Search results for the GEO ID: GSE42295  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1037284 | GPL1355 |
|
Cartilage, OA, 2 weeks, rep1
|
knee articular cartilage
|
surgery: OA
time after surgery: 2 weeks
|
Gene expression data from knee articular cartilage chondrocytes 2 weeks after induction of OA
|
| Sample_geo_accession | GSM1037284
| | Sample_status | Public on Nov 15 2012
| | Sample_submission_date | Nov 14 2012
| | Sample_last_update_date | Nov 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See surgical description above and in Appleton, CT et al, 2007, Arthritis Res Ther 9:R13
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cartilage from knee joints was homogenized in TRIzol and subsequently extracted from the aqueous phase using QIAgen RNA isolation columns (RNeasy Mini Kit), subjected to quantification using Nanodrop system (Thermo Scientific) and quality assessment using 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | Raw expression data files were imported into GeneSpring 7.2 software (Silicon Genetics, Redwood City, CA) and underwent GC-RMA pre-processing. Raw data processing included transformation (values < 0.01 were set to 0.01), per-chip normalization (to 50th percentile), and per-gene normalization (to median values). Probes demonstrating reliable signal were identified using the GeneSpring 7.2 SG1a-1 signal intensity quality control script and fold-change filtering was performed on these lists.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Tom,,Appleton
| | Sample_contact_email | cappleto@uwo.ca
| | Sample_contact_laboratory | Frank Beier
| | Sample_contact_department | Physiology & Pharmacology
| | Sample_contact_institute | The University of Western Ontario
| | Sample_contact_address | Rm 0061 DSB The University of Western Ontario
| | Sample_contact_city | London
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | N6A5C1
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1037nnn/GSM1037284/suppl/GSM1037284.CEL.gz
| | Sample_series_id | GSE42295
| | Sample_data_row_count | 31099
| | |
|
GSM1037285 | GPL1355 |
|
Cartilage, OA, 2 weeks, rep2
|
knee articular cartilage
|
surgery: OA
time after surgery: 2 weeks
|
Gene expression data from knee articular cartilage chondrocytes 2 weeks after induction of OA
|
| Sample_geo_accession | GSM1037285
| | Sample_status | Public on Nov 15 2012
| | Sample_submission_date | Nov 14 2012
| | Sample_last_update_date | Nov 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See surgical description above and in Appleton, CT et al, 2007, Arthritis Res Ther 9:R13
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cartilage from knee joints was homogenized in TRIzol and subsequently extracted from the aqueous phase using QIAgen RNA isolation columns (RNeasy Mini Kit), subjected to quantification using Nanodrop system (Thermo Scientific) and quality assessment using 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | Raw expression data files were imported into GeneSpring 7.2 software (Silicon Genetics, Redwood City, CA) and underwent GC-RMA pre-processing. Raw data processing included transformation (values < 0.01 were set to 0.01), per-chip normalization (to 50th percentile), and per-gene normalization (to median values). Probes demonstrating reliable signal were identified using the GeneSpring 7.2 SG1a-1 signal intensity quality control script and fold-change filtering was performed on these lists.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Tom,,Appleton
| | Sample_contact_email | cappleto@uwo.ca
| | Sample_contact_laboratory | Frank Beier
| | Sample_contact_department | Physiology & Pharmacology
| | Sample_contact_institute | The University of Western Ontario
| | Sample_contact_address | Rm 0061 DSB The University of Western Ontario
| | Sample_contact_city | London
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | N6A5C1
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1037nnn/GSM1037285/suppl/GSM1037285.CEL.gz
| | Sample_series_id | GSE42295
| | Sample_data_row_count | 31099
| | |
|
GSM1037286 | GPL1355 |
|
Cartilage, OA, 2 weeks, rep3
|
knee articular cartilage
|
surgery: OA
time after surgery: 2 weeks
|
Gene expression data from knee articular cartilage chondrocytes 2 weeks after induction of OA
|
| Sample_geo_accession | GSM1037286
| | Sample_status | Public on Nov 15 2012
| | Sample_submission_date | Nov 14 2012
| | Sample_last_update_date | Nov 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See surgical description above and in Appleton, CT et al, 2007, Arthritis Res Ther 9:R13
