values at T12.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | Synovial biopsies were obtained by needle-arthroscopy of knee of the patients at T12. For each procedure, 4 to 8 synovial samples were snap-frozen in liquid nitrogen and stored at –80°C for later RNA extraction. The same amount of tissue was kept at -80°C for immunostaining experiments on frozen sections. The remaining material was fixed in 10% formalin and paraffin embedded for conventional optical evaluation and immunostaining of selected markers. All the experiments (RNA extraction, histology, immunohistochemistry) were performed on at least 4 biopsies harvested during every procedure in order to correct for variations related to the potential heterogeneous distribution of synovial inflammation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from the synovial biopsies using the Nucleospin® RNA II extraction kit (Macherey-Nagel), including DNase treatment of the samples. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent Technologies Inc). All samples had a 28s/18s ratio > 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling of RNA (cRNA synthesis) was performed according to a standard Affymetrix® procedure (One-Cycle Target Labeling kit, Affymetrix UK Ltd., High Wycombe, UK); briefly total RNA was first reverse transcribed into single-stranded cDNA using a T7-Oligo(dT) Promoter Primer and Superscript II reverse transcriptase. Next, RNase H was added together with E. Coli DNA polymerase I and E. Coli DNA ligase, followed by a short incubation with T4 DNA polymerase in order to achieve synthesis of the second-strand cDNA. The purified double-stranded cDNA served as the template for the in vitro transcription reaction, which was carried out overnight in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. At the end of this procedure, the biotinylated complementary RNA (cRNA) was cleaned, and fragmented by a 35-minute incubation at 95°c.
| | Sample_hyb_protocol | GeneChip® Human genome U133 Plus 2.0 Arrays (spotted with 1,300,000 oligonucleotides informative for 47,000 transcripts originated from 39,000 genes, Affymetrix UK Ltd, High Wycombe, UK) were hybridized overnight at 45°c in monoplicates with 10 μg cRNA. The slides were then washed and stained using the EukGE-WS2v5 Fluidics protocol on the Genechip® Fluidics Station (Affymetrix) before being scanned on a Genechip® Scanner 3000.
| | Sample_scan_protocol | The slides were scanned on a Genechip® Scanner 3000.
| | Sample_data_processing | For the initial normalization and analysis steps, data were retrieved on Affymetrix GCOS software. The frequency of positive genes (genes with a flag present) was between 45 and 55% on each slide. After scaling of all probe sets to a value of 100, the amplification scale was reported inferior to 3.0 for all slides. The signals yielded by the poly-A RNA, hybridization and housekeeping controls (GAPDH 3’/5’ ratio < 2) were indicative of the good quality of the amplification and hybridization procedures.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernard,Robert,Lauwerys
| | Sample_contact_email | Bernard.Lauwerys@ruma.ucl.ac.be
| | Sample_contact_phone | +32.2.764.53.91
| | Sample_contact_fax | +32.2.764.53.74
| | Sample_contact_laboratory | Rheumatology Unit
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Université catholique de Louvain
| | Sample_contact_address | Avenue Hippocrate 10
| | Sample_contact_city | Brussels
| | Sample_contact_zip/postal_code | 1200
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM390nnn/GSM390154/suppl/GSM390154.CEL.gz
| | Sample_series_id | GSE15602
| | Sample_data_row_count | 54675
| | |
|
GSM390155 | GPL570 |
|
RA Synovial biopsy T12 post-adalimumab therapy, Moderate Responder 3
|
Synovial biopsy, RA patient, 12 weeks after adalimumab therapy, moderate responder
|
tissue: synovial tissue from knee
disease: rheumatoid arthritis
|
Patient has rheumatoid arthritis (RA), according to the American College of rheumatology criteria for the diagnosis of RA. All patients included in this study had active disease at the time of initiation of adalimumab therapy and were resistant to conventional therapy. They all had erosive changes imaged on conventional x-rays of the hands and/or feet. All patients were treated with disease-modifying antirheumatic drugs (DMARD’s), 23 with methotrexate (median dose 15 mg/week, range 7.5 – 20 mg/week), and 2 with leflunomide (20 mg/day); 18 of them were treated with low-dose steroids (prednisolone ≤ 7.5 mg/day). Six patients had been included in double-blind clinical trials before inclusion in the present study (1 in a Golimumab versus placebo trial, 3 in a MapKinase inhibitor versus placebo trial and 2 in a TACE-inhibitor versus placebo trial). These trials were stopped at least 3 months prior to initiation of TNF-blocking therapy. All drug dosages were stable from at least 3 months prior to initiation of TNF blocking therapy until completion of the study. No steroid injections were allowed during the duration of the study.
|
| Sample_geo_accession | GSM390155
| | Sample_status | Public on Apr 15 2009
| | Sample_submission_date | Apr 08 2009
| | Sample_last_update_date | Apr 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Adalimumab therapy was initiated at a dosage of 40 mg subcutaneously every other week. Disease activity at baseline and 12 weeks after initiation of therapy (T12) was evaluated using DAS(28)-CRP (3- and 4-variables) scores, and response to therapy was assessed according to the EULAR response criteria that categorize patients in responders (good- or moderate-) and non- (or poor-) responders based on changes in DAS activity between T0 and T12 and absolute DAS values at T12.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | Synovial biopsies were obtained by needle-arthroscopy of knee of the patients at T12. For each procedure, 4 to 8 synovial samples were snap-frozen in liquid nitrogen and stored at –80°C for later RNA extraction. The same amount of tissue was kept at -80°C for immunostaining experiments on frozen sections. The remaining material was fixed in 10% formalin and paraffin embedded for conventional optical evaluation and immunostaining of selected markers. All the experiments (RNA extraction, histology, immunohistochemistry) were performed on at least 4 biopsies harvested during every procedure in order to correct for variations related to the potential heterogeneous distribution of synovial inflammation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from the synovial biopsies using the Nucleospin® RNA II extraction kit (Macherey-Nagel), including DNase treatment of the samples. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent Technologies Inc). All samples had a 28s/18s ratio > 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling of RNA (cRNA synthesis) was performed according to a standard Affymetrix® procedure (One-Cycle Target Labeling kit, Affymetrix UK Ltd., High Wycombe, UK); briefly total RNA was first reverse transcribed into single-stranded cDNA using a T7-Oligo(dT) Promoter Primer and Superscript II reverse transcriptase. Next, RNase H was added together with E. Coli DNA polymerase I and E. Coli DNA ligase, followed by a short incubation with T4 DNA polymerase in order to achieve synthesis of the second-strand cDNA. The purified double-stranded cDNA served as the template for the in vitro transcription reaction, which was carried out overnight in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. At the end of this procedure, the biotinylated complementary RNA (cRNA) was cleaned, and fragmented by a 35-minute incubation at 95°c.
