Search results for the GEO ID: GSE37191  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM913332 | GPL1261 |
|
WT mouse dura mater, EAE, technical replicate 1
|
WT mouse, experimental autoimmune encephalomyelitis, dura mater
|
background strain: WBB6F1/J
genotype/variation: wild type
tissue: dura mater
disease status: day 6 experimental autoimmune encephalomyelitis
|
Gene expression data from WT mouse dura mater with experimental autoimmune encephalomyelitis
|
| Sample_geo_accession | GSM913332
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Apr 11 2012
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were immunized subcutaneously with 100 μg MOG35-55 peptide emulsified in 5mg/mL CFA (Incomplete Freund’s Adjuvant with dessicated M. Tuberculosis H37 RA, VWR). On Days 0 and 2, animals received i.p. injections of 250 ng pertussis toxin (List Biologicals.) Immunized WT and Kit W/Wv mice were sacrificed on Day 6 post-immunization and perfused with PBS as were naïve littermate PBS control mice. The dura mater was immediately removed from the calvarium of the skull and pooled (10 mice/group).
| | Sample_growth_protocol_ch1 | Female KitW/Wv mice (WBB6F1/J-KitW/KitW-v) and littermate controls were purchased from Jackson Laboratories at 3-5 weeks of age and housed in the barrier facility at Northwestern University. HDC-/- mice were originally generated by Dr. Hiroshi Ohtsu (Tohoku University) and were the kind gift of Dr. Paul Bryce (206 BAS). All experiments were approved by the Northwestern University Animal Care Committee and all mice were housed in an Association for Assessment and Accreditation of Laboratory Animal Care–approved facility.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the dura mater using SV Total RNA Isolation System (Promega).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix 900432) and cRNA was synthesized, labeled, fragmented and hybridized to The GeneChip Mouse Genome 430 2.0 Array in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA)
| | Sample_scan_protocol | After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner
| | Sample_data_processing | Image data were analyzed with Affymetrix Expression Console™ software and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The mean fold change was calculated from the 3 independent technical replicates for each of the four experimental conditions (12 arrays total) and assessed by a non-parametric rank product test. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R (http://www.r-product.org/).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM913nnn/GSM913332/suppl/GSM913332_WT_day6EAE_4_090604_MelB.CEL.gz
| | Sample_series_id | GSE37191
| | Sample_data_row_count | 45101
| | |
|
GSM913333 | GPL1261 |
|
WT mouse dura mater, EAE, technical replicate 2
|
WT mouse, experimental autoimmune encephalomyelitis, dura mater
|
background strain: WBB6F1/J
genotype/variation: wild type
tissue: dura mater
disease status: day 6 experimental autoimmune encephalomyelitis
|
Gene expression data from WT mouse dura mater with experimental autoimmune encephalomyelitis
|
| Sample_geo_accession | GSM913333
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Apr 11 2012
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were immunized subcutaneously with 100 μg MOG35-55 peptide emulsified in 5mg/mL CFA (Incomplete Freund’s Adjuvant with dessicated M. Tuberculosis H37 RA, VWR). On Days 0 and 2, animals received i.p. injections of 250 ng pertussis toxin (List Biologicals.) Immunized WT and Kit W/Wv mice were sacrificed on Day 6 post-immunization and perfused with PBS as were naïve littermate PBS control mice. The dura mater was immediately removed from the calvarium of the skull and pooled (10 mice/group).
