Search results for the GEO ID: GSE6119  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM143126 | GPL1355 |
|
Glucosamine treatment_a
|
rat chondrocyte cultured in presence of glucosamine
|
Genotype: Rattus norvegicus
Age: 2 months
|
Gene expression data from rat chondrocyte cultured in presence of 20mM glucosamine
|
| Sample_geo_accession | GSM143126
| | Sample_status | Public on Oct 30 2006
| | Sample_submission_date | Oct 30 2006
| | Sample_last_update_date | Oct 30 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Articular cartilage was isolated from the femoral heads of male Wistar rats under aseptic conditions (Charles River Laboratories). Chondrocytes were obtained by sequential digestion of the cartilage with pronase and type II collagenase. After filtration to remove tissue debris, the cells were cultured in 75-cm2 flasks in complete Dulbecco’s Modified Eagle Medium (DMEM; supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_growth_protocol_ch1 | Experiments were performed with second-passage cultures whereby the cells from the large cultures were trypsinized, pooled and seeded into twenty 25 cm2 flasks. These were then 1/4 were cultured in presence of 20mM glucosamine for 20 hours (n=2/group).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | streptavidin-phycoerythryn
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, fifteen micrograms of adjusted cRNA from each sample was hybridized for 16 hours at 45°C to Affymetrix GeneChip Rat Genome 230 2.0 arrays.
| | Sample_scan_protocol | GeneChips were scanned using the Genearray Scanner, Agilent Technologies
| | Sample_data_processing | Microarray Suite, version 5 (Affymetrix), was used to generate *.cel files, and a computer program (Probe Profiler, ver.1.3.11; Corimbia, Inc.) developed specifically for the GeneChip system (Affymetrix) was used to convert intensity data into quantitative estimates, globally scaled to 100, of gene expression for each probe set.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | jean noel,,gouze
| | Sample_contact_laboratory | gene therapy
| | Sample_contact_department | orthopaedics
| | Sample_contact_institute | university of florida
| | Sample_contact_address | 1600 SW archer rd
| | Sample_contact_city | gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143126/suppl/GSM143126.CEL.gz
| | Sample_series_id | GSE6119
| | Sample_data_row_count | 31099
| | |
|
GSM143127 | GPL1355 |
|
Glucosamine treatment_b
|
rat chondrocyte cultured in presence of glucosamine
|
Genotype: Rattus norvegicus
Age: 2 months
|
Gene expression data from rat chondrocyte cultured in presence of 20mM glucosamine
|
| Sample_geo_accession | GSM143127
| | Sample_status | Public on Oct 30 2006
| | Sample_submission_date | Oct 30 2006
| | Sample_last_update_date | Oct 30 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Articular cartilage was isolated from the femoral heads of male Wistar rats under aseptic conditions (Charles River Laboratories). Chondrocytes were obtained by sequential digestion of the cartilage with pronase and type II collagenase. After filtration to remove tissue debris, the cells were cultured in 75-cm2 flasks in complete Dulbecco’s Modified Eagle Medium (DMEM; supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_growth_protocol_ch1 | Experiments were performed with second-passage cultures whereby the cells from the large cultures were trypsinized, pooled and seeded into twenty 25 cm2 flasks. These were then 1/4 were cultured in presence of 20mM glucosamine for 20 hours (n=2/group).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | streptavidin-phycoerythryn
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, fifteen micrograms of adjusted cRNA from each sample was hybridized for 16 hours at 45°C to Affymetrix GeneChip Rat Genome 230 2.0 arrays.
