Search results for the GEO ID: GSE14903  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM372275 | GPL1355 |
|
Rat_prefrontal_cortex-rep1-expt2
|
Rat Prefrontal cortex, individual #1
|
gender: Male
strain: Lewis
tissue: prefrontal cortex
weight: 200-250g
light cycle: 800-2000h
startle: 394.1333333
locomotion: 17044.87
plus maze: 12.1
sugar feeding: 1.95
ppi: 6.799729364
|
experiment 2
|
| Sample_geo_accession | GSM372275
| | Sample_status | Public on Nov 24 2009
| | Sample_submission_date | Feb 19 2009
| | Sample_last_update_date | Feb 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | No treatments applied
| | Sample_growth_protocol_ch1 | Experiment 1: 20 male Lewis rats (200-250g, Charles River, Montreal, Canada) underwent three behavioural tests: SF, locomotion, and ASR. Experiment 2: 40 male Lewis rats (200-250g, Charles River) underwent four behaviour tests: SF, locomotion, ASR, and PPI. Rats were acclimated one week before testing, singly housed in clear Plexiglas cages with food and water ad libitum, except as described during the SF test. Light cycle was from 0800-2000h, temperature at 21°C +/-1°C. Testing occurred between 0900-1700h. Procedures were approved by the Department of Zoology animal care committee, and conformed to ethical standards of the University of Toronto and the Canadian Council on Animal Care.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed in a random order by decapitation 12 days (Experiment 1) and 6 days after the last testing day (Experiment 2). Brains were removed, and PFC dissected: Fr1and Fr2 anterior to Bregma +4.0mm without olfactory bulb, snap frozen on dry ice and stored at -80°C until RNA extraction. 30-35mg of PFC was added to a pre-chilled cuvette containing 600μl Trizol (Invitrogen, Carlsbad, CA) and mechanically homogenized. The homogenate was then centrifuged at 14,000rpm for 10min, 4°C. Chloroform (VWR International, Mississauga, ON) was added to the supernatant (20% v/v Trizol), shaken and incubated 15s at 21°C, then centrifuged at 14,000rpm for 15min at 4°C. RNA was precipitated by adding an equal volume of 70% ethanol at room temperature then vortexed. The Absolutely RNeasy® RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) was used to purify precipitated RNA, and RNA was eluted then concentrated to 1.2μg/μl using the Microcron YM-10 centrifugal filter device kit (Millipore Corp., Bedford, MA). RNA quality assurance was obtained via the Agilent BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA) or NanoDrop ND-8000 (Wilmington, DE) spectrophotometer, verifying the 18s and 28s ribosomal RNA bands. Quality assurance was conducted at the Centre for Applied Genomics TCAG facilities at the Hospital for Sick Children (Toronto, ON, Canada) before preparation for microarray hybridization at the same facility.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).
| | Sample_hyb_protocol | Hybridization was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).
| | Sample_scan_protocol | Array images were captured with the Agilent 2500 scanner using the Affymetrix Microarray Suite software (v5.0).
| | Sample_data_processing | Data were loaded into the R statistical environment (v2.6.2) using the affy pacakge (v1.16.0) of the BioConductor open-source library. Arrays were tested for spatial and distributional heterogeneity; none were excluded. Pre-processing employed the GCRNA algorithm, as implemented in the gcrma package of BioConductor (v2.10.0).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Paul,C,Boutros
| | Sample_contact_email | Paul.Boutros@utoronto.ca
| | Sample_contact_institute | Ontario Institute for Cancer Research
| | Sample_contact_address | 101 College Street, Suite 800
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G 0A3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM372nnn/GSM372275/suppl/GSM372275.CEL.gz
| | Sample_series_id | GSE14903
| | Sample_series_id | GSE14904
| | Sample_data_row_count | 31099
| | |
|
GSM372276 | GPL1355 |
|
Rat_prefrontal_cortex-rep2-expt2
|
Rat Prefrontal cortex, individual #2
|
gender: Male
strain: Lewis
tissue: prefrontal cortex
weight: 200-250g
light cycle: 800-2000h
startle: 362.5333333
locomotion: 13933.46
plus maze: 0
sugar feeding: 1.65
ppi: 10.73924237
|
experiment 2
|
| Sample_geo_accession | GSM372276
| | Sample_status | Public on Nov 24 2009
| | Sample_submission_date | Feb 19 2009
| | Sample_last_update_date | Feb 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | No treatments applied
| | Sample_growth_protocol_ch1 | Experiment 1: 20 male Lewis rats (200-250g, Charles River, Montreal, Canada) underwent three behavioural tests: SF, locomotion, and ASR. Experiment 2: 40 male Lewis rats (200-250g, Charles River) underwent four behaviour tests: SF, locomotion, ASR, and PPI. Rats were acclimated one week before testing, singly housed in clear Plexiglas cages with food and water ad libitum, except as described during the SF test. Light cycle was from 0800-2000h, temperature at 21°C +/-1°C. Testing occurred between 0900-1700h. Procedures were approved by the Department of Zoology animal care committee, and conformed to ethical standards of the University of Toronto and the Canadian Council on Animal Care.