| | Sample_growth_protocol_ch1 | Female KitW/Wv mice (WBB6F1/J-KitW/KitW-v) and littermate controls were purchased from Jackson Laboratories at 3-5 weeks of age and housed in the barrier facility at Northwestern University. HDC-/- mice were originally generated by Dr. Hiroshi Ohtsu (Tohoku University) and were the kind gift of Dr. Paul Bryce (206 BAS). All experiments were approved by the Northwestern University Animal Care Committee and all mice were housed in an Association for Assessment and Accreditation of Laboratory Animal Care–approved facility.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the dura mater using SV Total RNA Isolation System (Promega).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix 900432) and cRNA was synthesized, labeled, fragmented and hybridized to The GeneChip Mouse Genome 430 2.0 Array in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA)
| | Sample_scan_protocol | After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner
| | Sample_data_processing | Image data were analyzed with Affymetrix Expression Console™ software and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The mean fold change was calculated from the 3 independent technical replicates for each of the four experimental conditions (12 arrays total) and assessed by a non-parametric rank product test. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R (http://www.r-product.org/).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM913nnn/GSM913333/suppl/GSM913333_WT_day6EAE_5_090604_MelB.CEL.gz
| | Sample_series_id | GSE37191
| | Sample_data_row_count | 45101
| | |
|
GSM913334 | GPL1261 |
|
WT mouse dura mater, EAE, technical replicate 3
|
WT mouse, experimental autoimmune encephalomyelitis, dura mater
|
background strain: WBB6F1/J
genotype/variation: wild type
tissue: dura mater
disease status: day 6 experimental autoimmune encephalomyelitis
|
Gene expression data from WT mouse dura mater with experimental autoimmune encephalomyelitis
|
| Sample_geo_accession | GSM913334
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Apr 11 2012
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were immunized subcutaneously with 100 μg MOG35-55 peptide emulsified in 5mg/mL CFA (Incomplete Freund’s Adjuvant with dessicated M. Tuberculosis H37 RA, VWR). On Days 0 and 2, animals received i.p. injections of 250 ng pertussis toxin (List Biologicals.) Immunized WT and Kit W/Wv mice were sacrificed on Day 6 post-immunization and perfused with PBS as were naïve littermate PBS control mice. The dura mater was immediately removed from the calvarium of the skull and pooled (10 mice/group).
| | Sample_growth_protocol_ch1 | Female KitW/Wv mice (WBB6F1/J-KitW/KitW-v) and littermate controls were purchased from Jackson Laboratories at 3-5 weeks of age and housed in the barrier facility at Northwestern University. HDC-/- mice were originally generated by Dr. Hiroshi Ohtsu (Tohoku University) and were the kind gift of Dr. Paul Bryce (206 BAS). All experiments were approved by the Northwestern University Animal Care Committee and all mice were housed in an Association for Assessment and Accreditation of Laboratory Animal Care–approved facility.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the dura mater using SV Total RNA Isolation System (Promega).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix 900432) and cRNA was synthesized, labeled, fragmented and hybridized to The GeneChip Mouse Genome 430 2.0 Array in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA)
| | Sample_scan_protocol | After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner
| | Sample_data_processing | Image data were analyzed with Affymetrix Expression Console™ software and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The mean fold change was calculated from the 3 independent technical replicates for each of the four experimental conditions (12 arrays total) and assessed by a non-parametric rank product test. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R (http://www.r-product.org/).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM913nnn/GSM913334/suppl/GSM913334_WT_day6EAE_6_090604_MelB.CEL.gz
| | Sample_series_id | GSE37191
| | Sample_data_row_count | 45101
| | |
|
GSM913335 | GPL1261 |
|
WT mouse dura mater, naïve control, technical replicate 1
|
WT mouse, naïve control, dura mater
|
background strain: WBB6F1/J
genotype/variation: wild type
tissue: dura mater
disease status: control
|
Gene expression data from WT mouse dura mater treated as a naïve control
|
| Sample_geo_accession | GSM913335
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Apr 11 2012
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were immunized subcutaneously with 100 μg MOG35-55 peptide emulsified in 5mg/mL CFA (Incomplete Freund’s Adjuvant with dessicated M. Tuberculosis H37 RA, VWR). On Days 0 and 2, animals received i.p. injections of 250 ng pertussis toxin (List Biologicals.) Immunized WT and Kit W/Wv mice were sacrificed on Day 6 post-immunization and perfused with PBS as were naïve littermate PBS control mice. The dura mater was immediately removed from the calvarium of the skull and pooled (10 mice/group).
