Search results for the GEO ID: GSE13148  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM329261 | GPL1261 |
|
spleen, old, arthritic, biological replicate 1
|
spleen, old, arthritic, biological replicate 1
|
Strain: BALB/c
Gender: female
Age: 9-month-old
Arthritic
|
spleen, old, arthritic, biological replicate 1
|
| Sample_geo_accession | GSM329261
| | Sample_status | Public on Oct 09 2009
| | Sample_submission_date | Oct 10 2008
| | Sample_last_update_date | Oct 10 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Spleens were harvested at the end of the experiment. 50 mg pieces were used for RNA preparation.
| | Sample_growth_protocol_ch1 | Siblings of 1 to 11 months of age were immunized i.p. with an emulsion of cartilage PG (100 µg protein) and 2 mg dimethyldioctadecyl-ammonium bromide (DDA) adjuvant on days 0, 21 and 42 (Glant,T.T. and Mikecz,K., Proteoglycan aggrecan-induced arthritis. A murine autoimmune model of rheumatoid arthritis. Methods Mol.Med. 2004. 102: 313-338.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with TriReagent (Sigma) according to the manufacturers instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to standard Affymetrix recommended protocols from 2 to 5 ug total RNA (Affymetrix Expression Analysis Technical Manual, P/N 702232 Rev.2).
| | Sample_hyb_protocol | Following fragmentation, 15ug of labeled cRNA were hybridized according to standard Affymetrix protocols on Affymetrix GeneChip ‘Mouse Genome 430 2.0’ arrays using ‘GeneChip Fluidics Station 450’.
| | Sample_scan_protocol | Affymetrix GeneChip arrays were scanned according to standard Affymetrix protocols on an ‘Affymetrix GeneChip Scanner 3000 7G’. Each array was analyzed for the following quality metrics: total background, raw noise(Q), average signal present, signal intensity of species-specific house-keeping genes, 3’/5’ signal ratio of house-keeping genes, relative signal intensities of labeling controls, and absolute signal intensities of hybridization controls.
| | Sample_data_processing | Data was analyzed in ‘S-Plus’ 6.2 statistical package with the ‘S+ArrayAnalyzer’ v2.0.1 (TIBCO Software Inc.). Data was summarized using the Robust Multi-array Average (RMA) (Irizarry, 2003) and normalized by quantiles. Statistical significance of differential expression between sample types was determined using Local Pooled Error (LPE) test (Thatte, 2003). Statistacal test p-values were corrected for False Discovery Rate (FDR) by Benjamini-Hochberg (BH) procedure. Differentially expressed transcripts were annotated according to the most current revision of data in Affymetrix’s ‘NetAffx Analysis Center’.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tibor,T,Glant
| | Sample_contact_email | Tibor_Glant@rush.edu, Katalin_Mikecz@rush.edu
| | Sample_contact_laboratory | Molecular Medicine
| | Sample_contact_department | Orthopedic Surgery
| | Sample_contact_institute | Rush University Medical Center
| | Sample_contact_address | 1735 West Harrison
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60612
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM329nnn/GSM329261/suppl/GSM329261.CEL.gz
| | Sample_series_id | GSE13148
| | Sample_data_row_count | 45101
| | |
|
GSM329262 | GPL1261 |
|
spleen, old, arthritic, biological replicate 2
|
spleen, old, arthritic, biological replicate 2
|
Strain: BALB/c
Gender: female
Age: 9-month-old
Arthritic
|
spleen, old, arthritic, biological replicate 2
|
| Sample_geo_accession | GSM329262
| | Sample_status | Public on Oct 09 2009
| | Sample_submission_date | Oct 10 2008
| | Sample_last_update_date | Oct 10 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Spleens were harvested at the end of the experiment. 50 mg pieces were used for RNA preparation.
