Result

Search results for the GEO ID: GSE14902

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Title

Source name

Description

Characteristics

GSM372266

GPL341

Rat_prefrontal_cortex-rep1-expt1

Rat Prefrontal cortex, individual #1

gender: Male strain: Lewis tissue: prefrontal cortex weight: 200-250g light cycle: 800-2000h startle: 458.6,Locomotion: 1102 plus maze: 9 sugar feeding: 2.4

experiment 1

Sample_geo_accession	GSM372266
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	GPL341
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/GSM372266/suppl/GSM372266.CEL.gz
Sample_series_id	GSE14902
Sample_series_id	GSE14904
Sample_data_row_count	15923

GSM372267

GPL341

Rat_prefrontal_cortex-rep2-expt1

Rat Prefrontal cortex, individual #2

gender: Male strain: Lewis tissue: prefrontal cortex weight: 200-250g light cycle: 800-2000h startle: 295.8,Locomotion: 787 plus maze: 18.7 sugar feeding: 1.7

experiment 1

Sample_geo_accession	GSM372267
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	GPL341
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/GSM372267/suppl/GSM372267.CEL.gz
Sample_series_id	GSE14902
Sample_series_id	GSE14904
Sample_data_row_count	15923

GSM372268

GPL341

Rat_prefrontal_cortex-rep3-expt1

Rat Prefrontal cortex, individual #3

gender: Male strain: Lewis tissue: prefrontal cortex weight: 200-250g light cycle: 800-2000h startle: 501,Locomotion: 536 plus maze: 0 sugar feeding: 1.8

experiment 1

Sample_geo_accession	GSM372268
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	GPL341
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/GSM372268/suppl/GSM372268.CEL.gz
Sample_series_id	GSE14902
Sample_series_id	GSE14904
Sample_data_row_count	15923

GSM372269

GPL341

Rat_prefrontal_cortex-rep4-expt1

Rat Prefrontal cortex, individual #4

gender: Male strain: Lewis tissue: prefrontal cortex weight: 200-250g light cycle: 800-2000h startle: 244.7,Locomotion: 805 plus maze: 3 sugar feeding: 4.7

experiment 1

Sample_geo_accession	GSM372269
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	GPL341
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/GSM372269/suppl/GSM372269.CEL.gz
Sample_series_id	GSE14902
Sample_series_id	GSE14904
Sample_data_row_count	15923

GSM372270

GPL341

Rat_prefrontal_cortex-rep5-expt1

Rat Prefrontal cortex, individual #5

gender: Male strain: Lewis tissue: prefrontal cortex weight: 200-250g light cycle: 800-2000h startle: 175.4,Locomotion: 706 plus maze: 2.7 sugar feeding: 1.4

experiment 1

Sample_geo_accession	GSM372270
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	GPL341
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/GSM372270/suppl/GSM372270.CEL.gz
Sample_series_id	GSE14902
Sample_series_id	GSE14904
Sample_data_row_count	15923

GSM372271

GPL341

Rat_prefrontal_cortex-rep6-expt1

Rat Prefrontal cortex, individual #6

gender: Male strain: Lewis tissue: prefrontal cortex weight: 200-250g light cycle: 800-2000h startle: 352.9,Locomotion: 634 plus maze: 18.7 sugar feeding: 0.8

experiment 1

Sample_geo_accession	GSM372271
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	GPL341
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/GSM372271/suppl/GSM372271.CEL.gz
Sample_series_id	GSE14902
Sample_series_id	GSE14904
Sample_data_row_count	15923

GSM372272

GPL341

Rat_prefrontal_cortex-rep7-expt1

Rat Prefrontal cortex, individual #7

gender: Male strain: Lewis tissue: prefrontal cortex weight: 200-250g light cycle: 800-2000h startle: 153.7,Locomotion: 635 plus maze: 2.3 sugar feeding: 1.3

experiment 1

Sample_geo_accession	GSM372272
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	GPL341
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/GSM372272/suppl/GSM372272.CEL.gz
Sample_series_id	GSE14902
Sample_series_id	GSE14904
Sample_data_row_count	15923

GSM372273

GPL341

Rat_prefrontal_cortex-rep8-expt1

Rat Prefrontal cortex, individual #8

gender: Male strain: Lewis tissue: prefrontal cortex weight: 200-250g light cycle: 800-2000h startle: 67.7,Locomotion: 946 plus maze: 5.7 sugar feeding: 3.3

experiment 1

Sample_geo_accession	GSM372273
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	GPL341
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/GSM372273/suppl/GSM372273.CEL.gz
Sample_series_id	GSE14902
Sample_series_id	GSE14904
Sample_data_row_count	15923

GSM372274

GPL341

Rat_prefrontal_cortex-rep9-expt1

Rat Prefrontal cortex, individual #9

gender: Male strain: Lewis tissue: prefrontal cortex weight: 200-250g light cycle: 800-2000h startle: 230,Locomotion: 793 plus maze: 0 sugar feeding: 2.1

experiment 1

Sample_geo_accession	GSM372274
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	GPL341
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/GSM372274/suppl/GSM372274.CEL.gz
Sample_series_id	GSE14902
Sample_series_id	GSE14904
Sample_data_row_count	15923

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