| | Sample_growth_protocol_ch1 | Female KitW/Wv mice (WBB6F1/J-KitW/KitW-v) and littermate controls were purchased from Jackson Laboratories at 3-5 weeks of age and housed in the barrier facility at Northwestern University. HDC-/- mice were originally generated by Dr. Hiroshi Ohtsu (Tohoku University) and were the kind gift of Dr. Paul Bryce (206 BAS). All experiments were approved by the Northwestern University Animal Care Committee and all mice were housed in an Association for Assessment and Accreditation of Laboratory Animal Care–approved facility.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the dura mater using SV Total RNA Isolation System (Promega).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix 900432) and cRNA was synthesized, labeled, fragmented and hybridized to The GeneChip Mouse Genome 430 2.0 Array in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA)
| | Sample_scan_protocol | After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner
| | Sample_data_processing | Image data were analyzed with Affymetrix Expression Console™ software and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The mean fold change was calculated from the 3 independent technical replicates for each of the four experimental conditions (12 arrays total) and assessed by a non-parametric rank product test. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R (http://www.r-product.org/).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM913nnn/GSM913335/suppl/GSM913335_WT_naive_1_090604_MelB.CEL.gz
| | Sample_series_id | GSE37191
| | Sample_data_row_count | 45101
| | |
|
GSM913336 | GPL1261 |
|
WT mouse dura mater, naïve control, technical replicate 2
|
WT mouse, naïve control, dura mater
|
background strain: WBB6F1/J
genotype/variation: wild type
tissue: dura mater
disease status: control
|
Gene expression data from WT mouse dura mater treated as a naïve control
|
| Sample_geo_accession | GSM913336
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Apr 11 2012
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were immunized subcutaneously with 100 μg MOG35-55 peptide emulsified in 5mg/mL CFA (Incomplete Freund’s Adjuvant with dessicated M. Tuberculosis H37 RA, VWR). On Days 0 and 2, animals received i.p. injections of 250 ng pertussis toxin (List Biologicals.) Immunized WT and Kit W/Wv mice were sacrificed on Day 6 post-immunization and perfused with PBS as were naïve littermate PBS control mice. The dura mater was immediately removed from the calvarium of the skull and pooled (10 mice/group).
| | Sample_growth_protocol_ch1 | Female KitW/Wv mice (WBB6F1/J-KitW/KitW-v) and littermate controls were purchased from Jackson Laboratories at 3-5 weeks of age and housed in the barrier facility at Northwestern University. HDC-/- mice were originally generated by Dr. Hiroshi Ohtsu (Tohoku University) and were the kind gift of Dr. Paul Bryce (206 BAS). All experiments were approved by the Northwestern University Animal Care Committee and all mice were housed in an Association for Assessment and Accreditation of Laboratory Animal Care–approved facility.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the dura mater using SV Total RNA Isolation System (Promega).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix 900432) and cRNA was synthesized, labeled, fragmented and hybridized to The GeneChip Mouse Genome 430 2.0 Array in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA)
| | Sample_scan_protocol | After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner
| | Sample_data_processing | Image data were analyzed with Affymetrix Expression Console™ software and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The mean fold change was calculated from the 3 independent technical replicates for each of the four experimental conditions (12 arrays total) and assessed by a non-parametric rank product test. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R (http://www.r-product.org/).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM913nnn/GSM913336/suppl/GSM913336_WT_naive_2_090604_MelB.CEL.gz
| | Sample_series_id | GSE37191
| | Sample_data_row_count | 45101
| | |
|
GSM913337 | GPL1261 |
|
WT mouse dura mater, naïve control, technical replicate 3
|
WT mouse, naïve control, dura mater
|
background strain: WBB6F1/J
genotype/variation: wild type
tissue: dura mater
disease status: control
|
Gene expression data from WT mouse dura mater treated as a naïve control
|
| Sample_geo_accession | GSM913337
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Apr 11 2012
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were immunized subcutaneously with 100 μg MOG35-55 peptide emulsified in 5mg/mL CFA (Incomplete Freund’s Adjuvant with dessicated M. Tuberculosis H37 RA, VWR). On Days 0 and 2, animals received i.p. injections of 250 ng pertussis toxin (List Biologicals.) Immunized WT and Kit W/Wv mice were sacrificed on Day 6 post-immunization and perfused with PBS as were naïve littermate PBS control mice. The dura mater was immediately removed from the calvarium of the skull and pooled (10 mice/group).