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cartilage from knee joints was homogenized in TRIzol and subsequently extracted from the aqueous phase using QIAgen RNA isolation columns (RNeasy Mini Kit), subjected to quantification using Nanodrop system (Thermo Scientific) and quality assessment using 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | Raw expression data files were imported into GeneSpring 7.2 software (Silicon Genetics, Redwood City, CA) and underwent GC-RMA pre-processing. Raw data processing included transformation (values < 0.01 were set to 0.01), per-chip normalization (to 50th percentile), and per-gene normalization (to median values). Probes demonstrating reliable signal were identified using the GeneSpring 7.2 SG1a-1 signal intensity quality control script and fold-change filtering was performed on these lists.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Tom,,Appleton
| | Sample_contact_email | cappleto@uwo.ca
| | Sample_contact_laboratory | Frank Beier
| | Sample_contact_department | Physiology & Pharmacology
| | Sample_contact_institute | The University of Western Ontario
| | Sample_contact_address | Rm 0061 DSB The University of Western Ontario
| | Sample_contact_city | London
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | N6A5C1
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1037nnn/GSM1037286/suppl/GSM1037286.CEL.gz
| | Sample_series_id | GSE42295
| | Sample_data_row_count | 31099
| | |
|
GSM1037287 | GPL1355 |
|
Cartilage, Sham, 2 weeks, rep1
|
knee articular cartilage
|
surgery: Sham
time after surgery: 2 weeks
|
Gene expression data from knee articular cartilage chondrocytes 2 weeks after Sham surgery
|
| Sample_geo_accession | GSM1037287
| | Sample_status | Public on Nov 15 2012
| | Sample_submission_date | Nov 14 2012
| | Sample_last_update_date | Nov 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See surgical description above and in Appleton, CT et al, 2007, Arthritis Res Ther 9:R13
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cartilage from knee joints was homogenized in TRIzol and subsequently extracted from the aqueous phase using QIAgen RNA isolation columns (RNeasy Mini Kit), subjected to quantification using Nanodrop system (Thermo Scientific) and quality assessment using 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | Raw expression data files were imported into GeneSpring 7.2 software (Silicon Genetics, Redwood City, CA) and underwent GC-RMA pre-processing. Raw data processing included transformation (values < 0.01 were set to 0.01), per-chip normalization (to 50th percentile), and per-gene normalization (to median values). Probes demonstrating reliable signal were identified using the GeneSpring 7.2 SG1a-1 signal intensity quality control script and fold-change filtering was performed on these lists.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Tom,,Appleton
| | Sample_contact_email | cappleto@uwo.ca
| | Sample_contact_laboratory | Frank Beier
| | Sample_contact_department | Physiology & Pharmacology
| | Sample_contact_institute | The University of Western Ontario
| | Sample_contact_address | Rm 0061 DSB The University of Western Ontario
| | Sample_contact_city | London
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | N6A5C1
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1037nnn/GSM1037287/suppl/GSM1037287.CEL.gz
| | Sample_series_id | GSE42295
| | Sample_data_row_count | 31099
| | |
|
GSM1037288 | GPL1355 |
|
Cartilage, Sham, 2 weeks, rep2
|
knee articular cartilage
|
surgery: Sham
time after surgery: 2 weeks
|
Gene expression data from knee articular cartilage chondrocytes 2 weeks after Sham surgery
|
| Sample_geo_accession | GSM1037288
| | Sample_status | Public on Nov 15 2012
| | Sample_submission_date | Nov 14 2012
| | Sample_last_update_date | Nov 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See surgical description above and in Appleton, CT et al, 2007, Arthritis Res Ther 9:R13
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cartilage from knee joints was homogenized in TRIzol and subsequently extracted from the aqueous phase using QIAgen RNA isolation columns (RNeasy Mini Kit), subjected to quantification using Nanodrop system (Thermo Scientific) and quality assessment using 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | Raw expression data files were imported into GeneSpring 7.2 software (Silicon Genetics, Redwood City, CA) and underwent GC-RMA pre-processing. Raw data processing included transformation (values < 0.01 were set to 0.01), per-chip normalization (to 50th percentile), and per-gene normalization (to median values). Probes demonstrating reliable signal were identified using the GeneSpring 7.2 SG1a-1 signal intensity quality control script and fold-change filtering was performed on these lists.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Tom,,Appleton
| | Sample_contact_email | cappleto@uwo.ca
| | Sample_contact_laboratory | Frank Beier
| | Sample_contact_department | Physiology & Pharmacology
| | Sample_contact_institute | The University of Western Ontario
| | Sample_contact_address | Rm 0061 DSB The University of Western Ontario