| | Sample_growth_protocol_ch1 | Siblings of 1 to 11 months of age were immunized i.p. with an emulsion of cartilage PG (100 µg protein) and 2 mg dimethyldioctadecyl-ammonium bromide (DDA) adjuvant on days 0, 21 and 42 (Glant,T.T. and Mikecz,K., Proteoglycan aggrecan-induced arthritis. A murine autoimmune model of rheumatoid arthritis. Methods Mol.Med. 2004. 102: 313-338.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with TriReagent (Sigma) according to the manufacturers instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to standard Affymetrix recommended protocols from 2 to 5 ug total RNA (Affymetrix Expression Analysis Technical Manual, P/N 702232 Rev.2).
| | Sample_hyb_protocol | Following fragmentation, 15ug of labeled cRNA were hybridized according to standard Affymetrix protocols on Affymetrix GeneChip ‘Mouse Genome 430 2.0’ arrays using ‘GeneChip Fluidics Station 450’.
| | Sample_scan_protocol | Affymetrix GeneChip arrays were scanned according to standard Affymetrix protocols on an ‘Affymetrix GeneChip Scanner 3000 7G’. Each array was analyzed for the following quality metrics: total background, raw noise(Q), average signal present, signal intensity of species-specific house-keeping genes, 3’/5’ signal ratio of house-keeping genes, relative signal intensities of labeling controls, and absolute signal intensities of hybridization controls.
| | Sample_data_processing | Data was analyzed in ‘S-Plus’ 6.2 statistical package with the ‘S+ArrayAnalyzer’ v2.0.1 (TIBCO Software Inc.). Data was summarized using the Robust Multi-array Average (RMA) (Irizarry, 2003) and normalized by quantiles. Statistical significance of differential expression between sample types was determined using Local Pooled Error (LPE) test (Thatte, 2003). Statistacal test p-values were corrected for False Discovery Rate (FDR) by Benjamini-Hochberg (BH) procedure. Differentially expressed transcripts were annotated according to the most current revision of data in Affymetrix’s ‘NetAffx Analysis Center’.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tibor,T,Glant
| | Sample_contact_email | Tibor_Glant@rush.edu, Katalin_Mikecz@rush.edu
| | Sample_contact_laboratory | Molecular Medicine
| | Sample_contact_department | Orthopedic Surgery
| | Sample_contact_institute | Rush University Medical Center
| | Sample_contact_address | 1735 West Harrison
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60612
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM329nnn/GSM329262/suppl/GSM329262.CEL.gz
| | Sample_series_id | GSE13148
| | Sample_data_row_count | 45101
| | |
|
GSM329263 | GPL1261 |
|
spleen, old, non-arthritic, biological replicate 1
|
spleen, old, non-arthritic, biological replicate 1
|
Strain: BALB/c
Gender: female
Age: 7-month-old
Non-arthritic
|
spleen, old, non-arthritic, biological replicate 1
|
| Sample_geo_accession | GSM329263
| | Sample_status | Public on Oct 09 2009
| | Sample_submission_date | Oct 10 2008
| | Sample_last_update_date | Oct 10 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Spleens were harvested at the end of the experiment. 50 mg pieces were used for RNA preparation.
| | Sample_growth_protocol_ch1 | Siblings of 1 to 11 months of age were immunized i.p. with an emulsion of cartilage PG (100 µg protein) and 2 mg dimethyldioctadecyl-ammonium bromide (DDA) adjuvant on days 0, 21 and 42 (Glant,T.T. and Mikecz,K., Proteoglycan aggrecan-induced arthritis. A murine autoimmune model of rheumatoid arthritis. Methods Mol.Med. 2004. 102: 313-338.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with TriReagent (Sigma) according to the manufacturers instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to standard Affymetrix recommended protocols from 2 to 5 ug total RNA (Affymetrix Expression Analysis Technical Manual, P/N 702232 Rev.2).
| | Sample_hyb_protocol | Following fragmentation, 15ug of labeled cRNA were hybridized according to standard Affymetrix protocols on Affymetrix GeneChip ‘Mouse Genome 430 2.0’ arrays using ‘GeneChip Fluidics Station 450’.