| | Sample_hyb_protocol | GeneChip® Human genome U133 Plus 2.0 Arrays (spotted with 1,300,000 oligonucleotides informative for 47,000 transcripts originated from 39,000 genes, Affymetrix UK Ltd, High Wycombe, UK) were hybridized overnight at 45°c in monoplicates with 10 μg cRNA. The slides were then washed and stained using the EukGE-WS2v5 Fluidics protocol on the Genechip® Fluidics Station (Affymetrix) before being scanned on a Genechip® Scanner 3000.
| | Sample_scan_protocol | The slides were scanned on a Genechip® Scanner 3000.
| | Sample_data_processing | For the initial normalization and analysis steps, data were retrieved on Affymetrix GCOS software. The frequency of positive genes (genes with a flag present) was between 45 and 55% on each slide. After scaling of all probe sets to a value of 100, the amplification scale was reported inferior to 3.0 for all slides. The signals yielded by the poly-A RNA, hybridization and housekeeping controls (GAPDH 3’/5’ ratio < 2) were indicative of the good quality of the amplification and hybridization procedures.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernard,Robert,Lauwerys
| | Sample_contact_email | Bernard.Lauwerys@ruma.ucl.ac.be
| | Sample_contact_phone | +32.2.764.53.91
| | Sample_contact_fax | +32.2.764.53.74
| | Sample_contact_laboratory | Rheumatology Unit
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Université catholique de Louvain
| | Sample_contact_address | Avenue Hippocrate 10
| | Sample_contact_city | Brussels
| | Sample_contact_zip/postal_code | 1200
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM390nnn/GSM390155/suppl/GSM390155.CEL.gz
| | Sample_series_id | GSE15602
| | Sample_data_row_count | 54675
| | |
|
GSM390156 | GPL570 |
|
RA Synovial biopsy T12 post-adalimumab therapy, Moderate Responder 4
|
Synovial biopsy, RA patient, 12 weeks after adalimumab therapy, moderate responder
|
tissue: synovial tissue from knee
disease: rheumatoid arthritis
|
Patient has rheumatoid arthritis (RA), according to the American College of rheumatology criteria for the diagnosis of RA. All patients included in this study had active disease at the time of initiation of adalimumab therapy and were resistant to conventional therapy. They all had erosive changes imaged on conventional x-rays of the hands and/or feet. All patients were treated with disease-modifying antirheumatic drugs (DMARD’s), 23 with methotrexate (median dose 15 mg/week, range 7.5 – 20 mg/week), and 2 with leflunomide (20 mg/day); 18 of them were treated with low-dose steroids (prednisolone ≤ 7.5 mg/day). Six patients had been included in double-blind clinical trials before inclusion in the present study (1 in a Golimumab versus placebo trial, 3 in a MapKinase inhibitor versus placebo trial and 2 in a TACE-inhibitor versus placebo trial). These trials were stopped at least 3 months prior to initiation of TNF-blocking therapy. All drug dosages were stable from at least 3 months prior to initiation of TNF blocking therapy until completion of the study. No steroid injections were allowed during the duration of the study.
|
| Sample_geo_accession | GSM390156
| | Sample_status | Public on Apr 15 2009
| | Sample_submission_date | Apr 08 2009
| | Sample_last_update_date | Apr 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Adalimumab therapy was initiated at a dosage of 40 mg subcutaneously every other week. Disease activity at baseline and 12 weeks after initiation of therapy (T12) was evaluated using DAS(28)-CRP (3- and 4-variables) scores, and response to therapy was assessed according to the EULAR response criteria that categorize patients in responders (good- or moderate-) and non- (or poor-) responders based on changes in DAS activity between T0 and T12 and absolute DAS values at T12.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | Synovial biopsies were obtained by needle-arthroscopy of knee of the patients at T12. For each procedure, 4 to 8 synovial samples were snap-frozen in liquid nitrogen and stored at –80°C for later RNA extraction. The same amount of tissue was kept at -80°C for immunostaining experiments on frozen sections. The remaining material was fixed in 10% formalin and paraffin embedded for conventional optical evaluation and immunostaining of selected markers. All the experiments (RNA extraction, histology, immunohistochemistry) were performed on at least 4 biopsies harvested during every procedure in order to correct for variations related to the potential heterogeneous distribution of synovial inflammation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from the synovial biopsies using the Nucleospin® RNA II extraction kit (Macherey-Nagel), including DNase treatment of the samples. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent Technologies Inc). All samples had a 28s/18s ratio > 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling of RNA (cRNA synthesis) was performed according to a standard Affymetrix® procedure (One-Cycle Target Labeling kit, Affymetrix UK Ltd., High Wycombe, UK); briefly total RNA was first reverse transcribed into single-stranded cDNA using a T7-Oligo(dT) Promoter Primer and Superscript II reverse transcriptase. Next, RNase H was added together with E. Coli DNA polymerase I and E. Coli DNA ligase, followed by a short incubation with T4 DNA polymerase in order to achieve synthesis of the second-strand cDNA. The purified double-stranded cDNA served as the template for the in vitro transcription reaction, which was carried out overnight in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. At the end of this procedure, the biotinylated complementary RNA (cRNA) was cleaned, and fragmented by a 35-minute incubation at 95°c.
| | Sample_hyb_protocol | GeneChip® Human genome U133 Plus 2.0 Arrays (spotted with 1,300,000 oligonucleotides informative for 47,000 transcripts originated from 39,000 genes, Affymetrix UK Ltd, High Wycombe, UK) were hybridized overnight at 45°c in monoplicates with 10 μg cRNA. The slides were then washed and stained using the EukGE-WS2v5 Fluidics protocol on the Genechip® Fluidics Station (Affymetrix) before being scanned on a Genechip® Scanner 3000.
| | Sample_scan_protocol | The slides were scanned on a Genechip® Scanner 3000.