| | Sample_contact_city | London
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | N6A5C1
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1037nnn/GSM1037288/suppl/GSM1037288.CEL.gz
| | Sample_series_id | GSE42295
| | Sample_data_row_count | 31099
| | |
|
GSM1037289 | GPL1355 |
|
Cartilage, Sham, 2 weeks, rep3
|
knee articular cartilage
|
surgery: Sham
time after surgery: 2 weeks
|
Gene expression data from knee articular cartilage chondrocytes 2 weeks after Sham surgery
|
| Sample_geo_accession | GSM1037289
| | Sample_status | Public on Nov 15 2012
| | Sample_submission_date | Nov 14 2012
| | Sample_last_update_date | Nov 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See surgical description above and in Appleton, CT et al, 2007, Arthritis Res Ther 9:R13
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cartilage from knee joints was homogenized in TRIzol and subsequently extracted from the aqueous phase using QIAgen RNA isolation columns (RNeasy Mini Kit), subjected to quantification using Nanodrop system (Thermo Scientific) and quality assessment using 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | Raw expression data files were imported into GeneSpring 7.2 software (Silicon Genetics, Redwood City, CA) and underwent GC-RMA pre-processing. Raw data processing included transformation (values < 0.01 were set to 0.01), per-chip normalization (to 50th percentile), and per-gene normalization (to median values). Probes demonstrating reliable signal were identified using the GeneSpring 7.2 SG1a-1 signal intensity quality control script and fold-change filtering was performed on these lists.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Tom,,Appleton
| | Sample_contact_email | cappleto@uwo.ca
| | Sample_contact_laboratory | Frank Beier
| | Sample_contact_department | Physiology & Pharmacology
| | Sample_contact_institute | The University of Western Ontario
| | Sample_contact_address | Rm 0061 DSB The University of Western Ontario
| | Sample_contact_city | London
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | N6A5C1
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1037nnn/GSM1037289/suppl/GSM1037289.CEL.gz
| | Sample_series_id | GSE42295
| | Sample_data_row_count | 31099
| | |
|
GSM1037290 | GPL1355 |
|
Cartilage, OA, 8 weeks, rep1
|
knee articular cartilage
|
surgery: OA
time after surgery: 8 weeks
|
Gene expression data from knee articular cartilage chondrocytes 8 weeks after induction of OA
|
| Sample_geo_accession | GSM1037290
| | Sample_status | Public on Nov 15 2012
| | Sample_submission_date | Nov 14 2012
| | Sample_last_update_date | Nov 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See surgical description above and in Appleton, CT et al, 2007, Arthritis Res Ther 9:R13
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cartilage from knee joints was homogenized in TRIzol and subsequently extracted from the aqueous phase using QIAgen RNA isolation columns (RNeasy Mini Kit), subjected to quantification using Nanodrop system (Thermo Scientific) and quality assessment using 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | Raw expression data files were imported into GeneSpring 7.2 software (Silicon Genetics, Redwood City, CA) and underwent GC-RMA pre-processing. Raw data processing included transformation (values < 0.01 were set to 0.01), per-chip normalization (to 50th percentile), and per-gene normalization (to median values). Probes demonstrating reliable signal were identified using the GeneSpring 7.2 SG1a-1 signal intensity quality control script and fold-change filtering was performed on these lists.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Tom,,Appleton
| | Sample_contact_email | cappleto@uwo.ca
| | Sample_contact_laboratory | Frank Beier
| | Sample_contact_department | Physiology & Pharmacology
| | Sample_contact_institute | The University of Western Ontario
| | Sample_contact_address | Rm 0061 DSB The University of Western Ontario
| | Sample_contact_city | London
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | N6A5C1
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1037nnn/GSM1037290/suppl/GSM1037290.CEL.gz
| | Sample_series_id | GSE42295
| | Sample_data_row_count | 31099
| | |
|
GSM1037291 | GPL1355 |
|
Cartilage, OA, 8 weeks, rep2
|
knee articular cartilage
|
surgery: OA
time after surgery: 8 weeks
|
Gene expression data from knee articular cartilage chondrocytes 8 weeks after induction of OA
|
| Sample_geo_accession | GSM1037291
| | Sample_status | Public on Nov 15 2012
| | Sample_submission_date | Nov 14 2012
| | Sample_last_update_date | Nov 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See surgical description above and in Appleton, CT et al, 2007, Arthritis Res Ther 9:R13