| | Sample_scan_protocol | Affymetrix GeneChip arrays were scanned according to standard Affymetrix protocols on an ‘Affymetrix GeneChip Scanner 3000 7G’. Each array was analyzed for the following quality metrics: total background, raw noise(Q), average signal present, signal intensity of species-specific house-keeping genes, 3’/5’ signal ratio of house-keeping genes, relative signal intensities of labeling controls, and absolute signal intensities of hybridization controls.
| | Sample_data_processing | Data was analyzed in ‘S-Plus’ 6.2 statistical package with the ‘S+ArrayAnalyzer’ v2.0.1 (TIBCO Software Inc.). Data was summarized using the Robust Multi-array Average (RMA) (Irizarry, 2003) and normalized by quantiles. Statistical significance of differential expression between sample types was determined using Local Pooled Error (LPE) test (Thatte, 2003). Statistacal test p-values were corrected for False Discovery Rate (FDR) by Benjamini-Hochberg (BH) procedure. Differentially expressed transcripts were annotated according to the most current revision of data in Affymetrix’s ‘NetAffx Analysis Center’.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tibor,T,Glant
| | Sample_contact_email | Tibor_Glant@rush.edu, Katalin_Mikecz@rush.edu
| | Sample_contact_laboratory | Molecular Medicine
| | Sample_contact_department | Orthopedic Surgery
| | Sample_contact_institute | Rush University Medical Center
| | Sample_contact_address | 1735 West Harrison
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60612
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM329nnn/GSM329263/suppl/GSM329263.CEL.gz
| | Sample_series_id | GSE13148
| | Sample_data_row_count | 45101
| | |
|
GSM329264 | GPL1261 |
|
spleen, old, non-arthritic, biological replicate 2
|
spleen, old, non-arthritic, biological replicate 2
|
Strain: BALB/c
Gender: female
Age: 5-month-old
Non-arthritic
|
spleen, old, non-arthritic, biological replicate 2
|
| Sample_geo_accession | GSM329264
| | Sample_status | Public on Oct 09 2009
| | Sample_submission_date | Oct 10 2008
| | Sample_last_update_date | Oct 10 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Spleens were harvested at the end of the experiment. 50 mg pieces were used for RNA preparation.
| | Sample_growth_protocol_ch1 | Siblings of 1 to 11 months of age were immunized i.p. with an emulsion of cartilage PG (100 µg protein) and 2 mg dimethyldioctadecyl-ammonium bromide (DDA) adjuvant on days 0, 21 and 42 (Glant,T.T. and Mikecz,K., Proteoglycan aggrecan-induced arthritis. A murine autoimmune model of rheumatoid arthritis. Methods Mol.Med. 2004. 102: 313-338.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with TriReagent (Sigma) according to the manufacturers instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to standard Affymetrix recommended protocols from 2 to 5 ug total RNA (Affymetrix Expression Analysis Technical Manual, P/N 702232 Rev.2).
| | Sample_hyb_protocol | Following fragmentation, 15ug of labeled cRNA were hybridized according to standard Affymetrix protocols on Affymetrix GeneChip ‘Mouse Genome 430 2.0’ arrays using ‘GeneChip Fluidics Station 450’.
| | Sample_scan_protocol | Affymetrix GeneChip arrays were scanned according to standard Affymetrix protocols on an ‘Affymetrix GeneChip Scanner 3000 7G’. Each array was analyzed for the following quality metrics: total background, raw noise(Q), average signal present, signal intensity of species-specific house-keeping genes, 3’/5’ signal ratio of house-keeping genes, relative signal intensities of labeling controls, and absolute signal intensities of hybridization controls.