| | Sample_scan_protocol | GeneChips were scanned using the Genearray Scanner, Agilent Technologies
| | Sample_data_processing | Microarray Suite, version 5 (Affymetrix), was used to generate *.cel files, and a computer program (Probe Profiler, ver.1.3.11; Corimbia, Inc.) developed specifically for the GeneChip system (Affymetrix) was used to convert intensity data into quantitative estimates, globally scaled to 100, of gene expression for each probe set.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | jean noel,,gouze
| | Sample_contact_laboratory | gene therapy
| | Sample_contact_department | orthopaedics
| | Sample_contact_institute | university of florida
| | Sample_contact_address | 1600 SW archer rd
| | Sample_contact_city | gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143127/suppl/GSM143127.CEL.gz
| | Sample_series_id | GSE6119
| | Sample_data_row_count | 31099
| | |
|
GSM143128 | GPL1355 |
|
Glucosamine and IL-1 beta treatment_a
|
rat chondrocyte cultured in presence of glucosamine and IL-1
|
Genotype: Rattus norvegicus
Age: 2 months
|
Gene expression data from rat chondrocyte cultured in presence of 20mM glucosamine
|
| Sample_geo_accession | GSM143128
| | Sample_status | Public on Oct 30 2006
| | Sample_submission_date | Oct 30 2006
| | Sample_last_update_date | Oct 30 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Articular cartilage was isolated from the femoral heads of male Wistar rats under aseptic conditions (Charles River Laboratories). Chondrocytes were obtained by sequential digestion of the cartilage with pronase and type II collagenase. After filtration to remove tissue debris, the cells were cultured in 75-cm2 flasks in complete Dulbecco’s Modified Eagle Medium (DMEM; supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_growth_protocol_ch1 | Experiments were performed with second-passage cultures whereby the cells from the large cultures were trypsinized, pooled and seeded into twenty 25 cm2 flasks. These were then 1/4 were cultured in presence of 20mM glucosamine for 6 hours then stimulated with IL-1 beta for 14 hours (10ng/ml) (n=4/group).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | streptavidin-phycoerythryn
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, fifteen micrograms of adjusted cRNA from each sample was hybridized for 16 hours at 45°C to Affymetrix GeneChip Rat Genome 230 2.0 arrays.
| | Sample_scan_protocol | GeneChips were scanned using the Genearray Scanner, Agilent Technologies
| | Sample_data_processing | Microarray Suite, version 5 (Affymetrix), was used to generate *.cel files, and a computer program (Probe Profiler, ver.1.3.11; Corimbia, Inc.) developed specifically for the GeneChip system (Affymetrix) was used to convert intensity data into quantitative estimates, globally scaled to 100, of gene expression for each probe set.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | jean noel,,gouze
| | Sample_contact_laboratory | gene therapy
| | Sample_contact_department | orthopaedics
| | Sample_contact_institute | university of florida
| | Sample_contact_address | 1600 SW archer rd
| | Sample_contact_city | gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143128/suppl/GSM143128.CEL.gz
| | Sample_series_id | GSE6119
| | Sample_data_row_count | 31099
| | |
|
GSM143129 | GPL1355 |
|
Glucosamine and IL-1 beta treatment_b
|
rat chondrocyte cultured in presence of glucosamine and IL-1
|
Genotype: Rattus norvegicus
Age: 2 months
|
Gene expression data from rat chondrocyte cultured in presence of 20mM glucosamine
|
| Sample_geo_accession | GSM143129
| | Sample_status | Public on Oct 30 2006
| | Sample_submission_date | Oct 30 2006
| | Sample_last_update_date | Oct 30 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Articular cartilage was isolated from the femoral heads of male Wistar rats under aseptic conditions (Charles River Laboratories). Chondrocytes were obtained by sequential digestion of the cartilage with pronase and type II collagenase. After filtration to remove tissue debris, the cells were cultured in 75-cm2 flasks in complete Dulbecco’s Modified Eagle Medium (DMEM; supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_growth_protocol_ch1 | Experiments were performed with second-passage cultures whereby the cells from the large cultures were trypsinized, pooled and seeded into twenty 25 cm2 flasks. These were then 1/4 were cultured in presence of 20mM glucosamine for 6 hours then stimulated with IL-1 beta for 14 hours (10ng/ml) (n=4/group).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | streptavidin-phycoerythryn
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, fifteen micrograms of adjusted cRNA from each sample was hybridized for 16 hours at 45°C to Affymetrix GeneChip Rat Genome 230 2.0 arrays.