| | Sample_data_processing | For the initial normalization and analysis steps, data were retrieved on Affymetrix GCOS software. The frequency of positive genes (genes with a flag present) was between 45 and 55% on each slide. After scaling of all probe sets to a value of 100, the amplification scale was reported inferior to 3.0 for all slides. The signals yielded by the poly-A RNA, hybridization and housekeeping controls (GAPDH 3’/5’ ratio < 2) were indicative of the good quality of the amplification and hybridization procedures.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernard,Robert,Lauwerys
| | Sample_contact_email | Bernard.Lauwerys@ruma.ucl.ac.be
| | Sample_contact_phone | +32.2.764.53.91
| | Sample_contact_fax | +32.2.764.53.74
| | Sample_contact_laboratory | Rheumatology Unit
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Université catholique de Louvain
| | Sample_contact_address | Avenue Hippocrate 10
| | Sample_contact_city | Brussels
| | Sample_contact_zip/postal_code | 1200
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM390nnn/GSM390156/suppl/GSM390156.CEL.gz
| | Sample_series_id | GSE15602
| | Sample_data_row_count | 54675
| | |
|
GSM390157 | GPL570 |
|
RA Synovial biopsy T12 post-adalimumab therapy, Moderate Responder 5
|
Synovial biopsy, RA patient, 12 weeks after adalimumab therapy, moderate responder
|
tissue: synovial tissue from knee
disease: rheumatoid arthritis
|
Patient has rheumatoid arthritis (RA), according to the American College of rheumatology criteria for the diagnosis of RA. All patients included in this study had active disease at the time of initiation of adalimumab therapy and were resistant to conventional therapy. They all had erosive changes imaged on conventional x-rays of the hands and/or feet. All patients were treated with disease-modifying antirheumatic drugs (DMARD’s), 23 with methotrexate (median dose 15 mg/week, range 7.5 – 20 mg/week), and 2 with leflunomide (20 mg/day); 18 of them were treated with low-dose steroids (prednisolone ≤ 7.5 mg/day). Six patients had been included in double-blind clinical trials before inclusion in the present study (1 in a Golimumab versus placebo trial, 3 in a MapKinase inhibitor versus placebo trial and 2 in a TACE-inhibitor versus placebo trial). These trials were stopped at least 3 months prior to initiation of TNF-blocking therapy. All drug dosages were stable from at least 3 months prior to initiation of TNF blocking therapy until completion of the study. No steroid injections were allowed during the duration of the study.
|
| Sample_geo_accession | GSM390157
| | Sample_status | Public on Apr 15 2009
| | Sample_submission_date | Apr 08 2009
| | Sample_last_update_date | Apr 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Adalimumab therapy was initiated at a dosage of 40 mg subcutaneously every other week. Disease activity at baseline and 12 weeks after initiation of therapy (T12) was evaluated using DAS(28)-CRP (3- and 4-variables) scores, and response to therapy was assessed according to the EULAR response criteria that categorize patients in responders (good- or moderate-) and non- (or poor-) responders based on changes in DAS activity between T0 and T12 and absolute DAS values at T12.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | Synovial biopsies were obtained by needle-arthroscopy of knee of the patients at T12. For each procedure, 4 to 8 synovial samples were snap-frozen in liquid nitrogen and stored at –80°C for later RNA extraction. The same amount of tissue was kept at -80°C for immunostaining experiments on frozen sections. The remaining material was fixed in 10% formalin and paraffin embedded for conventional optical evaluation and immunostaining of selected markers. All the experiments (RNA extraction, histology, immunohistochemistry) were performed on at least 4 biopsies harvested during every procedure in order to correct for variations related to the potential heterogeneous distribution of synovial inflammation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from the synovial biopsies using the Nucleospin® RNA II extraction kit (Macherey-Nagel), including DNase treatment of the samples. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent Technologies Inc). All samples had a 28s/18s ratio > 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling of RNA (cRNA synthesis) was performed according to a standard Affymetrix® procedure (One-Cycle Target Labeling kit, Affymetrix UK Ltd., High Wycombe, UK); briefly total RNA was first reverse transcribed into single-stranded cDNA using a T7-Oligo(dT) Promoter Primer and Superscript II reverse transcriptase. Next, RNase H was added together with E. Coli DNA polymerase I and E. Coli DNA ligase, followed by a short incubation with T4 DNA polymerase in order to achieve synthesis of the second-strand cDNA. The purified double-stranded cDNA served as the template for the in vitro transcription reaction, which was carried out overnight in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. At the end of this procedure, the biotinylated complementary RNA (cRNA) was cleaned, and fragmented by a 35-minute incubation at 95°c.
| | Sample_hyb_protocol | GeneChip® Human genome U133 Plus 2.0 Arrays (spotted with 1,300,000 oligonucleotides informative for 47,000 transcripts originated from 39,000 genes, Affymetrix UK Ltd, High Wycombe, UK) were hybridized overnight at 45°c in monoplicates with 10 μg cRNA. The slides were then washed and stained using the EukGE-WS2v5 Fluidics protocol on the Genechip® Fluidics Station (Affymetrix) before being scanned on a Genechip® Scanner 3000.
| | Sample_scan_protocol | The slides were scanned on a Genechip® Scanner 3000.
