Search results for the GEO ID: GSE4675  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM105450 | GPL339 |
|
Semeralul_PFC_Development_Week2_Batch2_Animal_1
|
Prefrontal Cortex, Week 2 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 2 weeks', 'Tissue: prefrontal cortex', 'Batch: 2'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105450
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL® Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 L Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 L of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20oC and centrifuged at 14,000 rpm for 10 minutes at 4oC. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 g/L RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105450/suppl/GSM105450.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105450/suppl/GSM105450.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105451 | GPL339 |
|
Semeralul_PFC_Development_Week2_Batch2_Animal_2
|
Prefrontal Cortex, Week 2 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 2 weeks', 'Tissue: prefrontal cortex', 'Batch: 2'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105451
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL® Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 L Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 L of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20oC and centrifuged at 14,000 rpm for 10 minutes at 4oC. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 g/L RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105451/suppl/GSM105451.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105451/suppl/GSM105451.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105452 | GPL339 |
|
Semeralul_PFC_Development_Week2_Batch1_Animal_3
|
Prefrontal Cortex, Week 2 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 2 weeks', 'Tissue: prefrontal cortex', 'Batch: 1'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105452
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL® Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 L Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 L of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20oC and centrifuged at 14,000 rpm for 10 minutes at 4oC. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 g/L RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105452/suppl/GSM105452.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105452/suppl/GSM105452.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105453 | GPL339 |
|
Semeralul_PFC_Development_Week2_Batch1_Animal_4
|
Prefrontal Cortex, Week 2 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 2 weeks', 'Tissue: prefrontal cortex', 'Batch: 1'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105453
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL® Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 L Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 L of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20oC and centrifuged at 14,000 rpm for 10 minutes at 4oC. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 g/L RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105453/suppl/GSM105453.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105453/suppl/GSM105453.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105454 | GPL339 |
|
Semeralul_PFC_Development_Week2_Batch1_Animal_5
|
Prefrontal Cortex, Week 2 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 2 weeks', 'Tissue: prefrontal cortex', 'Batch: 1'
|
Week 2 Batch 2 Animal 2
|
| Sample_geo_accession | GSM105454
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL® Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 L Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 L of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20oC and centrifuged at 14,000 rpm for 10 minutes at 4oC. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 g/L RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105454/suppl/GSM105454.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105454/suppl/GSM105454.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105455 | GPL339 |
|
Semeralul_PFC_Development_Week2_Batch1_Animal_6
|
Prefrontal Cortex, Week 2 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 2 weeks', 'Tissue: prefrontal cortex', 'Batch: 1'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105455
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4 C. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4 C. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105455/suppl/GSM105455.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105455/suppl/GSM105455.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105456 | GPL339 |
|
Semeralul_PFC_Development_Week3_Batch1_Animal_2
|
Prefrontal Cortex, Week 3 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 3 weeks', 'Tissue: prefrontal cortex', 'Batch: 1'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105456
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4 C. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4oC. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105456/suppl/GSM105456.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105456/suppl/GSM105456.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105457 | GPL339 |
|
Semeralul_PFC_Development_Week3_Batch1_Animal_3
|
Prefrontal Cortex, Week 3 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 3 weeks', 'Tissue: prefrontal cortex', 'Batch: 1'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105457
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL® Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4 C. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105457/suppl/GSM105457.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105457/suppl/GSM105457.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105458 | GPL339 |
|
Semeralul_PFC_Development_Week3_Batch1_Animal_5
|
Prefrontal Cortex, Week 3 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 3 weeks', 'Tissue: prefrontal cortex', 'Batch: 1'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105458
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL® Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4 C. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105458/suppl/GSM105458.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105458/suppl/GSM105458.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105459 | GPL339 |
|
Semeralul_PFC_Development_Week3_Batch1_Animal_6
|
Prefrontal Cortex, Week 3 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 3 weeks', 'Tissue: prefrontal cortex', 'Batch: 1'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105459
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL® Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4 C. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105459/suppl/GSM105459.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105459/suppl/GSM105459.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105460 | GPL339 |
|
Semeralul_PFC_Development_Week4_Batch1_Animal_1
|
Prefrontal Cortex, Week 4 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 4 weeks', 'Tissue: prefrontal cortex', 'Batch: 1'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105460
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4 C. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105460/suppl/GSM105460.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105460/suppl/GSM105460.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105461 | GPL339 |
|
Semeralul_PFC_Development_Week4_Batch1_Animal_2
|
Prefrontal Cortex, Week 4 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 4 weeks', 'Tissue: prefrontal cortex', 'Batch: 1'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105461
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4 C. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105461/suppl/GSM105461.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105461/suppl/GSM105461.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105462 | GPL339 |
|