| | Sample_scan_protocol | GeneChips were scanned using the Genearray Scanner, Agilent Technologies
| | Sample_data_processing | Microarray Suite, version 5 (Affymetrix), was used to generate *.cel files, and a computer program (Probe Profiler, ver.1.3.11; Corimbia, Inc.) developed specifically for the GeneChip system (Affymetrix) was used to convert intensity data into quantitative estimates, globally scaled to 100, of gene expression for each probe set.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | jean noel,,gouze
| | Sample_contact_laboratory | gene therapy
| | Sample_contact_department | orthopaedics
| | Sample_contact_institute | university of florida
| | Sample_contact_address | 1600 SW archer rd
| | Sample_contact_city | gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143129/suppl/GSM143129.CEL.gz
| | Sample_series_id | GSE6119
| | Sample_data_row_count | 31099
| | |
|
GSM143130 | GPL1355 |
|
Glucosamine and IL-1 beta treatment_c
|
rat chondrocyte cultured in presence of glucosamine and IL-1
|
Genotype: Rattus norvegicus
Age: 2 months
|
Gene expression data from rat chondrocyte cultured in presence of 20mM glucosamine
|
| Sample_geo_accession | GSM143130
| | Sample_status | Public on Oct 30 2006
| | Sample_submission_date | Oct 30 2006
| | Sample_last_update_date | Oct 30 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Articular cartilage was isolated from the femoral heads of male Wistar rats under aseptic conditions (Charles River Laboratories). Chondrocytes were obtained by sequential digestion of the cartilage with pronase and type II collagenase. After filtration to remove tissue debris, the cells were cultured in 75-cm2 flasks in complete Dulbecco’s Modified Eagle Medium (DMEM; supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_growth_protocol_ch1 | Experiments were performed with second-passage cultures whereby the cells from the large cultures were trypsinized, pooled and seeded into twenty 25 cm2 flasks. These were then 1/4 were cultured in presence of 20mM glucosamine for 6 hours then stimulated with IL-1 beta for 14 hours (10ng/ml) (n=4/group).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | streptavidin-phycoerythryn
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, fifteen micrograms of adjusted cRNA from each sample was hybridized for 16 hours at 45°C to Affymetrix GeneChip Rat Genome 230 2.0 arrays.
| | Sample_scan_protocol | GeneChips were scanned using the Genearray Scanner, Agilent Technologies
| | Sample_data_processing | Microarray Suite, version 5 (Affymetrix), was used to generate *.cel files, and a computer program (Probe Profiler, ver.1.3.11; Corimbia, Inc.) developed specifically for the GeneChip system (Affymetrix) was used to convert intensity data into quantitative estimates, globally scaled to 100, of gene expression for each probe set.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | jean noel,,gouze
| | Sample_contact_laboratory | gene therapy
| | Sample_contact_department | orthopaedics
| | Sample_contact_institute | university of florida
| | Sample_contact_address | 1600 SW archer rd
| | Sample_contact_city | gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143130/suppl/GSM143130.CEL.gz
| | Sample_series_id | GSE6119
| | Sample_data_row_count | 31099
| | |
|
GSM143131 | GPL1355 |
|
Glucosamine and IL-1 beta treatment_d
|
rat chondrocyte cultured in presence of glucosamine and IL-1
|
Genotype: Rattus norvegicus
Age: 2 months
|
Gene expression data from rat chondrocyte cultured in presence of 20mM glucosamine
|
| Sample_geo_accession | GSM143131
| | Sample_status | Public on Oct 30 2006
| | Sample_submission_date | Oct 30 2006
| | Sample_last_update_date | Oct 30 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Articular cartilage was isolated from the femoral heads of male Wistar rats under aseptic conditions (Charles River Laboratories). Chondrocytes were obtained by sequential digestion of the cartilage with pronase and type II collagenase. After filtration to remove tissue debris, the cells were cultured in 75-cm2 flasks in complete Dulbecco’s Modified Eagle Medium (DMEM; supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_growth_protocol_ch1 | Experiments were performed with second-passage cultures whereby the cells from the large cultures were trypsinized, pooled and seeded into twenty 25 cm2 flasks. These were then 1/4 were cultured in presence of 20mM glucosamine for 6 hours then stimulated with IL-1 beta for 14 hours (10ng/ml) (n=4/group).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | streptavidin-phycoerythryn
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, fifteen micrograms of adjusted cRNA from each sample was hybridized for 16 hours at 45°C to Affymetrix GeneChip Rat Genome 230 2.0 arrays.