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed in a random order by decapitation 12 days (Experiment 1) and 6 days after the last testing day (Experiment 2). Brains were removed, and PFC dissected: Fr1and Fr2 anterior to Bregma +4.0mm without olfactory bulb, snap frozen on dry ice and stored at -80°C until RNA extraction. 30-35mg of PFC was added to a pre-chilled cuvette containing 600μl Trizol (Invitrogen, Carlsbad, CA) and mechanically homogenized. The homogenate was then centrifuged at 14,000rpm for 10min, 4°C. Chloroform (VWR International, Mississauga, ON) was added to the supernatant (20% v/v Trizol), shaken and incubated 15s at 21°C, then centrifuged at 14,000rpm for 15min at 4°C. RNA was precipitated by adding an equal volume of 70% ethanol at room temperature then vortexed. The Absolutely RNeasy® RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) was used to purify precipitated RNA, and RNA was eluted then concentrated to 1.2μg/μl using the Microcron YM-10 centrifugal filter device kit (Millipore Corp., Bedford, MA). RNA quality assurance was obtained via the Agilent BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA) or NanoDrop ND-8000 (Wilmington, DE) spectrophotometer, verifying the 18s and 28s ribosomal RNA bands. Quality assurance was conducted at the Centre for Applied Genomics TCAG facilities at the Hospital for Sick Children (Toronto, ON, Canada) before preparation for microarray hybridization at the same facility.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).
| | Sample_hyb_protocol | Hybridization was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).
| | Sample_scan_protocol | Array images were captured with the Agilent 2500 scanner using the Affymetrix Microarray Suite software (v5.0).
| | Sample_data_processing | Data were loaded into the R statistical environment (v2.6.2) using the affy pacakge (v1.16.0) of the BioConductor open-source library. Arrays were tested for spatial and distributional heterogeneity; none were excluded. Pre-processing employed the GCRNA algorithm, as implemented in the gcrma package of BioConductor (v2.10.0).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Paul,C,Boutros
| | Sample_contact_email | Paul.Boutros@utoronto.ca
| | Sample_contact_institute | Ontario Institute for Cancer Research
| | Sample_contact_address | 101 College Street, Suite 800
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G 0A3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM372nnn/GSM372276/suppl/GSM372276.CEL.gz
| | Sample_series_id | GSE14903
| | Sample_series_id | GSE14904
| | Sample_data_row_count | 31099
| | |
|
GSM372277 | GPL1355 |
|
Rat_prefrontal_cortex-rep3-expt2
|
Rat Prefrontal cortex, individual #3
|
gender: Male
strain: Lewis
tissue: prefrontal cortex
weight: 200-250g
light cycle: 800-2000h
startle: 687.2
locomotion: 12984.58
plus maze: NA
sugar feeding: 2
ppi: 18.38377959
|
experiment 2
|
| Sample_geo_accession | GSM372277
| | Sample_status | Public on Nov 24 2009
| | Sample_submission_date | Feb 19 2009
| | Sample_last_update_date | Feb 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | No treatments applied
| | Sample_growth_protocol_ch1 | Experiment 1: 20 male Lewis rats (200-250g, Charles River, Montreal, Canada) underwent three behavioural tests: SF, locomotion, and ASR. Experiment 2: 40 male Lewis rats (200-250g, Charles River) underwent four behaviour tests: SF, locomotion, ASR, and PPI. Rats were acclimated one week before testing, singly housed in clear Plexiglas cages with food and water ad libitum, except as described during the SF test. Light cycle was from 0800-2000h, temperature at 21°C +/-1°C. Testing occurred between 0900-1700h. Procedures were approved by the Department of Zoology animal care committee, and conformed to ethical standards of the University of Toronto and the Canadian Council on Animal Care.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed in a random order by decapitation 12 days (Experiment 1) and 6 days after the last testing day (Experiment 2). Brains were removed, and PFC dissected: Fr1and Fr2 anterior to Bregma +4.0mm without olfactory bulb, snap frozen on dry ice and stored at -80°C until RNA extraction. 30-35mg of PFC was added to a pre-chilled cuvette containing 600μl Trizol (Invitrogen, Carlsbad, CA) and mechanically homogenized. The homogenate was then centrifuged at 14,000rpm for 10min, 4°C. Chloroform (VWR International, Mississauga, ON) was added to the supernatant (20% v/v Trizol), shaken and incubated 15s at 21°C, then centrifuged at 14,000rpm for 15min at 4°C. RNA was precipitated by adding an equal volume of 70% ethanol at room temperature then vortexed. The Absolutely RNeasy® RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) was used to purify precipitated RNA, and RNA was eluted then concentrated to 1.2μg/μl using the Microcron YM-10 centrifugal filter device kit (Millipore Corp., Bedford, MA). RNA quality assurance was obtained via the Agilent BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA) or NanoDrop ND-8000 (Wilmington, DE) spectrophotometer, verifying the 18s and 28s ribosomal RNA bands. Quality assurance was conducted at the Centre for Applied Genomics TCAG facilities at the Hospital for Sick Children (Toronto, ON, Canada) before preparation for microarray hybridization at the same facility.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).