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cartilage from knee joints was homogenized in TRIzol and subsequently extracted from the aqueous phase using QIAgen RNA isolation columns (RNeasy Mini Kit), subjected to quantification using Nanodrop system (Thermo Scientific) and quality assessment using 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | Raw expression data files were imported into GeneSpring 7.2 software (Silicon Genetics, Redwood City, CA) and underwent GC-RMA pre-processing. Raw data processing included transformation (values < 0.01 were set to 0.01), per-chip normalization (to 50th percentile), and per-gene normalization (to median values). Probes demonstrating reliable signal were identified using the GeneSpring 7.2 SG1a-1 signal intensity quality control script and fold-change filtering was performed on these lists.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Tom,,Appleton
| | Sample_contact_email | cappleto@uwo.ca
| | Sample_contact_laboratory | Frank Beier
| | Sample_contact_department | Physiology & Pharmacology
| | Sample_contact_institute | The University of Western Ontario
| | Sample_contact_address | Rm 0061 DSB The University of Western Ontario
| | Sample_contact_city | London
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | N6A5C1
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1037nnn/GSM1037291/suppl/GSM1037291.CEL.gz
| | Sample_series_id | GSE42295
| | Sample_data_row_count | 31099
| | |
|
GSM1037292 | GPL1355 |
|
Cartilage, OA, 8 weeks, rep3
|
knee articular cartilage
|
surgery: OA
time after surgery: 8 weeks
|
Gene expression data from knee articular cartilage chondrocytes 8 weeks after induction of OA
|
| Sample_geo_accession | GSM1037292
| | Sample_status | Public on Nov 15 2012
| | Sample_submission_date | Nov 14 2012
| | Sample_last_update_date | Nov 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See surgical description above and in Appleton, CT et al, 2007, Arthritis Res Ther 9:R13
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cartilage from knee joints was homogenized in TRIzol and subsequently extracted from the aqueous phase using QIAgen RNA isolation columns (RNeasy Mini Kit), subjected to quantification using Nanodrop system (Thermo Scientific) and quality assessment using 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | Raw expression data files were imported into GeneSpring 7.2 software (Silicon Genetics, Redwood City, CA) and underwent GC-RMA pre-processing. Raw data processing included transformation (values < 0.01 were set to 0.01), per-chip normalization (to 50th percentile), and per-gene normalization (to median values). Probes demonstrating reliable signal were identified using the GeneSpring 7.2 SG1a-1 signal intensity quality control script and fold-change filtering was performed on these lists.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Tom,,Appleton
| | Sample_contact_email | cappleto@uwo.ca
| | Sample_contact_laboratory | Frank Beier
| | Sample_contact_department | Physiology & Pharmacology
| | Sample_contact_institute | The University of Western Ontario
| | Sample_contact_address | Rm 0061 DSB The University of Western Ontario
| | Sample_contact_city | London
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | N6A5C1
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1037nnn/GSM1037292/suppl/GSM1037292.CEL.gz
| | Sample_series_id | GSE42295
| | Sample_data_row_count | 31099
| | |
|
GSM1037293 | GPL1355 |
|
Cartilage, Sham, 8 weeks, rep1
|
knee articular cartilage
|
surgery: Sham
time after surgery: 8 weeks
|
Gene expression data from knee articular cartilage chondrocytes 8 weeks after Sham surgery
|
| Sample_geo_accession | GSM1037293
| | Sample_status | Public on Nov 15 2012
| | Sample_submission_date | Nov 14 2012
| | Sample_last_update_date | Nov 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See surgical description above and in Appleton, CT et al, 2007, Arthritis Res Ther 9:R13
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cartilage from knee joints was homogenized in TRIzol and subsequently extracted from the aqueous phase using QIAgen RNA isolation columns (RNeasy Mini Kit), subjected to quantification using Nanodrop system (Thermo Scientific) and quality assessment using 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | Raw expression data files were imported into GeneSpring 7.2 software (Silicon Genetics, Redwood City, CA) and underwent GC-RMA pre-processing. Raw data processing included transformation (values < 0.01 were set to 0.01), per-chip normalization (to 50th percentile), and per-gene normalization (to median values). Probes demonstrating reliable signal were identified using the GeneSpring 7.2 SG1a-1 signal intensity quality control script and fold-change filtering was performed on these lists.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Tom,,Appleton
| | Sample_contact_email | cappleto@uwo.ca
| | Sample_contact_laboratory | Frank Beier
| | Sample_contact_department | Physiology & Pharmacology