| | Sample_data_processing | Data was analyzed in ‘S-Plus’ 6.2 statistical package with the ‘S+ArrayAnalyzer’ v2.0.1 (TIBCO Software Inc.). Data was summarized using the Robust Multi-array Average (RMA) (Irizarry, 2003) and normalized by quantiles. Statistical significance of differential expression between sample types was determined using Local Pooled Error (LPE) test (Thatte, 2003). Statistacal test p-values were corrected for False Discovery Rate (FDR) by Benjamini-Hochberg (BH) procedure. Differentially expressed transcripts were annotated according to the most current revision of data in Affymetrix’s ‘NetAffx Analysis Center’.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tibor,T,Glant
| | Sample_contact_email | Tibor_Glant@rush.edu, Katalin_Mikecz@rush.edu
| | Sample_contact_laboratory | Molecular Medicine
| | Sample_contact_department | Orthopedic Surgery
| | Sample_contact_institute | Rush University Medical Center
| | Sample_contact_address | 1735 West Harrison
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60612
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM329nnn/GSM329264/suppl/GSM329264.CEL.gz
| | Sample_series_id | GSE13148
| | Sample_data_row_count | 45101
| | |
|
GSM329265 | GPL1261 |
|
spleen, young, arthritic, biological replicate 1
|
spleen, young, arthritic, biological replicate 1
|
Strain: BALB/c
Gender: female
Age: 5-month-old
Arthritic
|
spleen, young, arthritic, biological replicate 1
|
| Sample_geo_accession | GSM329265
| | Sample_status | Public on Oct 09 2009
| | Sample_submission_date | Oct 10 2008
| | Sample_last_update_date | Oct 10 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Spleens were harvested at the end of the experiment. 50 mg pieces were used for RNA preparation.
| | Sample_growth_protocol_ch1 | Siblings of 1 to 11 months of age were immunized i.p. with an emulsion of cartilage PG (100 µg protein) and 2 mg dimethyldioctadecyl-ammonium bromide (DDA) adjuvant on days 0, 21 and 42 (Glant,T.T. and Mikecz,K., Proteoglycan aggrecan-induced arthritis. A murine autoimmune model of rheumatoid arthritis. Methods Mol.Med. 2004. 102: 313-338.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with TriReagent (Sigma) according to the manufacturers instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to standard Affymetrix recommended protocols from 2 to 5 ug total RNA (Affymetrix Expression Analysis Technical Manual, P/N 702232 Rev.2).
| | Sample_hyb_protocol | Following fragmentation, 15ug of labeled cRNA were hybridized according to standard Affymetrix protocols on Affymetrix GeneChip ‘Mouse Genome 430 2.0’ arrays using ‘GeneChip Fluidics Station 450’.
| | Sample_scan_protocol | Affymetrix GeneChip arrays were scanned according to standard Affymetrix protocols on an ‘Affymetrix GeneChip Scanner 3000 7G’. Each array was analyzed for the following quality metrics: total background, raw noise(Q), average signal present, signal intensity of species-specific house-keeping genes, 3’/5’ signal ratio of house-keeping genes, relative signal intensities of labeling controls, and absolute signal intensities of hybridization controls.
| | Sample_data_processing | Data was analyzed in ‘S-Plus’ 6.2 statistical package with the ‘S+ArrayAnalyzer’ v2.0.1 (TIBCO Software Inc.). Data was summarized using the Robust Multi-array Average (RMA) (Irizarry, 2003) and normalized by quantiles. Statistical significance of differential expression between sample types was determined using Local Pooled Error (LPE) test (Thatte, 2003). Statistacal test p-values were corrected for False Discovery Rate (FDR) by Benjamini-Hochberg (BH) procedure. Differentially expressed transcripts were annotated according to the most current revision of data in Affymetrix’s ‘NetAffx Analysis Center’.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tibor,T,Glant
| | Sample_contact_email | Tibor_Glant@rush.edu, Katalin_Mikecz@rush.edu
| | Sample_contact_laboratory | Molecular Medicine
| | Sample_contact_department | Orthopedic Surgery
| | Sample_contact_institute | Rush University Medical Center
| | Sample_contact_address | 1735 West Harrison
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60612
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM329nnn/GSM329265/suppl/GSM329265.CEL.gz
| | Sample_series_id | GSE13148
| | Sample_data_row_count | 45101
| | |
|
GSM329266 | GPL1261 |
|
spleen, young, arthritic, biological replicate 2
|
spleen, young, arthritic, biological replicate 2
|
Strain: BALB/c
Gender: female
Age: 4-month-old
Arthritic
|
spleen, young, arthritic, biological replicate 2
|
| Sample_geo_accession | GSM329266
| | Sample_status | Public on Oct 09 2009
| | Sample_submission_date | Oct 10 2008
| | Sample_last_update_date | Oct 10 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Spleens were harvested at the end of the experiment. 50 mg pieces were used for RNA preparation.