Semeralul_PFC_Development_Week4_Batch1_Animal_3
|
Prefrontal Cortex, Week 4 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 4 weeks', 'Tissue: prefrontal cortex', 'Batch: 1'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105462
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4 C. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105462/suppl/GSM105462.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105462/suppl/GSM105462.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105463 | GPL339 |
|
Semeralul_PFC_Development_Week4_Batch1_Animal_6
|
Prefrontal Cortex, Week 4 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 4 weeks', 'Tissue: prefrontal cortex', 'Batch: 1'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105463
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4 C. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105463/suppl/GSM105463.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105463/suppl/GSM105463.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105464 | GPL339 |
|
Semeralul_PFC_Development_Week5_Batch1_Animal_2
|
Prefrontal Cortex, Week 5 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 5 weeks', 'Tissue: prefrontal cortex', 'Batch: 1'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105464
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4 C. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105464/suppl/GSM105464.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105464/suppl/GSM105464.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105465 | GPL339 |
|
Semeralul_PFC_Development_Week5_Batch2_Animal_2
|
Prefrontal Cortex, Week 5 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 5 weeks', 'Tissue: prefrontal cortex', 'Batch: 2'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105465
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4 C. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105465/suppl/GSM105465.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105465/suppl/GSM105465.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105466 | GPL339 |
|
Semeralul_PFC_Development_Week5_Batch2_Animal_4
|
Prefrontal Cortex, Week 5 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 5 weeks', 'Tissue: prefrontal cortex', 'Batch: 2'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105466
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4 C. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105466/suppl/GSM105466.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105466/suppl/GSM105466.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105467 | GPL339 |
|
Semeralul_PFC_Development_Week5_Batch1_Animal_7
|
Prefrontal Cortex, Week 5 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 5 weeks', 'Tissue: prefrontal cortex', 'Batch: 1'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105467
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4 C. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105467/suppl/GSM105467.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105467/suppl/GSM105467.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105468 | GPL339 |
|
Semeralul_PFC_Development_Week5_Batch1_Animal_8
|
Prefrontal Cortex, Week 5 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 5 weeks', 'Tissue: prefrontal cortex', 'Batch: 1'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105468
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4 C. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105468/suppl/GSM105468.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105468/suppl/GSM105468.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105469 | GPL339 |
|
Semeralul_PFC_Development_Week10_Batch1_Animal_1
|
Prefrontal Cortex, Week 10 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 10 weeks', 'Tissue: prefrontal cortex', 'Batch: 1'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105469
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4 C. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105469/suppl/GSM105469.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105469/suppl/GSM105469.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105470 | GPL339 |
|
Semeralul_PFC_Development_Week10_Batch1_Animal_6
|
Prefrontal Cortex, Week 10 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 10 weeks', 'Tissue: prefrontal cortex', 'Batch: 1'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105470
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4 C. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105470/suppl/GSM105470.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105470/suppl/GSM105470.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105471 | GPL339 |
|
Semeralul_PFC_Development_Week10_Batch1_Animal_7
|
Prefrontal Cortex, Week 10 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 10 weeks', 'Tissue: prefrontal cortex', 'Batch: 1'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105471
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4 C. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105471/suppl/GSM105471.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105471/suppl/GSM105471.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
|
GSM105472 | GPL339 |
|
Semeralul_PFC_Development_Week10_Batch1_Animal_8
|
Prefrontal Cortex, Week 10 Postnatal
|
'Strain: C57BL/6', 'Gender: male', 'Age: 10 weeks', 'Tissue: prefrontal cortex', 'Batch: 1'
|
Prefrontal Cortex
|
| Sample_geo_accession | GSM105472
| | Sample_status | Public on May 15 2006
| | Sample_submission_date | Apr 15 2006
| | Sample_last_update_date | Apr 17 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Adult, wild-type C57BL/6 breeder mice were purchased at five weeks of age from Charles River Laboratories (Wilmington, MA). After seven days of acclimatization, timed matings were set up to generate offspring within our colony. Four to six male C57BL/6 mice were sacrificed on weeks 1-10, inclusive. Mice were killed by cervical dislocation, decapitated and the whole brain was removed from the skull. The PFC was dissected with a coronal cut approximately 3 mm caudal of the frontal pole (Franklin and Paxinos, 1997), and snap-frozen on dry ice, labeled and stored at -80oC.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was prepared using a combination of two common protocols, with slight modifications. TRIZOL Reagent was used for isolation of RNA (Invitrogen Life Technologies Corp., Carlsbad, CA) (Chomczynski, 1993) followed by purification using the Absolutely RNeasy RT-PCR Miniprep kit (Stratagene Inc., La Jolla, CA) (Dolter, 2000). Approximately, 20-35 mg of PFC tissue was homogenized and completely lysed in 600 uL Trizol, followed by centrifugation at 14,000 rpm for 10 minutes at 4oC. The pellet was discarded; 120 uL of chloroform was added to the supernatant, vigorously shaken, incubated for 2-3 minutes at 20 C and centrifuged at 14,000 rpm for 10 minutes at 4 C. The aqueous phase containing RNA was transferred to a fresh 1.5 mL microcentrifuge tube and washed with an equal volume of pre-chilled 70% ethanol. RNA was then purified using Stratagene’s Absolutely RNeasy RT-PCR Miniprep kit. After estimating the yield of total RNA, the solution was concentrated to 1.2 ug/uL RNA using Microcron YM-10 centrifugal filter devices (Millipore Corp., Bedford, MA). RNA integrity was verified by visualization of the 18S and 28S ribosomal RNA bands using the Agilent bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Extracts with evidence of RNA degradation - as indicated by smearing of 28S and 18S ribosomal RNA on agarose/formaldehyde gel electrophoresis - were discarded.
| | Sample_label_ch1 | Affymetrix
| | Sample_data_processing | GCRMA Normalization
| | Sample_platform_id | GPL339
| | 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/GSM105nnn/GSM105472/suppl/GSM105472.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM105nnn/GSM105472/suppl/GSM105472.EXP.gz
| | Sample_series_id | GSE4675
| | Sample_data_row_count | 22690
| | |
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