| | Sample_contact_institute | The University of Western Ontario
| | Sample_contact_address | Rm 0061 DSB The University of Western Ontario
| | Sample_contact_city | London
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | N6A5C1
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1037nnn/GSM1037293/suppl/GSM1037293.CEL.gz
| | Sample_series_id | GSE42295
| | Sample_data_row_count | 31099
| | |
|
GSM1037294 | GPL1355 |
|
Cartilage, Sham, 8 weeks, rep2
|
knee articular cartilage
|
surgery: Sham
time after surgery: 8 weeks
|
Gene expression data from knee articular cartilage chondrocytes 8 weeks after Sham surgery
|
| Sample_geo_accession | GSM1037294
| | Sample_status | Public on Nov 15 2012
| | Sample_submission_date | Nov 14 2012
| | Sample_last_update_date | Nov 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See surgical description above and in Appleton, CT et al, 2007, Arthritis Res Ther 9:R13
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cartilage from knee joints was homogenized in TRIzol and subsequently extracted from the aqueous phase using QIAgen RNA isolation columns (RNeasy Mini Kit), subjected to quantification using Nanodrop system (Thermo Scientific) and quality assessment using 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | Raw expression data files were imported into GeneSpring 7.2 software (Silicon Genetics, Redwood City, CA) and underwent GC-RMA pre-processing. Raw data processing included transformation (values < 0.01 were set to 0.01), per-chip normalization (to 50th percentile), and per-gene normalization (to median values). Probes demonstrating reliable signal were identified using the GeneSpring 7.2 SG1a-1 signal intensity quality control script and fold-change filtering was performed on these lists.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Tom,,Appleton
| | Sample_contact_email | cappleto@uwo.ca
| | Sample_contact_laboratory | Frank Beier
| | Sample_contact_department | Physiology & Pharmacology
| | Sample_contact_institute | The University of Western Ontario
| | Sample_contact_address | Rm 0061 DSB The University of Western Ontario
| | Sample_contact_city | London
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | N6A5C1
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1037nnn/GSM1037294/suppl/GSM1037294.CEL.gz
| | Sample_series_id | GSE42295
| | Sample_data_row_count | 31099
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GSM1037295 | GPL1355 |
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Cartilage, Sham, 8 weeks, rep3
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knee articular cartilage
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surgery: Sham
time after surgery: 8 weeks
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Gene expression data from knee articular cartilage chondrocytes 8 weeks after Sham surgery
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| Sample_geo_accession | GSM1037295
| | Sample_status | Public on Nov 15 2012
| | Sample_submission_date | Nov 14 2012
| | Sample_last_update_date | Nov 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | See surgical description above and in Appleton, CT et al, 2007, Arthritis Res Ther 9:R13
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cartilage from knee joints was homogenized in TRIzol and subsequently extracted from the aqueous phase using QIAgen RNA isolation columns (RNeasy Mini Kit), subjected to quantification using Nanodrop system (Thermo Scientific) and quality assessment using 2100 Bioanalyzer (Agilent).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix protocol
| | Sample_hyb_protocol | Affymetrix protocol
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | Raw expression data files were imported into GeneSpring 7.2 software (Silicon Genetics, Redwood City, CA) and underwent GC-RMA pre-processing. Raw data processing included transformation (values < 0.01 were set to 0.01), per-chip normalization (to 50th percentile), and per-gene normalization (to median values). Probes demonstrating reliable signal were identified using the GeneSpring 7.2 SG1a-1 signal intensity quality control script and fold-change filtering was performed on these lists.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Tom,,Appleton
| | Sample_contact_email | cappleto@uwo.ca
| | Sample_contact_laboratory | Frank Beier
| | Sample_contact_department | Physiology & Pharmacology
| | Sample_contact_institute | The University of Western Ontario
| | Sample_contact_address | Rm 0061 DSB The University of Western Ontario
| | Sample_contact_city | London
| | Sample_contact_state | ON
| | Sample_contact_zip/postal_code | N6A5C1
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1037nnn/GSM1037295/suppl/GSM1037295.CEL.gz
| | Sample_series_id | GSE42295
| | Sample_data_row_count | 31099
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