| | Sample_growth_protocol_ch1 | Female KitW/Wv mice (WBB6F1/J-KitW/KitW-v) and littermate controls were purchased from Jackson Laboratories at 3-5 weeks of age and housed in the barrier facility at Northwestern University. HDC-/- mice were originally generated by Dr. Hiroshi Ohtsu (Tohoku University) and were the kind gift of Dr. Paul Bryce (206 BAS). All experiments were approved by the Northwestern University Animal Care Committee and all mice were housed in an Association for Assessment and Accreditation of Laboratory Animal Care–approved facility.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the dura mater using SV Total RNA Isolation System (Promega).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix 900432) and cRNA was synthesized, labeled, fragmented and hybridized to The GeneChip Mouse Genome 430 2.0 Array in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA)
| | Sample_scan_protocol | After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner
| | Sample_data_processing | Image data were analyzed with Affymetrix Expression Console™ software and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The mean fold change was calculated from the 3 independent technical replicates for each of the four experimental conditions (12 arrays total) and assessed by a non-parametric rank product test. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R (http://www.r-product.org/).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM913nnn/GSM913337/suppl/GSM913337_WT_naive_3_090604_MelB.CEL.gz
| | Sample_series_id | GSE37191
| | Sample_data_row_count | 45101
| | |
|
GSM913338 | GPL1261 |
|
Kit W/Wv mouse dura mater, EAE, technical replicate 1
|
Kit W/Wv mouse, experimental autoimmune encephalomyelitis, dura mater
|
background strain: WBB6F1/J
genotype/variation: KitW/Wv mice (WBB6F1/J-KitW/KitW-v)
tissue: dura mater
disease status: day 6 experimental autoimmune encephalomyelitis
|
Gene expression data from Kit W/Wv mouse dura mater with experimental autoimmune encephalomyelitis
|
| Sample_geo_accession | GSM913338
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Apr 11 2012
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were immunized subcutaneously with 100 μg MOG35-55 peptide emulsified in 5mg/mL CFA (Incomplete Freund’s Adjuvant with dessicated M. Tuberculosis H37 RA, VWR). On Days 0 and 2, animals received i.p. injections of 250 ng pertussis toxin (List Biologicals.) Immunized WT and Kit W/Wv mice were sacrificed on Day 6 post-immunization and perfused with PBS as were naïve littermate PBS control mice. The dura mater was immediately removed from the calvarium of the skull and pooled (10 mice/group).
| | Sample_growth_protocol_ch1 | Female KitW/Wv mice (WBB6F1/J-KitW/KitW-v) and littermate controls were purchased from Jackson Laboratories at 3-5 weeks of age and housed in the barrier facility at Northwestern University. HDC-/- mice were originally generated by Dr. Hiroshi Ohtsu (Tohoku University) and were the kind gift of Dr. Paul Bryce (206 BAS). All experiments were approved by the Northwestern University Animal Care Committee and all mice were housed in an Association for Assessment and Accreditation of Laboratory Animal Care–approved facility.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the dura mater using SV Total RNA Isolation System (Promega).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix 900432) and cRNA was synthesized, labeled, fragmented and hybridized to The GeneChip Mouse Genome 430 2.0 Array in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA)
| | Sample_scan_protocol | After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner
| | Sample_data_processing | Image data were analyzed with Affymetrix Expression Console™ software and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The mean fold change was calculated from the 3 independent technical replicates for each of the four experimental conditions (12 arrays total) and assessed by a non-parametric rank product test. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R (http://www.r-product.org/).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM913nnn/GSM913338/suppl/GSM913338_Wwv_day6EAE_10_090604_MelB.CEL.gz
| | Sample_series_id | GSE37191
| | Sample_data_row_count | 45101
| | |
|
GSM913339 | GPL1261 |
|
Kit W/Wv mouse dura mater, EAE, technical replicate 2
|
Kit W/Wv mouse, experimental autoimmune encephalomyelitis, dura mater
|
background strain: WBB6F1/J
genotype/variation: KitW/Wv mice (WBB6F1/J-KitW/KitW-v)
tissue: dura mater
disease status: day 6 experimental autoimmune encephalomyelitis
|
Gene expression data from Kit W/Wv mouse dura mater with experimental autoimmune encephalomyelitis
|
| Sample_geo_accession | GSM913339
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Apr 11 2012
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were immunized subcutaneously with 100 μg MOG35-55 peptide emulsified in 5mg/mL CFA (Incomplete Freund’s Adjuvant with dessicated M. Tuberculosis H37 RA, VWR). On Days 0 and 2, animals received i.p. injections of 250 ng pertussis toxin (List Biologicals.) Immunized WT and Kit W/Wv mice were sacrificed on Day 6 post-immunization and perfused with PBS as were naïve littermate PBS control mice. The dura mater was immediately removed from the calvarium of the skull and pooled (10 mice/group).