| | Sample_hyb_protocol | Hybridization was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).
| | Sample_scan_protocol | Array images were captured with the Agilent 2500 scanner using the Affymetrix Microarray Suite software (v5.0).
| | Sample_data_processing | Data were loaded into the R statistical environment (v2.6.2) using the affy pacakge (v1.16.0) of the BioConductor open-source library. Arrays were tested for spatial and distributional heterogeneity; none were excluded. Pre-processing employed the GCRNA algorithm, as implemented in the gcrma package of BioConductor (v2.10.0).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Paul,C,Boutros
| | Sample_contact_email | Paul.Boutros@utoronto.ca
| | Sample_contact_institute | Ontario Institute for Cancer Research
| | Sample_contact_address | 101 College Street, Suite 800
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G 0A3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM372nnn/GSM372277/suppl/GSM372277.CEL.gz
| | Sample_series_id | GSE14903
| | Sample_series_id | GSE14904
| | Sample_data_row_count | 31099
| | |
|
GSM372278 | GPL1355 |
|
Rat_prefrontal_cortex-rep4-expt2
|
Rat Prefrontal cortex, individual #4
|
gender: Male
strain: Lewis
tissue: prefrontal cortex
weight: 200-250g
light cycle: 800-2000h
startle: 510.1333333
locomotion: 17987.06
plus maze: 20.2
sugar feeding: 1.5
ppi: 42.52483011
|
experiment 2
|
| Sample_geo_accession | GSM372278
| | Sample_status | Public on Nov 24 2009
| | Sample_submission_date | Feb 19 2009
| | Sample_last_update_date | Feb 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | No treatments applied
| | Sample_growth_protocol_ch1 | Experiment 1: 20 male Lewis rats (200-250g, Charles River, Montreal, Canada) underwent three behavioural tests: SF, locomotion, and ASR. Experiment 2: 40 male Lewis rats (200-250g, Charles River) underwent four behaviour tests: SF, locomotion, ASR, and PPI. Rats were acclimated one week before testing, singly housed in clear Plexiglas cages with food and water ad libitum, except as described during the SF test. Light cycle was from 0800-2000h, temperature at 21°C +/-1°C. Testing occurred between 0900-1700h. Procedures were approved by the Department of Zoology animal care committee, and conformed to ethical standards of the University of Toronto and the Canadian Council on Animal Care.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed in a random order by decapitation 12 days (Experiment 1) and 6 days after the last testing day (Experiment 2). Brains were removed, and PFC dissected: Fr1and Fr2 anterior to Bregma +4.0mm without olfactory bulb, snap frozen on dry ice and stored at -80°C until RNA extraction. 30-35mg of PFC was added to a pre-chilled cuvette containing 600μl Trizol (Invitrogen, Carlsbad, CA) and mechanically homogenized. The homogenate was then centrifuged at 14,000rpm for 10min, 4°C. Chloroform (VWR International, Mississauga, ON) was added to the supernatant (20% v/v Trizol), shaken and incubated 15s at 21°C, then centrifuged at 14,000rpm for 15min at 4°C. RNA was precipitated by adding an equal volume of 70% ethanol at room temperature then vortexed. The Absolutely RNeasy® RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) was used to purify precipitated RNA, and RNA was eluted then concentrated to 1.2μg/μl using the Microcron YM-10 centrifugal filter device kit (Millipore Corp., Bedford, MA). RNA quality assurance was obtained via the Agilent BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA) or NanoDrop ND-8000 (Wilmington, DE) spectrophotometer, verifying the 18s and 28s ribosomal RNA bands. Quality assurance was conducted at the Centre for Applied Genomics TCAG facilities at the Hospital for Sick Children (Toronto, ON, Canada) before preparation for microarray hybridization at the same facility.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).
| | Sample_hyb_protocol | Hybridization was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).