| | Sample_data_processing | For the initial normalization and analysis steps, data were retrieved on Affymetrix GCOS software. The frequency of positive genes (genes with a flag present) was between 45 and 55% on each slide. After scaling of all probe sets to a value of 100, the amplification scale was reported inferior to 3.0 for all slides. The signals yielded by the poly-A RNA, hybridization and housekeeping controls (GAPDH 3’/5’ ratio < 2) were indicative of the good quality of the amplification and hybridization procedures.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernard,Robert,Lauwerys
| | Sample_contact_email | Bernard.Lauwerys@ruma.ucl.ac.be
| | Sample_contact_phone | +32.2.764.53.91
| | Sample_contact_fax | +32.2.764.53.74
| | Sample_contact_laboratory | Rheumatology Unit
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Université catholique de Louvain
| | Sample_contact_address | Avenue Hippocrate 10
| | Sample_contact_city | Brussels
| | Sample_contact_zip/postal_code | 1200
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM390nnn/GSM390157/suppl/GSM390157.CEL.gz
| | Sample_series_id | GSE15602
| | Sample_data_row_count | 54675
| | |
|
GSM390158 | GPL570 |
|
RA Synovial biopsy T12 post-adalimumab therapy, Good Responder 1
|
Synovial biopsy, RA patient, 12 weeks after adalimumab therapy, good responder
|
tissue: synovial tissue from knee
disease: rheumatoid arthritis
|
Patient has rheumatoid arthritis (RA), according to the American College of rheumatology criteria for the diagnosis of RA. All patients included in this study had active disease at the time of initiation of adalimumab therapy and were resistant to conventional therapy. They all had erosive changes imaged on conventional x-rays of the hands and/or feet. All patients were treated with disease-modifying antirheumatic drugs (DMARD’s), 23 with methotrexate (median dose 15 mg/week, range 7.5 – 20 mg/week), and 2 with leflunomide (20 mg/day); 18 of them were treated with low-dose steroids (prednisolone ≤ 7.5 mg/day). Six patients had been included in double-blind clinical trials before inclusion in the present study (1 in a Golimumab versus placebo trial, 3 in a MapKinase inhibitor versus placebo trial and 2 in a TACE-inhibitor versus placebo trial). These trials were stopped at least 3 months prior to initiation of TNF-blocking therapy. All drug dosages were stable from at least 3 months prior to initiation of TNF blocking therapy until completion of the study. No steroid injections were allowed during the duration of the study.
|
| Sample_geo_accession | GSM390158
| | Sample_status | Public on Apr 15 2009
| | Sample_submission_date | Apr 08 2009
| | Sample_last_update_date | Apr 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Adalimumab therapy was initiated at a dosage of 40 mg subcutaneously every other week. Disease activity at baseline and 12 weeks after initiation of therapy (T12) was evaluated using DAS(28)-CRP (3- and 4-variables) scores, and response to therapy was assessed according to the EULAR response criteria that categorize patients in responders (good- or moderate-) and non- (or poor-) responders based on changes in DAS activity between T0 and T12 and absolute DAS values at T12.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | Synovial biopsies were obtained by needle-arthroscopy of knee of the patients at T12. For each procedure, 4 to 8 synovial samples were snap-frozen in liquid nitrogen and stored at –80°C for later RNA extraction. The same amount of tissue was kept at -80°C for immunostaining experiments on frozen sections. The remaining material was fixed in 10% formalin and paraffin embedded for conventional optical evaluation and immunostaining of selected markers. All the experiments (RNA extraction, histology, immunohistochemistry) were performed on at least 4 biopsies harvested during every procedure in order to correct for variations related to the potential heterogeneous distribution of synovial inflammation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from the synovial biopsies using the Nucleospin® RNA II extraction kit (Macherey-Nagel), including DNase treatment of the samples. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent Technologies Inc). All samples had a 28s/18s ratio > 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling of RNA (cRNA synthesis) was performed according to a standard Affymetrix® procedure (One-Cycle Target Labeling kit, Affymetrix UK Ltd., High Wycombe, UK); briefly total RNA was first reverse transcribed into single-stranded cDNA using a T7-Oligo(dT) Promoter Primer and Superscript II reverse transcriptase. Next, RNase H was added together with E. Coli DNA polymerase I and E. Coli DNA ligase, followed by a short incubation with T4 DNA polymerase in order to achieve synthesis of the second-strand cDNA. The purified double-stranded cDNA served as the template for the in vitro transcription reaction, which was carried out overnight in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. At the end of this procedure, the biotinylated complementary RNA (cRNA) was cleaned, and fragmented by a 35-minute incubation at 95°c.
| | Sample_hyb_protocol | GeneChip® Human genome U133 Plus 2.0 Arrays (spotted with 1,300,000 oligonucleotides informative for 47,000 transcripts originated from 39,000 genes, Affymetrix UK Ltd, High Wycombe, UK) were hybridized overnight at 45°c in monoplicates with 10 μg cRNA. The slides were then washed and stained using the EukGE-WS2v5 Fluidics protocol on the Genechip® Fluidics Station (Affymetrix) before being scanned on a Genechip® Scanner 3000.
| | Sample_scan_protocol | The slides were scanned on a Genechip® Scanner 3000.
| | Sample_data_processing | For the initial normalization and analysis steps, data were retrieved on Affymetrix GCOS software. The frequency of positive genes (genes with a flag present) was between 45 and 55% on each slide. After scaling of all probe sets to a value of 100, the amplification scale was reported inferior to 3.0 for all slides. The signals yielded by the poly-A RNA, hybridization and housekeeping controls (GAPDH 3’/5’ ratio < 2) were indicative of the good quality of the amplification and hybridization procedures.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernard,Robert,Lauwerys
| | Sample_contact_email | Bernard.Lauwerys@ruma.ucl.ac.be
| | Sample_contact_phone | +32.2.764.53.91
| | Sample_contact_fax | +32.2.764.53.74
| | Sample_contact_laboratory | Rheumatology Unit
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Université catholique de Louvain
| | Sample_contact_address | Avenue Hippocrate 10
| | Sample_contact_city | Brussels
| | Sample_contact_zip/postal_code | 1200
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM390nnn/GSM390158/suppl/GSM390158.CEL.gz
| | Sample_series_id | GSE15602
| | Sample_data_row_count | 54675
| | |
|
GSM390159 | GPL570 |
|
RA Synovial biopsy T12 post-adalimumab therapy, Good Responder 2
|
Synovial biopsy, RA patient, 12 weeks after adalimumab therapy, good responder
|
tissue: synovial tissue from knee
disease: rheumatoid arthritis
|
Patient has rheumatoid arthritis (RA), according to the American College of rheumatology criteria for the diagnosis of RA. All patients included in this study had active disease at the time of initiation of adalimumab therapy and were resistant to conventional therapy. They all had erosive changes imaged on conventional x-rays of the hands and/or feet. All patients were treated with disease-modifying antirheumatic drugs (DMARD’s), 23 with methotrexate (median dose 15 mg/week, range 7.5 – 20 mg/week), and 2 with leflunomide (20 mg/day); 18 of them were treated with low-dose steroids (prednisolone ≤ 7.5 mg/day). Six patients had been included in double-blind clinical trials before inclusion in the present study (1 in a Golimumab versus placebo trial, 3 in a MapKinase inhibitor versus placebo trial and 2 in a TACE-inhibitor versus placebo trial). These trials were stopped at least 3 months prior to initiation of TNF-blocking therapy. All drug dosages were stable from at least 3 months prior to initiation of TNF blocking therapy until completion of the study. No steroid injections were allowed during the duration of the study.