| | Sample_scan_protocol | GeneChips were scanned using the Genearray Scanner, Agilent Technologies
| | Sample_data_processing | Microarray Suite, version 5 (Affymetrix), was used to generate *.cel files, and a computer program (Probe Profiler, ver.1.3.11; Corimbia, Inc.) developed specifically for the GeneChip system (Affymetrix) was used to convert intensity data into quantitative estimates, globally scaled to 100, of gene expression for each probe set.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | jean noel,,gouze
| | Sample_contact_laboratory | gene therapy
| | Sample_contact_department | orthopaedics
| | Sample_contact_institute | university of florida
| | Sample_contact_address | 1600 SW archer rd
| | Sample_contact_city | gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143131/suppl/GSM143131.CEL.gz
| | Sample_series_id | GSE6119
| | Sample_data_row_count | 31099
| | |
|
GSM143132 | GPL1355 |
|
IL-1 beta treatment_a
|
rat chondrocyte cultured in presence of IL-1
|
Genotype: Rattus norvegicus
Age: 2 months
|
Gene expression data from rat chondrocyte cultured in presence of 20mM glucosamine
|
| Sample_geo_accession | GSM143132
| | Sample_status | Public on Oct 30 2006
| | Sample_submission_date | Oct 30 2006
| | Sample_last_update_date | Oct 30 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Articular cartilage was isolated from the femoral heads of male Wistar rats under aseptic conditions (Charles River Laboratories). Chondrocytes were obtained by sequential digestion of the cartilage with pronase and type II collagenase. After filtration to remove tissue debris, the cells were cultured in 75-cm2 flasks in complete Dulbecco’s Modified Eagle Medium (DMEM; supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_growth_protocol_ch1 | Experiments were performed with second-passage cultures whereby the cells from the large cultures were trypsinized, pooled and seeded into twenty 25 cm2 flasks. These were then 1/4 were cultured in presence of IL-1 beta for 14 hours (10ng/ml) (n=4/group).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | streptavidin-phycoerythryn
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, fifteen micrograms of adjusted cRNA from each sample was hybridized for 16 hours at 45°C to Affymetrix GeneChip Rat Genome 230 2.0 arrays.
| | Sample_scan_protocol | GeneChips were scanned using the Genearray Scanner, Agilent Technologies
| | Sample_data_processing | Microarray Suite, version 5 (Affymetrix), was used to generate *.cel files, and a computer program (Probe Profiler, ver.1.3.11; Corimbia, Inc.) developed specifically for the GeneChip system (Affymetrix) was used to convert intensity data into quantitative estimates, globally scaled to 100, of gene expression for each probe set.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | jean noel,,gouze
| | Sample_contact_laboratory | gene therapy
| | Sample_contact_department | orthopaedics
| | Sample_contact_institute | university of florida
| | Sample_contact_address | 1600 SW archer rd
| | Sample_contact_city | gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143132/suppl/GSM143132.CEL.gz
| | Sample_series_id | GSE6119
| | Sample_data_row_count | 31099
| | |
|
GSM143133 | GPL1355 |
|
IL-1 beta treatment_b
|
rat chondrocyte cultured in presence of IL-1
|
Genotype: Rattus norvegicus
Age: 2 months
|
Gene expression data from rat chondrocyte cultured in presence of 20mM glucosamine
|
| Sample_geo_accession | GSM143133
| | Sample_status | Public on Oct 30 2006
| | Sample_submission_date | Oct 30 2006
| | Sample_last_update_date | Oct 30 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Articular cartilage was isolated from the femoral heads of male Wistar rats under aseptic conditions (Charles River Laboratories). Chondrocytes were obtained by sequential digestion of the cartilage with pronase and type II collagenase. After filtration to remove tissue debris, the cells were cultured in 75-cm2 flasks in complete Dulbecco’s Modified Eagle Medium (DMEM; supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_growth_protocol_ch1 | Experiments were performed with second-passage cultures whereby the cells from the large cultures were trypsinized, pooled and seeded into twenty 25 cm2 flasks. These were then 1/4 were cultured in presence of IL-1 beta for 14 hours (10ng/ml) (n=4/group).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | streptavidin-phycoerythryn
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, fifteen micrograms of adjusted cRNA from each sample was hybridized for 16 hours at 45°C to Affymetrix GeneChip Rat Genome 230 2.0 arrays.