| | Sample_scan_protocol | Array images were captured with the Agilent 2500 scanner using the Affymetrix Microarray Suite software (v5.0).
| | Sample_data_processing | Data were loaded into the R statistical environment (v2.6.2) using the affy pacakge (v1.16.0) of the BioConductor open-source library. Arrays were tested for spatial and distributional heterogeneity; none were excluded. Pre-processing employed the GCRNA algorithm, as implemented in the gcrma package of BioConductor (v2.10.0).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Paul,C,Boutros
| | Sample_contact_email | Paul.Boutros@utoronto.ca
| | Sample_contact_institute | Ontario Institute for Cancer Research
| | Sample_contact_address | 101 College Street, Suite 800
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G 0A3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM372nnn/GSM372278/suppl/GSM372278.CEL.gz
| | Sample_series_id | GSE14903
| | Sample_series_id | GSE14904
| | Sample_data_row_count | 31099
| | |
|
GSM372279 | GPL1355 |
|
Rat_prefrontal_cortex-rep5-expt2
|
Rat Prefrontal cortex, individual #5
|
gender: Male
strain: Lewis
tissue: prefrontal cortex
weight: 200-250g
light cycle: 800-2000h
startle: 764.6666667
locomotion: 11236.89
plus maze: 60.29219719
sugar feeding: 0
ppi: 39.3809939
|
experiment 2
|
| Sample_geo_accession | GSM372279
| | Sample_status | Public on Nov 24 2009
| | Sample_submission_date | Feb 19 2009
| | Sample_last_update_date | Feb 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | No treatments applied
| | Sample_growth_protocol_ch1 | Experiment 1: 20 male Lewis rats (200-250g, Charles River, Montreal, Canada) underwent three behavioural tests: SF, locomotion, and ASR. Experiment 2: 40 male Lewis rats (200-250g, Charles River) underwent four behaviour tests: SF, locomotion, ASR, and PPI. Rats were acclimated one week before testing, singly housed in clear Plexiglas cages with food and water ad libitum, except as described during the SF test. Light cycle was from 0800-2000h, temperature at 21°C +/-1°C. Testing occurred between 0900-1700h. Procedures were approved by the Department of Zoology animal care committee, and conformed to ethical standards of the University of Toronto and the Canadian Council on Animal Care.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed in a random order by decapitation 12 days (Experiment 1) and 6 days after the last testing day (Experiment 2). Brains were removed, and PFC dissected: Fr1and Fr2 anterior to Bregma +4.0mm without olfactory bulb, snap frozen on dry ice and stored at -80°C until RNA extraction. 30-35mg of PFC was added to a pre-chilled cuvette containing 600μl Trizol (Invitrogen, Carlsbad, CA) and mechanically homogenized. The homogenate was then centrifuged at 14,000rpm for 10min, 4°C. Chloroform (VWR International, Mississauga, ON) was added to the supernatant (20% v/v Trizol), shaken and incubated 15s at 21°C, then centrifuged at 14,000rpm for 15min at 4°C. RNA was precipitated by adding an equal volume of 70% ethanol at room temperature then vortexed. The Absolutely RNeasy® RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) was used to purify precipitated RNA, and RNA was eluted then concentrated to 1.2μg/μl using the Microcron YM-10 centrifugal filter device kit (Millipore Corp., Bedford, MA). RNA quality assurance was obtained via the Agilent BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA) or NanoDrop ND-8000 (Wilmington, DE) spectrophotometer, verifying the 18s and 28s ribosomal RNA bands. Quality assurance was conducted at the Centre for Applied Genomics TCAG facilities at the Hospital for Sick Children (Toronto, ON, Canada) before preparation for microarray hybridization at the same facility.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).
| | Sample_hyb_protocol | Hybridization was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).
| | Sample_scan_protocol | Array images were captured with the Agilent 2500 scanner using the Affymetrix Microarray Suite software (v5.0).