|
| Sample_geo_accession | GSM390159
| | Sample_status | Public on Apr 15 2009
| | Sample_submission_date | Apr 08 2009
| | Sample_last_update_date | Apr 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Adalimumab therapy was initiated at a dosage of 40 mg subcutaneously every other week. Disease activity at baseline and 12 weeks after initiation of therapy (T12) was evaluated using DAS(28)-CRP (3- and 4-variables) scores, and response to therapy was assessed according to the EULAR response criteria that categorize patients in responders (good- or moderate-) and non- (or poor-) responders based on changes in DAS activity between T0 and T12 and absolute DAS values at T12.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | Synovial biopsies were obtained by needle-arthroscopy of knee of the patients at T12. For each procedure, 4 to 8 synovial samples were snap-frozen in liquid nitrogen and stored at –80°C for later RNA extraction. The same amount of tissue was kept at -80°C for immunostaining experiments on frozen sections. The remaining material was fixed in 10% formalin and paraffin embedded for conventional optical evaluation and immunostaining of selected markers. All the experiments (RNA extraction, histology, immunohistochemistry) were performed on at least 4 biopsies harvested during every procedure in order to correct for variations related to the potential heterogeneous distribution of synovial inflammation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from the synovial biopsies using the Nucleospin® RNA II extraction kit (Macherey-Nagel), including DNase treatment of the samples. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent Technologies Inc). All samples had a 28s/18s ratio > 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling of RNA (cRNA synthesis) was performed according to a standard Affymetrix® procedure (One-Cycle Target Labeling kit, Affymetrix UK Ltd., High Wycombe, UK); briefly total RNA was first reverse transcribed into single-stranded cDNA using a T7-Oligo(dT) Promoter Primer and Superscript II reverse transcriptase. Next, RNase H was added together with E. Coli DNA polymerase I and E. Coli DNA ligase, followed by a short incubation with T4 DNA polymerase in order to achieve synthesis of the second-strand cDNA. The purified double-stranded cDNA served as the template for the in vitro transcription reaction, which was carried out overnight in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. At the end of this procedure, the biotinylated complementary RNA (cRNA) was cleaned, and fragmented by a 35-minute incubation at 95°c.
| | Sample_hyb_protocol | GeneChip® Human genome U133 Plus 2.0 Arrays (spotted with 1,300,000 oligonucleotides informative for 47,000 transcripts originated from 39,000 genes, Affymetrix UK Ltd, High Wycombe, UK) were hybridized overnight at 45°c in monoplicates with 10 μg cRNA. The slides were then washed and stained using the EukGE-WS2v5 Fluidics protocol on the Genechip® Fluidics Station (Affymetrix) before being scanned on a Genechip® Scanner 3000.
| | Sample_scan_protocol | The slides were scanned on a Genechip® Scanner 3000.
| | Sample_data_processing | For the initial normalization and analysis steps, data were retrieved on Affymetrix GCOS software. The frequency of positive genes (genes with a flag present) was between 45 and 55% on each slide. After scaling of all probe sets to a value of 100, the amplification scale was reported inferior to 3.0 for all slides. The signals yielded by the poly-A RNA, hybridization and housekeeping controls (GAPDH 3’/5’ ratio < 2) were indicative of the good quality of the amplification and hybridization procedures.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernard,Robert,Lauwerys
| | Sample_contact_email | Bernard.Lauwerys@ruma.ucl.ac.be
| | Sample_contact_phone | +32.2.764.53.91
| | Sample_contact_fax | +32.2.764.53.74
| | Sample_contact_laboratory | Rheumatology Unit
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Université catholique de Louvain
| | Sample_contact_address | Avenue Hippocrate 10
| | Sample_contact_city | Brussels
| | Sample_contact_zip/postal_code | 1200
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM390nnn/GSM390159/suppl/GSM390159.CEL.gz
| | Sample_series_id | GSE15602
| | Sample_data_row_count | 54675
| | |
|
GSM390160 | GPL570 |
|
RA Synovial biopsy T12 post-adalimumab therapy, Good Responder 3
|
Synovial biopsy, RA patient, 12 weeks after adalimumab therapy, good responder
|
tissue: synovial tissue from knee
disease: rheumatoid arthritis
|
Patient has rheumatoid arthritis (RA), according to the American College of rheumatology criteria for the diagnosis of RA. All patients included in this study had active disease at the time of initiation of adalimumab therapy and were resistant to conventional therapy. They all had erosive changes imaged on conventional x-rays of the hands and/or feet. All patients were treated with disease-modifying antirheumatic drugs (DMARD’s), 23 with methotrexate (median dose 15 mg/week, range 7.5 – 20 mg/week), and 2 with leflunomide (20 mg/day); 18 of them were treated with low-dose steroids (prednisolone ≤ 7.5 mg/day). Six patients had been included in double-blind clinical trials before inclusion in the present study (1 in a Golimumab versus placebo trial, 3 in a MapKinase inhibitor versus placebo trial and 2 in a TACE-inhibitor versus placebo trial). These trials were stopped at least 3 months prior to initiation of TNF-blocking therapy. All drug dosages were stable from at least 3 months prior to initiation of TNF blocking therapy until completion of the study. No steroid injections were allowed during the duration of the study.