| | Sample_growth_protocol_ch1 | Siblings of 1 to 11 months of age were immunized i.p. with an emulsion of cartilage PG (100 µg protein) and 2 mg dimethyldioctadecyl-ammonium bromide (DDA) adjuvant on days 0, 21 and 42 (Glant,T.T. and Mikecz,K., Proteoglycan aggrecan-induced arthritis. A murine autoimmune model of rheumatoid arthritis. Methods Mol.Med. 2004. 102: 313-338.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with TriReagent (Sigma) according to the manufacturers instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to standard Affymetrix recommended protocols from 2 to 5 ug total RNA (Affymetrix Expression Analysis Technical Manual, P/N 702232 Rev.2).
| | Sample_hyb_protocol | Following fragmentation, 15ug of labeled cRNA were hybridized according to standard Affymetrix protocols on Affymetrix GeneChip ‘Mouse Genome 430 2.0’ arrays using ‘GeneChip Fluidics Station 450’.
| | Sample_scan_protocol | Affymetrix GeneChip arrays were scanned according to standard Affymetrix protocols on an ‘Affymetrix GeneChip Scanner 3000 7G’. Each array was analyzed for the following quality metrics: total background, raw noise(Q), average signal present, signal intensity of species-specific house-keeping genes, 3’/5’ signal ratio of house-keeping genes, relative signal intensities of labeling controls, and absolute signal intensities of hybridization controls.
| | Sample_data_processing | Data was analyzed in ‘S-Plus’ 6.2 statistical package with the ‘S+ArrayAnalyzer’ v2.0.1 (TIBCO Software Inc.). Data was summarized using the Robust Multi-array Average (RMA) (Irizarry, 2003) and normalized by quantiles. Statistical significance of differential expression between sample types was determined using Local Pooled Error (LPE) test (Thatte, 2003). Statistacal test p-values were corrected for False Discovery Rate (FDR) by Benjamini-Hochberg (BH) procedure. Differentially expressed transcripts were annotated according to the most current revision of data in Affymetrix’s ‘NetAffx Analysis Center’.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tibor,T,Glant
| | Sample_contact_email | Tibor_Glant@rush.edu, Katalin_Mikecz@rush.edu
| | Sample_contact_laboratory | Molecular Medicine
| | Sample_contact_department | Orthopedic Surgery
| | Sample_contact_institute | Rush University Medical Center
| | Sample_contact_address | 1735 West Harrison
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60612
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM329nnn/GSM329266/suppl/GSM329266.CEL.gz
| | Sample_series_id | GSE13148
| | Sample_data_row_count | 45101
| | |
|
GSM329267 | GPL1261 |
|
spleen, young, non-arthritic, biological replicate 1
|
spleen, young, non-arthritic, biological replicate 1
|
Strain: BALB/c
Gender: female
Age: 3-month-old
Non-arthritic
|
spleen, young, non-arthritic, biological replicate 1
|
| Sample_geo_accession | GSM329267
| | Sample_status | Public on Oct 09 2009
| | Sample_submission_date | Oct 10 2008
| | Sample_last_update_date | Oct 10 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Spleens were harvested at the end of the experiment. 50 mg pieces were used for RNA preparation.