| | Sample_data_processing | Data were loaded into the R statistical environment (v2.6.2) using the affy pacakge (v1.16.0) of the BioConductor open-source library. Arrays were tested for spatial and distributional heterogeneity; none were excluded. Pre-processing employed the GCRNA algorithm, as implemented in the gcrma package of BioConductor (v2.10.0).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Paul,C,Boutros
| | Sample_contact_email | Paul.Boutros@utoronto.ca
| | Sample_contact_institute | Ontario Institute for Cancer Research
| | Sample_contact_address | 101 College Street, Suite 800
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G 0A3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM372nnn/GSM372279/suppl/GSM372279.CEL.gz
| | Sample_series_id | GSE14903
| | Sample_series_id | GSE14904
| | Sample_data_row_count | 31099
| | |
|
GSM372280 | GPL1355 |
|
Rat_prefrontal_cortex-rep6-expt2
|
Rat Prefrontal cortex, individual #6
|
gender: Male
strain: Lewis
tissue: prefrontal cortex
weight: 200-250g
light cycle: 800-2000h
startle: 855.2666667
locomotion: 10692.39
plus maze: NA
sugar feeding: 0.95
ppi: 25.35661392
|
experiment 2
|
| Sample_geo_accession | GSM372280
| | Sample_status | Public on Nov 24 2009
| | Sample_submission_date | Feb 19 2009
| | Sample_last_update_date | Feb 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | No treatments applied
| | Sample_growth_protocol_ch1 | Experiment 1: 20 male Lewis rats (200-250g, Charles River, Montreal, Canada) underwent three behavioural tests: SF, locomotion, and ASR. Experiment 2: 40 male Lewis rats (200-250g, Charles River) underwent four behaviour tests: SF, locomotion, ASR, and PPI. Rats were acclimated one week before testing, singly housed in clear Plexiglas cages with food and water ad libitum, except as described during the SF test. Light cycle was from 0800-2000h, temperature at 21°C +/-1°C. Testing occurred between 0900-1700h. Procedures were approved by the Department of Zoology animal care committee, and conformed to ethical standards of the University of Toronto and the Canadian Council on Animal Care.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed in a random order by decapitation 12 days (Experiment 1) and 6 days after the last testing day (Experiment 2). Brains were removed, and PFC dissected: Fr1and Fr2 anterior to Bregma +4.0mm without olfactory bulb, snap frozen on dry ice and stored at -80°C until RNA extraction. 30-35mg of PFC was added to a pre-chilled cuvette containing 600μl Trizol (Invitrogen, Carlsbad, CA) and mechanically homogenized. The homogenate was then centrifuged at 14,000rpm for 10min, 4°C. Chloroform (VWR International, Mississauga, ON) was added to the supernatant (20% v/v Trizol), shaken and incubated 15s at 21°C, then centrifuged at 14,000rpm for 15min at 4°C. RNA was precipitated by adding an equal volume of 70% ethanol at room temperature then vortexed. The Absolutely RNeasy® RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) was used to purify precipitated RNA, and RNA was eluted then concentrated to 1.2μg/μl using the Microcron YM-10 centrifugal filter device kit (Millipore Corp., Bedford, MA). RNA quality assurance was obtained via the Agilent BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA) or NanoDrop ND-8000 (Wilmington, DE) spectrophotometer, verifying the 18s and 28s ribosomal RNA bands. Quality assurance was conducted at the Centre for Applied Genomics TCAG facilities at the Hospital for Sick Children (Toronto, ON, Canada) before preparation for microarray hybridization at the same facility.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).
| | Sample_hyb_protocol | Hybridization was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).
| | Sample_scan_protocol | Array images were captured with the Agilent 2500 scanner using the Affymetrix Microarray Suite software (v5.0).
| | Sample_data_processing | Data were loaded into the R statistical environment (v2.6.2) using the affy pacakge (v1.16.0) of the BioConductor open-source library. Arrays were tested for spatial and distributional heterogeneity; none were excluded. Pre-processing employed the GCRNA algorithm, as implemented in the gcrma package of BioConductor (v2.10.0).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Paul,C,Boutros
| | Sample_contact_email | Paul.Boutros@utoronto.ca
| | Sample_contact_institute | Ontario Institute for Cancer Research
| | Sample_contact_address | 101 College Street, Suite 800
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G 0A3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM372nnn/GSM372280/suppl/GSM372280.CEL.gz
| | Sample_series_id | GSE14903
| | Sample_series_id | GSE14904
| | Sample_data_row_count | 31099
| | |
|
GSM372281 | GPL1355 |
|
Rat_prefrontal_cortex-rep7-expt2
|
Rat Prefrontal cortex, individual #7
|
gender: Male
strain: Lewis
tissue: prefrontal cortex
weight: 200-250g
light cycle: 800-2000h
startle: 942.5333333
locomotion: 13696.47
plus maze: 0
sugar feeding: 2.15
ppi: 26.68694299
|
experiment 2
|
| Sample_geo_accession | GSM372281
| | Sample_status | Public on Nov 24 2009
| | Sample_submission_date | Feb 19 2009
| | Sample_last_update_date | Feb 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | No treatments applied