| | Sample_growth_protocol_ch1 | Female KitW/Wv mice (WBB6F1/J-KitW/KitW-v) and littermate controls were purchased from Jackson Laboratories at 3-5 weeks of age and housed in the barrier facility at Northwestern University. HDC-/- mice were originally generated by Dr. Hiroshi Ohtsu (Tohoku University) and were the kind gift of Dr. Paul Bryce (206 BAS). All experiments were approved by the Northwestern University Animal Care Committee and all mice were housed in an Association for Assessment and Accreditation of Laboratory Animal Care–approved facility.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the dura mater using SV Total RNA Isolation System (Promega).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix 900432) and cRNA was synthesized, labeled, fragmented and hybridized to The GeneChip Mouse Genome 430 2.0 Array in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA)
| | Sample_scan_protocol | After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner
| | Sample_data_processing | Image data were analyzed with Affymetrix Expression Console™ software and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The mean fold change was calculated from the 3 independent technical replicates for each of the four experimental conditions (12 arrays total) and assessed by a non-parametric rank product test. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R (http://www.r-product.org/).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM913nnn/GSM913339/suppl/GSM913339_Wwv_day6EAE_11_090604_MelB.CEL.gz
| | Sample_series_id | GSE37191
| | Sample_data_row_count | 45101
| | |
|
GSM913340 | GPL1261 |
|
Kit W/Wv mouse dura mater, EAE, technical replicate 3
|
Kit W/Wv mouse, experimental autoimmune encephalomyelitis, dura mater
|
background strain: WBB6F1/J
genotype/variation: KitW/Wv mice (WBB6F1/J-KitW/KitW-v)
tissue: dura mater
disease status: day 6 experimental autoimmune encephalomyelitis
|
Gene expression data from Kit W/Wv mouse dura mater with experimental autoimmune encephalomyelitis
|
| Sample_geo_accession | GSM913340
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Apr 11 2012
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were immunized subcutaneously with 100 μg MOG35-55 peptide emulsified in 5mg/mL CFA (Incomplete Freund’s Adjuvant with dessicated M. Tuberculosis H37 RA, VWR). On Days 0 and 2, animals received i.p. injections of 250 ng pertussis toxin (List Biologicals.) Immunized WT and Kit W/Wv mice were sacrificed on Day 6 post-immunization and perfused with PBS as were naïve littermate PBS control mice. The dura mater was immediately removed from the calvarium of the skull and pooled (10 mice/group).