| | Sample_growth_protocol_ch1 | Siblings of 1 to 11 months of age were immunized i.p. with an emulsion of cartilage PG (100 µg protein) and 2 mg dimethyldioctadecyl-ammonium bromide (DDA) adjuvant on days 0, 21 and 42 (Glant,T.T. and Mikecz,K., Proteoglycan aggrecan-induced arthritis. A murine autoimmune model of rheumatoid arthritis. Methods Mol.Med. 2004. 102: 313-338.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with TriReagent (Sigma) according to the manufacturers instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to standard Affymetrix recommended protocols from 2 to 5 ug total RNA (Affymetrix Expression Analysis Technical Manual, P/N 702232 Rev.2).
| | Sample_hyb_protocol | Following fragmentation, 15ug of labeled cRNA were hybridized according to standard Affymetrix protocols on Affymetrix GeneChip ‘Mouse Genome 430 2.0’ arrays using ‘GeneChip Fluidics Station 450’.
| | Sample_scan_protocol | Affymetrix GeneChip arrays were scanned according to standard Affymetrix protocols on an ‘Affymetrix GeneChip Scanner 3000 7G’. Each array was analyzed for the following quality metrics: total background, raw noise(Q), average signal present, signal intensity of species-specific house-keeping genes, 3’/5’ signal ratio of house-keeping genes, relative signal intensities of labeling controls, and absolute signal intensities of hybridization controls.
| | Sample_data_processing | Data was analyzed in ‘S-Plus’ 6.2 statistical package with the ‘S+ArrayAnalyzer’ v2.0.1 (TIBCO Software Inc.). Data was summarized using the Robust Multi-array Average (RMA) (Irizarry, 2003) and normalized by quantiles. Statistical significance of differential expression between sample types was determined using Local Pooled Error (LPE) test (Thatte, 2003). Statistacal test p-values were corrected for False Discovery Rate (FDR) by Benjamini-Hochberg (BH) procedure. Differentially expressed transcripts were annotated according to the most current revision of data in Affymetrix’s ‘NetAffx Analysis Center’.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tibor,T,Glant
| | Sample_contact_email | Tibor_Glant@rush.edu, Katalin_Mikecz@rush.edu
| | Sample_contact_laboratory | Molecular Medicine
| | Sample_contact_department | Orthopedic Surgery
| | Sample_contact_institute | Rush University Medical Center
| | Sample_contact_address | 1735 West Harrison
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60612
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM329nnn/GSM329267/suppl/GSM329267.CEL.gz
| | Sample_series_id | GSE13148
| | Sample_data_row_count | 45101
| | |
|
GSM329268 | GPL1261 |
|
spleen, young, non-arthritic, biological replicate 2
|
spleen, young, non-arthritic, biological replicate 2
|
Strain: BALB/c
Gender: female
Age: 3-month-old
Non-arthritic
|
spleen, young, non-arthritic, biological replicate 2
|
| Sample_geo_accession | GSM329268
| | Sample_status | Public on Oct 09 2009
| | Sample_submission_date | Oct 10 2008
| | Sample_last_update_date | Oct 10 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Spleens were harvested at the end of the experiment. 50 mg pieces were used for RNA preparation.
| | Sample_growth_protocol_ch1 | Siblings of 1 to 11 months of age were immunized i.p. with an emulsion of cartilage PG (100 µg protein) and 2 mg dimethyldioctadecyl-ammonium bromide (DDA) adjuvant on days 0, 21 and 42 (Glant,T.T. and Mikecz,K., Proteoglycan aggrecan-induced arthritis. A murine autoimmune model of rheumatoid arthritis. Methods Mol.Med. 2004. 102: 313-338.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with TriReagent (Sigma) according to the manufacturers instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to standard Affymetrix recommended protocols from 2 to 5 ug total RNA (Affymetrix Expression Analysis Technical Manual, P/N 702232 Rev.2).
| | Sample_hyb_protocol | Following fragmentation, 15ug of labeled cRNA were hybridized according to standard Affymetrix protocols on Affymetrix GeneChip ‘Mouse Genome 430 2.0’ arrays using ‘GeneChip Fluidics Station 450’.