| | Sample_growth_protocol_ch1 | Experiment 1: 20 male Lewis rats (200-250g, Charles River, Montreal, Canada) underwent three behavioural tests: SF, locomotion, and ASR. Experiment 2: 40 male Lewis rats (200-250g, Charles River) underwent four behaviour tests: SF, locomotion, ASR, and PPI. Rats were acclimated one week before testing, singly housed in clear Plexiglas cages with food and water ad libitum, except as described during the SF test. Light cycle was from 0800-2000h, temperature at 21°C +/-1°C. Testing occurred between 0900-1700h. Procedures were approved by the Department of Zoology animal care committee, and conformed to ethical standards of the University of Toronto and the Canadian Council on Animal Care.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed in a random order by decapitation 12 days (Experiment 1) and 6 days after the last testing day (Experiment 2). Brains were removed, and PFC dissected: Fr1and Fr2 anterior to Bregma +4.0mm without olfactory bulb, snap frozen on dry ice and stored at -80°C until RNA extraction. 30-35mg of PFC was added to a pre-chilled cuvette containing 600μl Trizol (Invitrogen, Carlsbad, CA) and mechanically homogenized. The homogenate was then centrifuged at 14,000rpm for 10min, 4°C. Chloroform (VWR International, Mississauga, ON) was added to the supernatant (20% v/v Trizol), shaken and incubated 15s at 21°C, then centrifuged at 14,000rpm for 15min at 4°C. RNA was precipitated by adding an equal volume of 70% ethanol at room temperature then vortexed. The Absolutely RNeasy® RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) was used to purify precipitated RNA, and RNA was eluted then concentrated to 1.2μg/μl using the Microcron YM-10 centrifugal filter device kit (Millipore Corp., Bedford, MA). RNA quality assurance was obtained via the Agilent BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA) or NanoDrop ND-8000 (Wilmington, DE) spectrophotometer, verifying the 18s and 28s ribosomal RNA bands. Quality assurance was conducted at the Centre for Applied Genomics TCAG facilities at the Hospital for Sick Children (Toronto, ON, Canada) before preparation for microarray hybridization at the same facility.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).
| | Sample_hyb_protocol | Hybridization was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).
| | Sample_scan_protocol | Array images were captured with the Agilent 2500 scanner using the Affymetrix Microarray Suite software (v5.0).
| | Sample_data_processing | Data were loaded into the R statistical environment (v2.6.2) using the affy pacakge (v1.16.0) of the BioConductor open-source library. Arrays were tested for spatial and distributional heterogeneity; none were excluded. Pre-processing employed the GCRNA algorithm, as implemented in the gcrma package of BioConductor (v2.10.0).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Paul,C,Boutros
| | Sample_contact_email | Paul.Boutros@utoronto.ca
| | Sample_contact_institute | Ontario Institute for Cancer Research
| | Sample_contact_address | 101 College Street, Suite 800
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G 0A3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM372nnn/GSM372281/suppl/GSM372281.CEL.gz
| | Sample_series_id | GSE14903
| | Sample_series_id | GSE14904
| | Sample_data_row_count | 31099
| | |
|
GSM372282 | GPL1355 |
|
Rat_prefrontal_cortex-rep8-expt2
|
Rat Prefrontal cortex, individual #8
|
gender: Male
strain: Lewis
tissue: prefrontal cortex
weight: 200-250g
light cycle: 800-2000h
startle: 624.1333333
locomotion: 10277.71
plus maze: 5.005005005
sugar feeding: 0.5
ppi: 40.19440291
|
experiment 2
|
| Sample_geo_accession | GSM372282
| | Sample_status | Public on Nov 24 2009
| | Sample_submission_date | Feb 19 2009
| | Sample_last_update_date | Feb 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | No treatments applied
| | Sample_growth_protocol_ch1 | Experiment 1: 20 male Lewis rats (200-250g, Charles River, Montreal, Canada) underwent three behavioural tests: SF, locomotion, and ASR. Experiment 2: 40 male Lewis rats (200-250g, Charles River) underwent four behaviour tests: SF, locomotion, ASR, and PPI. Rats were acclimated one week before testing, singly housed in clear Plexiglas cages with food and water ad libitum, except as described during the SF test. Light cycle was from 0800-2000h, temperature at 21°C +/-1°C. Testing occurred between 0900-1700h. Procedures were approved by the Department of Zoology animal care committee, and conformed to ethical standards of the University of Toronto and the Canadian Council on Animal Care.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed in a random order by decapitation 12 days (Experiment 1) and 6 days after the last testing day (Experiment 2). Brains were removed, and PFC dissected: Fr1and Fr2 anterior to Bregma +4.0mm without olfactory bulb, snap frozen on dry ice and stored at -80°C until RNA extraction. 30-35mg of PFC was added to a pre-chilled cuvette containing 600μl Trizol (Invitrogen, Carlsbad, CA) and mechanically homogenized. The homogenate was then centrifuged at 14,000rpm for 10min, 4°C. Chloroform (VWR International, Mississauga, ON) was added to the supernatant (20% v/v Trizol), shaken and incubated 15s at 21°C, then centrifuged at 14,000rpm for 15min at 4°C. RNA was precipitated by adding an equal volume of 70% ethanol at room temperature then vortexed. The Absolutely RNeasy® RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) was used to purify precipitated RNA, and RNA was eluted then concentrated to 1.2μg/μl using the Microcron YM-10 centrifugal filter device kit (Millipore Corp., Bedford, MA). RNA quality assurance was obtained via the Agilent BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA) or NanoDrop ND-8000 (Wilmington, DE) spectrophotometer, verifying the 18s and 28s ribosomal RNA bands. Quality assurance was conducted at the Centre for Applied Genomics TCAG facilities at the Hospital for Sick Children (Toronto, ON, Canada) before preparation for microarray hybridization at the same facility.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).