| | Sample_scan_protocol | GeneChips were scanned using the Genearray Scanner, Agilent Technologies
| | Sample_data_processing | Microarray Suite, version 5 (Affymetrix), was used to generate *.cel files, and a computer program (Probe Profiler, ver.1.3.11; Corimbia, Inc.) developed specifically for the GeneChip system (Affymetrix) was used to convert intensity data into quantitative estimates, globally scaled to 100, of gene expression for each probe set.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | jean noel,,gouze
| | Sample_contact_laboratory | gene therapy
| | Sample_contact_department | orthopaedics
| | Sample_contact_institute | university of florida
| | Sample_contact_address | 1600 SW archer rd
| | Sample_contact_city | gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143133/suppl/GSM143133.CEL.gz
| | Sample_series_id | GSE6119
| | Sample_data_row_count | 31099
| | |
|
GSM143134 | GPL1355 |
|
IL-1 beta treatment_c
|
rat chondrocyte cultured in presence of IL-1
|
Genotype: Rattus norvegicus
Age: 2 months
|
Gene expression data from rat chondrocyte cultured in presence of 20mM glucosamine
|
| Sample_geo_accession | GSM143134
| | Sample_status | Public on Oct 30 2006
| | Sample_submission_date | Oct 30 2006
| | Sample_last_update_date | Oct 30 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Articular cartilage was isolated from the femoral heads of male Wistar rats under aseptic conditions (Charles River Laboratories). Chondrocytes were obtained by sequential digestion of the cartilage with pronase and type II collagenase. After filtration to remove tissue debris, the cells were cultured in 75-cm2 flasks in complete Dulbecco’s Modified Eagle Medium (DMEM; supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_growth_protocol_ch1 | Experiments were performed with second-passage cultures whereby the cells from the large cultures were trypsinized, pooled and seeded into twenty 25 cm2 flasks. These were then 1/4 were cultured in presence of IL-1 beta for 14 hours (10ng/ml) (n=4/group).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | streptavidin-phycoerythryn
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, fifteen micrograms of adjusted cRNA from each sample was hybridized for 16 hours at 45°C to Affymetrix GeneChip Rat Genome 230 2.0 arrays.
| | Sample_scan_protocol | GeneChips were scanned using the Genearray Scanner, Agilent Technologies
| | Sample_data_processing | Microarray Suite, version 5 (Affymetrix), was used to generate *.cel files, and a computer program (Probe Profiler, ver.1.3.11; Corimbia, Inc.) developed specifically for the GeneChip system (Affymetrix) was used to convert intensity data into quantitative estimates, globally scaled to 100, of gene expression for each probe set.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | jean noel,,gouze
| | Sample_contact_laboratory | gene therapy
| | Sample_contact_department | orthopaedics
| | Sample_contact_institute | university of florida
| | Sample_contact_address | 1600 SW archer rd
| | Sample_contact_city | gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143134/suppl/GSM143134.CEL.gz
| | Sample_series_id | GSE6119
| | Sample_data_row_count | 31099
| | |
|
GSM143135 | GPL1355 |
|
IL-1 beta treatment_d
|
rat chondrocyte cultured in presence of IL-1
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Genotype: Rattus norvegicus
Age: 2 months
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Gene expression data from rat chondrocyte cultured in presence of 20mM glucosamine
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| Sample_geo_accession | GSM143135
| | Sample_status | Public on Oct 30 2006
| | Sample_submission_date | Oct 30 2006
| | Sample_last_update_date | Oct 30 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Articular cartilage was isolated from the femoral heads of male Wistar rats under aseptic conditions (Charles River Laboratories). Chondrocytes were obtained by sequential digestion of the cartilage with pronase and type II collagenase. After filtration to remove tissue debris, the cells were cultured in 75-cm2 flasks in complete Dulbecco’s Modified Eagle Medium (DMEM; supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_growth_protocol_ch1 | Experiments were performed with second-passage cultures whereby the cells from the large cultures were trypsinized, pooled and seeded into twenty 25 cm2 flasks. These were then 1/4 were cultured in presence of IL-1 beta for 14 hours (10ng/ml) (n=4/group).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | streptavidin-phycoerythryn
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, fifteen micrograms of adjusted cRNA from each sample was hybridized for 16 hours at 45°C to Affymetrix GeneChip Rat Genome 230 2.0 arrays.