| | Sample_scan_protocol | Affymetrix GeneChip arrays were scanned according to standard Affymetrix protocols on an ‘Affymetrix GeneChip Scanner 3000 7G’. Each array was analyzed for the following quality metrics: total background, raw noise(Q), average signal present, signal intensity of species-specific house-keeping genes, 3’/5’ signal ratio of house-keeping genes, relative signal intensities of labeling controls, and absolute signal intensities of hybridization controls.
| | Sample_data_processing | Data was analyzed in ‘S-Plus’ 6.2 statistical package with the ‘S+ArrayAnalyzer’ v2.0.1 (TIBCO Software Inc.). Data was summarized using the Robust Multi-array Average (RMA) (Irizarry, 2003) and normalized by quantiles. Statistical significance of differential expression between sample types was determined using Local Pooled Error (LPE) test (Thatte, 2003). Statistacal test p-values were corrected for False Discovery Rate (FDR) by Benjamini-Hochberg (BH) procedure. Differentially expressed transcripts were annotated according to the most current revision of data in Affymetrix’s ‘NetAffx Analysis Center’.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tibor,T,Glant
| | Sample_contact_email | Tibor_Glant@rush.edu, Katalin_Mikecz@rush.edu
| | Sample_contact_laboratory | Molecular Medicine
| | Sample_contact_department | Orthopedic Surgery
| | Sample_contact_institute | Rush University Medical Center
| | Sample_contact_address | 1735 West Harrison
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60612
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM329nnn/GSM329268/suppl/GSM329268.CEL.gz
| | Sample_series_id | GSE13148
| | Sample_data_row_count | 45101
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GSM329269 | GPL1261 |
|
spleen, young, non-arthritic, biological replicate 3
|
spleen, young, non-arthritic, biological replicate 3
|
Strain: BALB/c
Gender: female
Age: 2-month-old
Non-arthritic
|
spleen, young, non-arthritic, biological replicate 3
|
| Sample_geo_accession | GSM329269
| | Sample_status | Public on Oct 09 2009
| | Sample_submission_date | Oct 10 2008
| | Sample_last_update_date | Oct 10 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Spleens were harvested at the end of the experiment. 50 mg pieces were used for RNA preparation.
| | Sample_growth_protocol_ch1 | Siblings of 1 to 11 months of age were immunized i.p. with an emulsion of cartilage PG (100 µg protein) and 2 mg dimethyldioctadecyl-ammonium bromide (DDA) adjuvant on days 0, 21 and 42 (Glant,T.T. and Mikecz,K., Proteoglycan aggrecan-induced arthritis. A murine autoimmune model of rheumatoid arthritis. Methods Mol.Med. 2004. 102: 313-338.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with TriReagent (Sigma) according to the manufacturers instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to standard Affymetrix recommended protocols from 2 to 5 ug total RNA (Affymetrix Expression Analysis Technical Manual, P/N 702232 Rev.2).
| | Sample_hyb_protocol | Following fragmentation, 15ug of labeled cRNA were hybridized according to standard Affymetrix protocols on Affymetrix GeneChip ‘Mouse Genome 430 2.0’ arrays using ‘GeneChip Fluidics Station 450’.
| | Sample_scan_protocol | Affymetrix GeneChip arrays were scanned according to standard Affymetrix protocols on an ‘Affymetrix GeneChip Scanner 3000 7G’. Each array was analyzed for the following quality metrics: total background, raw noise(Q), average signal present, signal intensity of species-specific house-keeping genes, 3’/5’ signal ratio of house-keeping genes, relative signal intensities of labeling controls, and absolute signal intensities of hybridization controls.