|
| Sample_geo_accession | GSM390160
| | Sample_status | Public on Apr 15 2009
| | Sample_submission_date | Apr 08 2009
| | Sample_last_update_date | Apr 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Adalimumab therapy was initiated at a dosage of 40 mg subcutaneously every other week. Disease activity at baseline and 12 weeks after initiation of therapy (T12) was evaluated using DAS(28)-CRP (3- and 4-variables) scores, and response to therapy was assessed according to the EULAR response criteria that categorize patients in responders (good- or moderate-) and non- (or poor-) responders based on changes in DAS activity between T0 and T12 and absolute DAS values at T12.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | Synovial biopsies were obtained by needle-arthroscopy of knee of the patients at T12. For each procedure, 4 to 8 synovial samples were snap-frozen in liquid nitrogen and stored at –80°C for later RNA extraction. The same amount of tissue was kept at -80°C for immunostaining experiments on frozen sections. The remaining material was fixed in 10% formalin and paraffin embedded for conventional optical evaluation and immunostaining of selected markers. All the experiments (RNA extraction, histology, immunohistochemistry) were performed on at least 4 biopsies harvested during every procedure in order to correct for variations related to the potential heterogeneous distribution of synovial inflammation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from the synovial biopsies using the Nucleospin® RNA II extraction kit (Macherey-Nagel), including DNase treatment of the samples. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent Technologies Inc). All samples had a 28s/18s ratio > 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling of RNA (cRNA synthesis) was performed according to a standard Affymetrix® procedure (One-Cycle Target Labeling kit, Affymetrix UK Ltd., High Wycombe, UK); briefly total RNA was first reverse transcribed into single-stranded cDNA using a T7-Oligo(dT) Promoter Primer and Superscript II reverse transcriptase. Next, RNase H was added together with E. Coli DNA polymerase I and E. Coli DNA ligase, followed by a short incubation with T4 DNA polymerase in order to achieve synthesis of the second-strand cDNA. The purified double-stranded cDNA served as the template for the in vitro transcription reaction, which was carried out overnight in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. At the end of this procedure, the biotinylated complementary RNA (cRNA) was cleaned, and fragmented by a 35-minute incubation at 95°c.
| | Sample_hyb_protocol | GeneChip® Human genome U133 Plus 2.0 Arrays (spotted with 1,300,000 oligonucleotides informative for 47,000 transcripts originated from 39,000 genes, Affymetrix UK Ltd, High Wycombe, UK) were hybridized overnight at 45°c in monoplicates with 10 μg cRNA. The slides were then washed and stained using the EukGE-WS2v5 Fluidics protocol on the Genechip® Fluidics Station (Affymetrix) before being scanned on a Genechip® Scanner 3000.
| | Sample_scan_protocol | The slides were scanned on a Genechip® Scanner 3000.
| | Sample_data_processing | For the initial normalization and analysis steps, data were retrieved on Affymetrix GCOS software. The frequency of positive genes (genes with a flag present) was between 45 and 55% on each slide. After scaling of all probe sets to a value of 100, the amplification scale was reported inferior to 3.0 for all slides. The signals yielded by the poly-A RNA, hybridization and housekeeping controls (GAPDH 3’/5’ ratio < 2) were indicative of the good quality of the amplification and hybridization procedures.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernard,Robert,Lauwerys
| | Sample_contact_email | Bernard.Lauwerys@ruma.ucl.ac.be
| | Sample_contact_phone | +32.2.764.53.91
| | Sample_contact_fax | +32.2.764.53.74
| | Sample_contact_laboratory | Rheumatology Unit
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Université catholique de Louvain
| | Sample_contact_address | Avenue Hippocrate 10
| | Sample_contact_city | Brussels
| | Sample_contact_zip/postal_code | 1200
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM390nnn/GSM390160/suppl/GSM390160.CEL.gz
| | Sample_series_id | GSE15602
| | Sample_data_row_count | 54675
| | |
|
GSM390170 | GPL570 |
|
RA Synovial biopsy T12 post-adalimumab therapy, Poor Responder 1
|
Synovial biopsy, RA patient, 12 weeks after adalimumab therapy, poor responder
|
tissue: synovial tissue from knee
disease: rheumatoid arthritis
|
Patient has rheumatoid arthritis (RA), according to the American College of rheumatology criteria for the diagnosis of RA. All patients included in this study had active disease at the time of initiation of adalimumab therapy and were resistant to conventional therapy. They all had erosive changes imaged on conventional x-rays of the hands and/or feet. All patients were treated with disease-modifying antirheumatic drugs (DMARD’s), 23 with methotrexate (median dose 15 mg/week, range 7.5 – 20 mg/week), and 2 with leflunomide (20 mg/day); 18 of them were treated with low-dose steroids (prednisolone ≤ 7.5 mg/day). Six patients had been included in double-blind clinical trials before inclusion in the present study (1 in a Golimumab versus placebo trial, 3 in a MapKinase inhibitor versus placebo trial and 2 in a TACE-inhibitor versus placebo trial). These trials were stopped at least 3 months prior to initiation of TNF-blocking therapy. All drug dosages were stable from at least 3 months prior to initiation of TNF blocking therapy until completion of the study. No steroid injections were allowed during the duration of the study.
|
| Sample_geo_accession | GSM390170
| | Sample_status | Public on Apr 15 2009
| | Sample_submission_date | Apr 08 2009
| | Sample_last_update_date | Apr 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Adalimumab therapy was initiated at a dosage of 40 mg subcutaneously every other week. Disease activity at baseline and 12 weeks after initiation of therapy (T12) was evaluated using DAS(28)-CRP (3- and 4-variables) scores, and response to therapy was assessed according to the EULAR response criteria that categorize patients in responders (good- or moderate-) and non- (or poor-) responders based on changes in DAS activity between T0 and T12 and absolute DAS values at T12.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | Synovial biopsies were obtained by needle-arthroscopy of knee of the patients at T12. For each procedure, 4 to 8 synovial samples were snap-frozen in liquid nitrogen and stored at –80°C for later RNA extraction. The same amount of tissue was kept at -80°C for immunostaining experiments on frozen sections. The remaining material was fixed in 10% formalin and paraffin embedded for conventional optical evaluation and immunostaining of selected markers. All the experiments (RNA extraction, histology, immunohistochemistry) were performed on at least 4 biopsies harvested during every procedure in order to correct for variations related to the potential heterogeneous distribution of synovial inflammation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from the synovial biopsies using the Nucleospin® RNA II extraction kit (Macherey-Nagel), including DNase treatment of the samples. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent Technologies Inc). All samples had a 28s/18s ratio > 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling of RNA (cRNA synthesis) was performed according to a standard Affymetrix® procedure (One-Cycle Target Labeling kit, Affymetrix UK Ltd., High Wycombe, UK); briefly total RNA was first reverse transcribed into single-stranded cDNA using a T7-Oligo(dT) Promoter Primer and Superscript II reverse transcriptase. Next, RNase H was added together with E. Coli DNA polymerase I and E. Coli DNA ligase, followed by a short incubation with T4 DNA polymerase in order to achieve synthesis of the second-strand cDNA. The purified double-stranded cDNA served as the template for the in vitro transcription reaction, which was carried out overnight in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. At the end of this procedure, the biotinylated complementary RNA (cRNA) was cleaned, and fragmented by a 35-minute incubation at 95°c.