| | Sample_hyb_protocol | Hybridization was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).
| | Sample_scan_protocol | Array images were captured with the Agilent 2500 scanner using the Affymetrix Microarray Suite software (v5.0).
| | Sample_data_processing | Data were loaded into the R statistical environment (v2.6.2) using the affy pacakge (v1.16.0) of the BioConductor open-source library. Arrays were tested for spatial and distributional heterogeneity; none were excluded. Pre-processing employed the GCRNA algorithm, as implemented in the gcrma package of BioConductor (v2.10.0).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Paul,C,Boutros
| | Sample_contact_email | Paul.Boutros@utoronto.ca
| | Sample_contact_institute | Ontario Institute for Cancer Research
| | Sample_contact_address | 101 College Street, Suite 800
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G 0A3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM372nnn/GSM372282/suppl/GSM372282.CEL.gz
| | Sample_series_id | GSE14903
| | Sample_series_id | GSE14904
| | Sample_data_row_count | 31099
| | |
|
GSM372283 | GPL1355 |
|
Rat_prefrontal_cortex-rep9-expt2
|
Rat Prefrontal cortex, individual #9
|
gender: Male
strain: Lewis
tissue: prefrontal cortex
weight: 200-250g
light cycle: 800-2000h
startle: 927.0666667
locomotion: 10284.08
plus maze: NA
sugar feeding: 0.65
ppi: 37.35078383
|
experiment 2
|
| Sample_geo_accession | GSM372283
| | Sample_status | Public on Nov 24 2009
| | Sample_submission_date | Feb 19 2009
| | Sample_last_update_date | Feb 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | No treatments applied
| | Sample_growth_protocol_ch1 | Experiment 1: 20 male Lewis rats (200-250g, Charles River, Montreal, Canada) underwent three behavioural tests: SF, locomotion, and ASR. Experiment 2: 40 male Lewis rats (200-250g, Charles River) underwent four behaviour tests: SF, locomotion, ASR, and PPI. Rats were acclimated one week before testing, singly housed in clear Plexiglas cages with food and water ad libitum, except as described during the SF test. Light cycle was from 0800-2000h, temperature at 21°C +/-1°C. Testing occurred between 0900-1700h. Procedures were approved by the Department of Zoology animal care committee, and conformed to ethical standards of the University of Toronto and the Canadian Council on Animal Care.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed in a random order by decapitation 12 days (Experiment 1) and 6 days after the last testing day (Experiment 2). Brains were removed, and PFC dissected: Fr1and Fr2 anterior to Bregma +4.0mm without olfactory bulb, snap frozen on dry ice and stored at -80°C until RNA extraction. 30-35mg of PFC was added to a pre-chilled cuvette containing 600μl Trizol (Invitrogen, Carlsbad, CA) and mechanically homogenized. The homogenate was then centrifuged at 14,000rpm for 10min, 4°C. Chloroform (VWR International, Mississauga, ON) was added to the supernatant (20% v/v Trizol), shaken and incubated 15s at 21°C, then centrifuged at 14,000rpm for 15min at 4°C. RNA was precipitated by adding an equal volume of 70% ethanol at room temperature then vortexed. The Absolutely RNeasy® RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) was used to purify precipitated RNA, and RNA was eluted then concentrated to 1.2μg/μl using the Microcron YM-10 centrifugal filter device kit (Millipore Corp., Bedford, MA). RNA quality assurance was obtained via the Agilent BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA) or NanoDrop ND-8000 (Wilmington, DE) spectrophotometer, verifying the 18s and 28s ribosomal RNA bands. Quality assurance was conducted at the Centre for Applied Genomics TCAG facilities at the Hospital for Sick Children (Toronto, ON, Canada) before preparation for microarray hybridization at the same facility.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).
| | Sample_hyb_protocol | Hybridization was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).