| | Sample_data_processing | Data was analyzed in ‘S-Plus’ 6.2 statistical package with the ‘S+ArrayAnalyzer’ v2.0.1 (TIBCO Software Inc.). Data was summarized using the Robust Multi-array Average (RMA) (Irizarry, 2003) and normalized by quantiles. Statistical significance of differential expression between sample types was determined using Local Pooled Error (LPE) test (Thatte, 2003). Statistacal test p-values were corrected for False Discovery Rate (FDR) by Benjamini-Hochberg (BH) procedure. Differentially expressed transcripts were annotated according to the most current revision of data in Affymetrix’s ‘NetAffx Analysis Center’.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tibor,T,Glant
| | Sample_contact_email | Tibor_Glant@rush.edu, Katalin_Mikecz@rush.edu
| | Sample_contact_laboratory | Molecular Medicine
| | Sample_contact_department | Orthopedic Surgery
| | Sample_contact_institute | Rush University Medical Center
| | Sample_contact_address | 1735 West Harrison
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60612
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM329nnn/GSM329269/suppl/GSM329269.CEL.gz
| | Sample_series_id | GSE13148
| | Sample_data_row_count | 45101
| | |
|
GSM329270 | GPL1261 |
|
spleen, young, non-arthritic, biological replicate 4
|
spleen, young, non-arthritic, biological replicate 4
|
Strain: BALB/c
Gender: female
Age: 1-month-old
Non-arthritic
|
spleen, young, non-arthritic, biological replicate 4
|
| Sample_geo_accession | GSM329270
| | Sample_status | Public on Oct 09 2009
| | Sample_submission_date | Oct 10 2008
| | Sample_last_update_date | Oct 10 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Spleens were harvested at the end of the experiment. 50 mg pieces were used for RNA preparation.
| | Sample_growth_protocol_ch1 | Siblings of 1 to 11 months of age were immunized i.p. with an emulsion of cartilage PG (100 µg protein) and 2 mg dimethyldioctadecyl-ammonium bromide (DDA) adjuvant on days 0, 21 and 42 (Glant,T.T. and Mikecz,K., Proteoglycan aggrecan-induced arthritis. A murine autoimmune model of rheumatoid arthritis. Methods Mol.Med. 2004. 102: 313-338.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated with TriReagent (Sigma) according to the manufacturers instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to standard Affymetrix recommended protocols from 2 to 5 ug total RNA (Affymetrix Expression Analysis Technical Manual, P/N 702232 Rev.2).
| | Sample_hyb_protocol | Following fragmentation, 15ug of labeled cRNA were hybridized according to standard Affymetrix protocols on Affymetrix GeneChip ‘Mouse Genome 430 2.0’ arrays using ‘GeneChip Fluidics Station 450’.
| | Sample_scan_protocol | Affymetrix GeneChip arrays were scanned according to standard Affymetrix protocols on an ‘Affymetrix GeneChip Scanner 3000 7G’. Each array was analyzed for the following quality metrics: total background, raw noise(Q), average signal present, signal intensity of species-specific house-keeping genes, 3’/5’ signal ratio of house-keeping genes, relative signal intensities of labeling controls, and absolute signal intensities of hybridization controls.
| | Sample_data_processing | Data was analyzed in ‘S-Plus’ 6.2 statistical package with the ‘S+ArrayAnalyzer’ v2.0.1 (TIBCO Software Inc.). Data was summarized using the Robust Multi-array Average (RMA) (Irizarry, 2003) and normalized by quantiles. Statistical significance of differential expression between sample types was determined using Local Pooled Error (LPE) test (Thatte, 2003). Statistacal test p-values were corrected for False Discovery Rate (FDR) by Benjamini-Hochberg (BH) procedure. Differentially expressed transcripts were annotated according to the most current revision of data in Affymetrix’s ‘NetAffx Analysis Center’.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Tibor,T,Glant
| | Sample_contact_email | Tibor_Glant@rush.edu, Katalin_Mikecz@rush.edu
| | Sample_contact_laboratory | Molecular Medicine
| | Sample_contact_department | Orthopedic Surgery
| | Sample_contact_institute | Rush University Medical Center
| | Sample_contact_address | 1735 West Harrison
| | Sample_contact_city | Chicago
| | Sample_contact_state | IL
| | Sample_contact_zip/postal_code | 60612
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM329nnn/GSM329270/suppl/GSM329270.CEL.gz
| | Sample_series_id | GSE13148
| | Sample_data_row_count | 45101
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