| | Sample_hyb_protocol | GeneChip® Human genome U133 Plus 2.0 Arrays (spotted with 1,300,000 oligonucleotides informative for 47,000 transcripts originated from 39,000 genes, Affymetrix UK Ltd, High Wycombe, UK) were hybridized overnight at 45°c in monoplicates with 10 μg cRNA. The slides were then washed and stained using the EukGE-WS2v5 Fluidics protocol on the Genechip® Fluidics Station (Affymetrix) before being scanned on a Genechip® Scanner 3000.
| | Sample_scan_protocol | The slides were scanned on a Genechip® Scanner 3000.
| | Sample_data_processing | For the initial normalization and analysis steps, data were retrieved on Affymetrix GCOS software. The frequency of positive genes (genes with a flag present) was between 45 and 55% on each slide. After scaling of all probe sets to a value of 100, the amplification scale was reported inferior to 3.0 for all slides. The signals yielded by the poly-A RNA, hybridization and housekeeping controls (GAPDH 3’/5’ ratio < 2) were indicative of the good quality of the amplification and hybridization procedures.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernard,Robert,Lauwerys
| | Sample_contact_email | Bernard.Lauwerys@ruma.ucl.ac.be
| | Sample_contact_phone | +32.2.764.53.91
| | Sample_contact_fax | +32.2.764.53.74
| | Sample_contact_laboratory | Rheumatology Unit
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Université catholique de Louvain
| | Sample_contact_address | Avenue Hippocrate 10
| | Sample_contact_city | Brussels
| | Sample_contact_zip/postal_code | 1200
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM390nnn/GSM390170/suppl/GSM390170.CEL.gz
| | Sample_series_id | GSE15602
| | Sample_data_row_count | 54675
| | |
|
GSM390171 | GPL570 |
|
RA Synovial biopsy T12 post-adalimumab therapy, Poor Responder 2
|
Synovial biopsy, RA patient, 12 weeks after adalimumab therapy, poor responder
|
tissue: synovial tissue from knee
disease: rheumatoid arthritis
|
Patient has rheumatoid arthritis (RA), according to the American College of rheumatology criteria for the diagnosis of RA. All patients included in this study had active disease at the time of initiation of adalimumab therapy and were resistant to conventional therapy. They all had erosive changes imaged on conventional x-rays of the hands and/or feet. All patients were treated with disease-modifying antirheumatic drugs (DMARD’s), 23 with methotrexate (median dose 15 mg/week, range 7.5 – 20 mg/week), and 2 with leflunomide (20 mg/day); 18 of them were treated with low-dose steroids (prednisolone ≤ 7.5 mg/day). Six patients had been included in double-blind clinical trials before inclusion in the present study (1 in a Golimumab versus placebo trial, 3 in a MapKinase inhibitor versus placebo trial and 2 in a TACE-inhibitor versus placebo trial). These trials were stopped at least 3 months prior to initiation of TNF-blocking therapy. All drug dosages were stable from at least 3 months prior to initiation of TNF blocking therapy until completion of the study. No steroid injections were allowed during the duration of the study.
|
| Sample_geo_accession | GSM390171
| | Sample_status | Public on Apr 15 2009
| | Sample_submission_date | Apr 08 2009
| | Sample_last_update_date | Apr 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Adalimumab therapy was initiated at a dosage of 40 mg subcutaneously every other week. Disease activity at baseline and 12 weeks after initiation of therapy (T12) was evaluated using DAS(28)-CRP (3- and 4-variables) scores, and response to therapy was assessed according to the EULAR response criteria that categorize patients in responders (good- or moderate-) and non- (or poor-) responders based on changes in DAS activity between T0 and T12 and absolute DAS values at T12.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | Synovial biopsies were obtained by needle-arthroscopy of knee of the patients at T12. For each procedure, 4 to 8 synovial samples were snap-frozen in liquid nitrogen and stored at –80°C for later RNA extraction. The same amount of tissue was kept at -80°C for immunostaining experiments on frozen sections. The remaining material was fixed in 10% formalin and paraffin embedded for conventional optical evaluation and immunostaining of selected markers. All the experiments (RNA extraction, histology, immunohistochemistry) were performed on at least 4 biopsies harvested during every procedure in order to correct for variations related to the potential heterogeneous distribution of synovial inflammation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from the synovial biopsies using the Nucleospin® RNA II extraction kit (Macherey-Nagel), including DNase treatment of the samples. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent Technologies Inc). All samples had a 28s/18s ratio > 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling of RNA (cRNA synthesis) was performed according to a standard Affymetrix® procedure (One-Cycle Target Labeling kit, Affymetrix UK Ltd., High Wycombe, UK); briefly total RNA was first reverse transcribed into single-stranded cDNA using a T7-Oligo(dT) Promoter Primer and Superscript II reverse transcriptase. Next, RNase H was added together with E. Coli DNA polymerase I and E. Coli DNA ligase, followed by a short incubation with T4 DNA polymerase in order to achieve synthesis of the second-strand cDNA. The purified double-stranded cDNA served as the template for the in vitro transcription reaction, which was carried out overnight in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. At the end of this procedure, the biotinylated complementary RNA (cRNA) was cleaned, and fragmented by a 35-minute incubation at 95°c.
| | Sample_hyb_protocol | GeneChip® Human genome U133 Plus 2.0 Arrays (spotted with 1,300,000 oligonucleotides informative for 47,000 transcripts originated from 39,000 genes, Affymetrix UK Ltd, High Wycombe, UK) were hybridized overnight at 45°c in monoplicates with 10 μg cRNA. The slides were then washed and stained using the EukGE-WS2v5 Fluidics protocol on the Genechip® Fluidics Station (Affymetrix) before being scanned on a Genechip® Scanner 3000.
| | Sample_scan_protocol | The slides were scanned on a Genechip® Scanner 3000.