| | Sample_scan_protocol | GeneChips were scanned using the Genearray Scanner, Agilent Technologies
| | Sample_data_processing | Microarray Suite, version 5 (Affymetrix), was used to generate *.cel files, and a computer program (Probe Profiler, ver.1.3.11; Corimbia, Inc.) developed specifically for the GeneChip system (Affymetrix) was used to convert intensity data into quantitative estimates, globally scaled to 100, of gene expression for each probe set.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | jean noel,,gouze
| | Sample_contact_laboratory | gene therapy
| | Sample_contact_department | orthopaedics
| | Sample_contact_institute | university of florida
| | Sample_contact_address | 1600 SW archer rd
| | Sample_contact_city | gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143135/suppl/GSM143135.CEL.gz
| | Sample_series_id | GSE6119
| | Sample_data_row_count | 31099
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GSM143136 | GPL1355 |
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control_a
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rat chondrocyte control
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Genotype: Rattus norvegicus
Age: 2 months
|
Gene expression data from rat chondrocyte cultured in presence of 20mM glucosamine
|
| Sample_geo_accession | GSM143136
| | Sample_status | Public on Oct 30 2006
| | Sample_submission_date | Oct 30 2006
| | Sample_last_update_date | Oct 30 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Articular cartilage was isolated from the femoral heads of male Wistar rats under aseptic conditions (Charles River Laboratories). Chondrocytes were obtained by sequential digestion of the cartilage with pronase and type II collagenase. After filtration to remove tissue debris, the cells were cultured in 75-cm2 flasks in complete Dulbecco’s Modified Eagle Medium (DMEM; supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_growth_protocol_ch1 | Experiments were performed with second-passage cultures whereby the cells from the large cultures were trypsinized, pooled and seeded into twenty 25 cm2 flasks. These were then 1/4 were cultured in complete DMEM (n=3/group).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | streptavidin-phycoerythryn
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, fifteen micrograms of adjusted cRNA from each sample was hybridized for 16 hours at 45°C to Affymetrix GeneChip Rat Genome 230 2.0 arrays.
| | Sample_scan_protocol | GeneChips were scanned using the Genearray Scanner, Agilent Technologies
| | Sample_data_processing | Microarray Suite, version 5 (Affymetrix), was used to generate *.cel files, and a computer program (Probe Profiler, ver.1.3.11; Corimbia, Inc.) developed specifically for the GeneChip system (Affymetrix) was used to convert intensity data into quantitative estimates, globally scaled to 100, of gene expression for each probe set.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | jean noel,,gouze
| | Sample_contact_laboratory | gene therapy
| | Sample_contact_department | orthopaedics
| | Sample_contact_institute | university of florida
| | Sample_contact_address | 1600 SW archer rd
| | Sample_contact_city | gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143136/suppl/GSM143136.CEL.gz
| | Sample_series_id | GSE6119
| | Sample_data_row_count | 31099
| | |
|
GSM143137 | GPL1355 |
|
control_b
|
rat chondrocyte control
|
Genotype: Rattus norvegicus
Age: 2 months
|
Gene expression data from rat chondrocyte cultured in presence of 20mM glucosamine
|
| Sample_geo_accession | GSM143137
| | Sample_status | Public on Oct 30 2006
| | Sample_submission_date | Oct 30 2006
| | Sample_last_update_date | Oct 30 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Articular cartilage was isolated from the femoral heads of male Wistar rats under aseptic conditions (Charles River Laboratories). Chondrocytes were obtained by sequential digestion of the cartilage with pronase and type II collagenase. After filtration to remove tissue debris, the cells were cultured in 75-cm2 flasks in complete Dulbecco’s Modified Eagle Medium (DMEM; supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_growth_protocol_ch1 | Experiments were performed with second-passage cultures whereby the cells from the large cultures were trypsinized, pooled and seeded into twenty 25 cm2 flasks. These were then 1/4 were cultured in complete DMEM (n=3/group).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | streptavidin-phycoerythryn
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, fifteen micrograms of adjusted cRNA from each sample was hybridized for 16 hours at 45°C to Affymetrix GeneChip Rat Genome 230 2.0 arrays.