| | Sample_growth_protocol_ch1 | Female KitW/Wv mice (WBB6F1/J-KitW/KitW-v) and littermate controls were purchased from Jackson Laboratories at 3-5 weeks of age and housed in the barrier facility at Northwestern University. HDC-/- mice were originally generated by Dr. Hiroshi Ohtsu (Tohoku University) and were the kind gift of Dr. Paul Bryce (206 BAS). All experiments were approved by the Northwestern University Animal Care Committee and all mice were housed in an Association for Assessment and Accreditation of Laboratory Animal Care–approved facility.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the dura mater using SV Total RNA Isolation System (Promega).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix 900432) and cRNA was synthesized, labeled, fragmented and hybridized to The GeneChip Mouse Genome 430 2.0 Array in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA)
| | Sample_scan_protocol | After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner
| | Sample_data_processing | Image data were analyzed with Affymetrix Expression Console™ software and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The mean fold change was calculated from the 3 independent technical replicates for each of the four experimental conditions (12 arrays total) and assessed by a non-parametric rank product test. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R (http://www.r-product.org/).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM913nnn/GSM913340/suppl/GSM913340_Wwv_day6EAE_12_090604_MelB.CEL.gz
| | Sample_series_id | GSE37191
| | Sample_data_row_count | 45101
| | |
|
GSM913341 | GPL1261 |
|
Kit W/Wv mouse dura mater, naïve control, technical replicate 1
|
Kit W/Wv mouse, naïve control, dura mater
|
background strain: WBB6F1/J
genotype/variation: KitW/Wv mice (WBB6F1/J-KitW/KitW-v)
tissue: dura mater
disease status: control
|
Gene expression data from Kit W/Wv mouse dura mater treated as a naïve control
|
| Sample_geo_accession | GSM913341
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Apr 11 2012
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were immunized subcutaneously with 100 μg MOG35-55 peptide emulsified in 5mg/mL CFA (Incomplete Freund’s Adjuvant with dessicated M. Tuberculosis H37 RA, VWR). On Days 0 and 2, animals received i.p. injections of 250 ng pertussis toxin (List Biologicals.) Immunized WT and Kit W/Wv mice were sacrificed on Day 6 post-immunization and perfused with PBS as were naïve littermate PBS control mice. The dura mater was immediately removed from the calvarium of the skull and pooled (10 mice/group).
| | Sample_growth_protocol_ch1 | Female KitW/Wv mice (WBB6F1/J-KitW/KitW-v) and littermate controls were purchased from Jackson Laboratories at 3-5 weeks of age and housed in the barrier facility at Northwestern University. HDC-/- mice were originally generated by Dr. Hiroshi Ohtsu (Tohoku University) and were the kind gift of Dr. Paul Bryce (206 BAS). All experiments were approved by the Northwestern University Animal Care Committee and all mice were housed in an Association for Assessment and Accreditation of Laboratory Animal Care–approved facility.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the dura mater using SV Total RNA Isolation System (Promega).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix 900432) and cRNA was synthesized, labeled, fragmented and hybridized to The GeneChip Mouse Genome 430 2.0 Array in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA)
| | Sample_scan_protocol | After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner
| | Sample_data_processing | Image data were analyzed with Affymetrix Expression Console™ software and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The mean fold change was calculated from the 3 independent technical replicates for each of the four experimental conditions (12 arrays total) and assessed by a non-parametric rank product test. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R (http://www.r-product.org/).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM913nnn/GSM913341/suppl/GSM913341_Wwv_naive_7_090604_MelB.CEL.gz
| | Sample_series_id | GSE37191
| | Sample_data_row_count | 45101
| | |
|
GSM913342 | GPL1261 |
|
Kit W/Wv mouse dura mater, naïve control, technical replicate 2
|
Kit W/Wv mouse, naïve control, dura mater
|
background strain: WBB6F1/J
genotype/variation: KitW/Wv mice (WBB6F1/J-KitW/KitW-v)
tissue: dura mater
disease status: control
|
Gene expression data from Kit W/Wv mouse dura mater treated as a naïve control
|
| Sample_geo_accession | GSM913342
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Apr 11 2012
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were immunized subcutaneously with 100 μg MOG35-55 peptide emulsified in 5mg/mL CFA (Incomplete Freund’s Adjuvant with dessicated M. Tuberculosis H37 RA, VWR). On Days 0 and 2, animals received i.p. injections of 250 ng pertussis toxin (List Biologicals.) Immunized WT and Kit W/Wv mice were sacrificed on Day 6 post-immunization and perfused with PBS as were naïve littermate PBS control mice. The dura mater was immediately removed from the calvarium of the skull and pooled (10 mice/group).