| | Sample_data_processing | For the initial normalization and analysis steps, data were retrieved on Affymetrix GCOS software. The frequency of positive genes (genes with a flag present) was between 45 and 55% on each slide. After scaling of all probe sets to a value of 100, the amplification scale was reported inferior to 3.0 for all slides. The signals yielded by the poly-A RNA, hybridization and housekeeping controls (GAPDH 3’/5’ ratio < 2) were indicative of the good quality of the amplification and hybridization procedures.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernard,Robert,Lauwerys
| | Sample_contact_email | Bernard.Lauwerys@ruma.ucl.ac.be
| | Sample_contact_phone | +32.2.764.53.91
| | Sample_contact_fax | +32.2.764.53.74
| | Sample_contact_laboratory | Rheumatology Unit
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Université catholique de Louvain
| | Sample_contact_address | Avenue Hippocrate 10
| | Sample_contact_city | Brussels
| | Sample_contact_zip/postal_code | 1200
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM390nnn/GSM390171/suppl/GSM390171.CEL.gz
| | Sample_series_id | GSE15602
| | Sample_data_row_count | 54675
| | |
|
GSM390173 | GPL570 |
|
RA Synovial biopsy T12 post-adalimumab therapy, Poor Responder 3
|
Synovial biopsy, RA patient, 12 weeks after adalimumab therapy, poor responder
|
tissue: synovial tissue from knee
disease: rheumatoid arthritis
|
Patient has rheumatoid arthritis (RA), according to the American College of rheumatology criteria for the diagnosis of RA. All patients included in this study had active disease at the time of initiation of adalimumab therapy and were resistant to conventional therapy. They all had erosive changes imaged on conventional x-rays of the hands and/or feet. All patients were treated with disease-modifying antirheumatic drugs (DMARD’s), 23 with methotrexate (median dose 15 mg/week, range 7.5 – 20 mg/week), and 2 with leflunomide (20 mg/day); 18 of them were treated with low-dose steroids (prednisolone ≤ 7.5 mg/day). Six patients had been included in double-blind clinical trials before inclusion in the present study (1 in a Golimumab versus placebo trial, 3 in a MapKinase inhibitor versus placebo trial and 2 in a TACE-inhibitor versus placebo trial). These trials were stopped at least 3 months prior to initiation of TNF-blocking therapy. All drug dosages were stable from at least 3 months prior to initiation of TNF blocking therapy until completion of the study. No steroid injections were allowed during the duration of the study.
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| Sample_geo_accession | GSM390173
| | Sample_status | Public on Apr 15 2009
| | Sample_submission_date | Apr 08 2009
| | Sample_last_update_date | Apr 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Adalimumab therapy was initiated at a dosage of 40 mg subcutaneously every other week. Disease activity at baseline and 12 weeks after initiation of therapy (T12) was evaluated using DAS(28)-CRP (3- and 4-variables) scores, and response to therapy was assessed according to the EULAR response criteria that categorize patients in responders (good- or moderate-) and non- (or poor-) responders based on changes in DAS activity between T0 and T12 and absolute DAS values at T12.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | Synovial biopsies were obtained by needle-arthroscopy of knee of the patients at T12. For each procedure, 4 to 8 synovial samples were snap-frozen in liquid nitrogen and stored at –80°C for later RNA extraction. The same amount of tissue was kept at -80°C for immunostaining experiments on frozen sections. The remaining material was fixed in 10% formalin and paraffin embedded for conventional optical evaluation and immunostaining of selected markers. All the experiments (RNA extraction, histology, immunohistochemistry) were performed on at least 4 biopsies harvested during every procedure in order to correct for variations related to the potential heterogeneous distribution of synovial inflammation.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from the synovial biopsies using the Nucleospin® RNA II extraction kit (Macherey-Nagel), including DNase treatment of the samples. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent Technologies Inc). All samples had a 28s/18s ratio > 1.8.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling of RNA (cRNA synthesis) was performed according to a standard Affymetrix® procedure (One-Cycle Target Labeling kit, Affymetrix UK Ltd., High Wycombe, UK); briefly total RNA was first reverse transcribed into single-stranded cDNA using a T7-Oligo(dT) Promoter Primer and Superscript II reverse transcriptase. Next, RNase H was added together with E. Coli DNA polymerase I and E. Coli DNA ligase, followed by a short incubation with T4 DNA polymerase in order to achieve synthesis of the second-strand cDNA. The purified double-stranded cDNA served as the template for the in vitro transcription reaction, which was carried out overnight in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. At the end of this procedure, the biotinylated complementary RNA (cRNA) was cleaned, and fragmented by a 35-minute incubation at 95°c.
| | Sample_hyb_protocol | GeneChip® Human genome U133 Plus 2.0 Arrays (spotted with 1,300,000 oligonucleotides informative for 47,000 transcripts originated from 39,000 genes, Affymetrix UK Ltd, High Wycombe, UK) were hybridized overnight at 45°c in monoplicates with 10 μg cRNA. The slides were then washed and stained using the EukGE-WS2v5 Fluidics protocol on the Genechip® Fluidics Station (Affymetrix) before being scanned on a Genechip® Scanner 3000.
| | Sample_scan_protocol | The slides were scanned on a Genechip® Scanner 3000.
| | Sample_data_processing | For the initial normalization and analysis steps, data were retrieved on Affymetrix GCOS software. The frequency of positive genes (genes with a flag present) was between 45 and 55% on each slide. After scaling of all probe sets to a value of 100, the amplification scale was reported inferior to 3.0 for all slides. The signals yielded by the poly-A RNA, hybridization and housekeeping controls (GAPDH 3’/5’ ratio < 2) were indicative of the good quality of the amplification and hybridization procedures.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bernard,Robert,Lauwerys
| | Sample_contact_email | Bernard.Lauwerys@ruma.ucl.ac.be
| | Sample_contact_phone | +32.2.764.53.91
| | Sample_contact_fax | +32.2.764.53.74
| | Sample_contact_laboratory | Rheumatology Unit
| | Sample_contact_department | Internal Medicine
| | Sample_contact_institute | Université catholique de Louvain
| | Sample_contact_address | Avenue Hippocrate 10
| | Sample_contact_city | Brussels
| | Sample_contact_zip/postal_code | 1200
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM390nnn/GSM390173/suppl/GSM390173.CEL.gz
| | Sample_series_id | GSE15602
| | Sample_data_row_count | 54675
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