| | Sample_scan_protocol | GeneChips were scanned using the Genearray Scanner, Agilent Technologies
| | Sample_data_processing | Microarray Suite, version 5 (Affymetrix), was used to generate *.cel files, and a computer program (Probe Profiler, ver.1.3.11; Corimbia, Inc.) developed specifically for the GeneChip system (Affymetrix) was used to convert intensity data into quantitative estimates, globally scaled to 100, of gene expression for each probe set.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | jean noel,,gouze
| | Sample_contact_laboratory | gene therapy
| | Sample_contact_department | orthopaedics
| | Sample_contact_institute | university of florida
| | Sample_contact_address | 1600 SW archer rd
| | Sample_contact_city | gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143137/suppl/GSM143137.CEL.gz
| | Sample_series_id | GSE6119
| | Sample_data_row_count | 31099
| | |
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GSM143138 | GPL1355 |
|
control_c
|
rat chondrocyte control
|
Genotype: Rattus norvegicus
Age: 2 months
|
Gene expression data from rat chondrocyte cultured in presence of 20mM glucosamine
|
| Sample_geo_accession | GSM143138
| | Sample_status | Public on Oct 30 2006
| | Sample_submission_date | Oct 30 2006
| | Sample_last_update_date | Oct 30 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Articular cartilage was isolated from the femoral heads of male Wistar rats under aseptic conditions (Charles River Laboratories). Chondrocytes were obtained by sequential digestion of the cartilage with pronase and type II collagenase. After filtration to remove tissue debris, the cells were cultured in 75-cm2 flasks in complete Dulbecco’s Modified Eagle Medium (DMEM; supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO2.
| | Sample_growth_protocol_ch1 | Experiments were performed with second-passage cultures whereby the cells from the large cultures were trypsinized, pooled and seeded into twenty 25 cm2 flasks. These were then 1/4 were cultured in complete DMEM (n=3/group).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | streptavidin-phycoerythryn
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, fifteen micrograms of adjusted cRNA from each sample was hybridized for 16 hours at 45°C to Affymetrix GeneChip Rat Genome 230 2.0 arrays.
| | Sample_scan_protocol | GeneChips were scanned using the Genearray Scanner, Agilent Technologies
| | Sample_data_processing | Microarray Suite, version 5 (Affymetrix), was used to generate *.cel files, and a computer program (Probe Profiler, ver.1.3.11; Corimbia, Inc.) developed specifically for the GeneChip system (Affymetrix) was used to convert intensity data into quantitative estimates, globally scaled to 100, of gene expression for each probe set.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | jean noel,,gouze
| | Sample_contact_laboratory | gene therapy
| | Sample_contact_department | orthopaedics
| | Sample_contact_institute | university of florida
| | Sample_contact_address | 1600 SW archer rd
| | Sample_contact_city | gainesville
| | Sample_contact_state | FL
| | Sample_contact_zip/postal_code | 32610
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM143nnn/GSM143138/suppl/GSM143138.CEL.gz
| | Sample_series_id | GSE6119
| | Sample_data_row_count | 31099
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