| | Sample_scan_protocol | Array images were captured with the Agilent 2500 scanner using the Affymetrix Microarray Suite software (v5.0).
| | Sample_data_processing | Data were loaded into the R statistical environment (v2.6.2) using the affy pacakge (v1.16.0) of the BioConductor open-source library. Arrays were tested for spatial and distributional heterogeneity; none were excluded. Pre-processing employed the GCRNA algorithm, as implemented in the gcrma package of BioConductor (v2.10.0).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Paul,C,Boutros
| | Sample_contact_email | Paul.Boutros@utoronto.ca
| | Sample_contact_institute | Ontario Institute for Cancer Research
| | Sample_contact_address | 101 College Street, Suite 800
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G 0A3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM372nnn/GSM372283/suppl/GSM372283.CEL.gz
| | Sample_series_id | GSE14903
| | Sample_series_id | GSE14904
| | Sample_data_row_count | 31099
| | |
|
GSM372284 | GPL1355 |
|
Rat_prefrontal_cortex-rep10-expt2
|
Rat Prefrontal cortex, individual #10
|
gender: Male
strain: Lewis
tissue: prefrontal cortex
weight: 200-250g
light cycle: 800-2000h
startle: 754.8
locomotion: 9420.13
plus maze: 3.301190166
sugar feeding: 1.15
ppi: 25.26938703
|
experiment 2
|
| Sample_geo_accession | GSM372284
| | Sample_status | Public on Nov 24 2009
| | Sample_submission_date | Feb 19 2009
| | Sample_last_update_date | Feb 19 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | No treatments applied
| | Sample_growth_protocol_ch1 | Experiment 1: 20 male Lewis rats (200-250g, Charles River, Montreal, Canada) underwent three behavioural tests: SF, locomotion, and ASR. Experiment 2: 40 male Lewis rats (200-250g, Charles River) underwent four behaviour tests: SF, locomotion, ASR, and PPI. Rats were acclimated one week before testing, singly housed in clear Plexiglas cages with food and water ad libitum, except as described during the SF test. Light cycle was from 0800-2000h, temperature at 21°C +/-1°C. Testing occurred between 0900-1700h. Procedures were approved by the Department of Zoology animal care committee, and conformed to ethical standards of the University of Toronto and the Canadian Council on Animal Care.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed in a random order by decapitation 12 days (Experiment 1) and 6 days after the last testing day (Experiment 2). Brains were removed, and PFC dissected: Fr1and Fr2 anterior to Bregma +4.0mm without olfactory bulb, snap frozen on dry ice and stored at -80°C until RNA extraction. 30-35mg of PFC was added to a pre-chilled cuvette containing 600μl Trizol (Invitrogen, Carlsbad, CA) and mechanically homogenized. The homogenate was then centrifuged at 14,000rpm for 10min, 4°C. Chloroform (VWR International, Mississauga, ON) was added to the supernatant (20% v/v Trizol), shaken and incubated 15s at 21°C, then centrifuged at 14,000rpm for 15min at 4°C. RNA was precipitated by adding an equal volume of 70% ethanol at room temperature then vortexed. The Absolutely RNeasy® RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) was used to purify precipitated RNA, and RNA was eluted then concentrated to 1.2μg/μl using the Microcron YM-10 centrifugal filter device kit (Millipore Corp., Bedford, MA). RNA quality assurance was obtained via the Agilent BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA) or NanoDrop ND-8000 (Wilmington, DE) spectrophotometer, verifying the 18s and 28s ribosomal RNA bands. Quality assurance was conducted at the Centre for Applied Genomics TCAG facilities at the Hospital for Sick Children (Toronto, ON, Canada) before preparation for microarray hybridization at the same facility.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).
| | Sample_hyb_protocol | Hybridization was performed according to manufacturer's instructions at the TCAG facility (Toronto, Canada).
| | Sample_scan_protocol | Array images were captured with the Agilent 2500 scanner using the Affymetrix Microarray Suite software (v5.0).
| | Sample_data_processing | Data were loaded into the R statistical environment (v2.6.2) using the affy pacakge (v1.16.0) of the BioConductor open-source library. Arrays were tested for spatial and distributional heterogeneity; none were excluded. Pre-processing employed the GCRNA algorithm, as implemented in the gcrma package of BioConductor (v2.10.0).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Paul,C,Boutros
| | Sample_contact_email | Paul.Boutros@utoronto.ca
| | Sample_contact_institute | Ontario Institute for Cancer Research
| | Sample_contact_address | 101 College Street, Suite 800
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G 0A3
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM372nnn/GSM372284/suppl/GSM372284.CEL.gz
| | Sample_series_id | GSE14903
| | Sample_series_id | GSE14904
| | Sample_data_row_count | 31099
| | |
|
| |
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