| | Sample_growth_protocol_ch1 | Female KitW/Wv mice (WBB6F1/J-KitW/KitW-v) and littermate controls were purchased from Jackson Laboratories at 3-5 weeks of age and housed in the barrier facility at Northwestern University. HDC-/- mice were originally generated by Dr. Hiroshi Ohtsu (Tohoku University) and were the kind gift of Dr. Paul Bryce (206 BAS). All experiments were approved by the Northwestern University Animal Care Committee and all mice were housed in an Association for Assessment and Accreditation of Laboratory Animal Care–approved facility.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the dura mater using SV Total RNA Isolation System (Promega).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix 900432) and cRNA was synthesized, labeled, fragmented and hybridized to The GeneChip Mouse Genome 430 2.0 Array in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA)
| | Sample_scan_protocol | After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner
| | Sample_data_processing | Image data were analyzed with Affymetrix Expression Console™ software and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The mean fold change was calculated from the 3 independent technical replicates for each of the four experimental conditions (12 arrays total) and assessed by a non-parametric rank product test. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R (http://www.r-product.org/).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM913nnn/GSM913342/suppl/GSM913342_Wwv_naive_8_090604_MelB.CEL.gz
| | Sample_series_id | GSE37191
| | Sample_data_row_count | 45101
| | |
|
GSM913343 | GPL1261 |
|
Kit W/Wv mouse dura mater, naïve control, technical replicate 3
|
Kit W/Wv mouse, naïve control, dura mater
|
background strain: WBB6F1/J
genotype/variation: KitW/Wv mice (WBB6F1/J-KitW/KitW-v)
tissue: dura mater
disease status: control
|
Gene expression data from Kit W/Wv mouse dura mater treated as a naïve control
|
| Sample_geo_accession | GSM913343
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Apr 11 2012
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Mice were immunized subcutaneously with 100 μg MOG35-55 peptide emulsified in 5mg/mL CFA (Incomplete Freund’s Adjuvant with dessicated M. Tuberculosis H37 RA, VWR). On Days 0 and 2, animals received i.p. injections of 250 ng pertussis toxin (List Biologicals.) Immunized WT and Kit W/Wv mice were sacrificed on Day 6 post-immunization and perfused with PBS as were naïve littermate PBS control mice. The dura mater was immediately removed from the calvarium of the skull and pooled (10 mice/group).
| | Sample_growth_protocol_ch1 | Female KitW/Wv mice (WBB6F1/J-KitW/KitW-v) and littermate controls were purchased from Jackson Laboratories at 3-5 weeks of age and housed in the barrier facility at Northwestern University. HDC-/- mice were originally generated by Dr. Hiroshi Ohtsu (Tohoku University) and were the kind gift of Dr. Paul Bryce (206 BAS). All experiments were approved by the Northwestern University Animal Care Committee and all mice were housed in an Association for Assessment and Accreditation of Laboratory Animal Care–approved facility.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated from the dura mater using SV Total RNA Isolation System (Promega).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix 900432) and cRNA was synthesized, labeled, fragmented and hybridized to The GeneChip Mouse Genome 430 2.0 Array in accordance to standard Affymetrix protocols (Affymetrix, Santa Clara, CA)
| | Sample_scan_protocol | After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner
| | Sample_data_processing | Image data were analyzed with Affymetrix Expression Console™ software and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The mean fold change was calculated from the 3 independent technical replicates for each of the four experimental conditions (12 arrays total) and assessed by a non-parametric rank product test. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R (http://www.r-product.org/).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM913nnn/GSM913343/suppl/GSM913343_Wwv_naive_9_090604_MelB.CEL.gz
| | Sample_series_id | GSE37191
| | Sample_data_row_count | 45101
| | |
|
| |
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