Search results for the GEO ID: GSE12679  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM318410 | GPL570 |
|
endothelial_rep1
|
human endothelial cells isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: endothelial, age:45, gender:male, diagnostic group: schizophrenia, PMI:35h
|
amplified RNA
|
| Sample_geo_accession | GSM318410
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318410/suppl/GSM318410.CEL.gz
| | Sample_relation | Reanalysis of: GSM309041
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318411 | GPL570 |
|
endothelial_rep2
|
human endothelial cells isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: endothelial, age:37, gender:male, diagnostic group: schizophrenia, PMI:30h
|
amplified RNA
|
| Sample_geo_accession | GSM318411
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318411/suppl/GSM318411.CEL.gz
| | Sample_relation | Reanalysis of: GSM309044
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318412 | GPL570 |
|
neuron_rep1
|
human neurons isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: neuronal, age:45, gender:male, diagnostic group: schizophrenia, PMI:35h
|
amplified RNA
|
| Sample_geo_accession | GSM318412
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318412/suppl/GSM318412.CEL.gz
| | Sample_relation | Reanalysis of: GSM309046
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318413 | GPL570 |
|
neuron_rep2
|
human neurons isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: neuronal, age:37, gender:male, diagnostic group: schizophrenia, PMI:30h
|
amplified RNA
|
| Sample_geo_accession | GSM318413
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318413/suppl/GSM318413.CEL.gz
| | Sample_relation | Reanalysis of: GSM309047
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318414 | GPL570 |
|
endothelial_rep3
|
human endothelial cells isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: endothelial, age:42, gender:male, diagnostic group: schizophrenia, PMI:37h
|
amplified RNA
|
| Sample_geo_accession | GSM318414
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318414/suppl/GSM318414.CEL.gz
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318415 | GPL570 |
|
endothelial_rep4
|
human endothelial cells isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: endothelial, age:32, gender:male, diagnostic group: control, PMI:13h
|
amplified RNA
|
| Sample_geo_accession | GSM318415
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318415/suppl/GSM318415.CEL.gz
| | Sample_relation | Reanalysis of: GSM309042
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318416 | GPL570 |
|
endothelial_rep5
|
human endothelial cells isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: endothelial, age:44, gender:male, diagnostic group: schizophrenia, PMI:9h
|
amplified RNA
|
| Sample_geo_accession | GSM318416
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318416/suppl/GSM318416.CEL.gz
| | Sample_relation | Reanalysis of: GSM309043
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318417 | GPL570 |
|
endothelial_rep6
|
human endothelial cells isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: endothelial, age:54, gender:male, diagnostic group: schizophrenia, PMI:38h
|
amplified RNA
|
| Sample_geo_accession | GSM318417
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318417/suppl/GSM318417.CEL.gz
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318418 | GPL570 |
|
endothelial_rep7
|
human endothelial cells isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: endothelial, age:45, gender:male, diagnostic group: schizophrenia, PMI:18h
|
amplified RNA
|
| Sample_geo_accession | GSM318418
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318418/suppl/GSM318418.CEL.gz
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318419 | GPL570 |
|
endothelial_rep8
|
human endothelial cells isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: endothelial, age:44, gender:female, diagnostic group: control, PMI:10h
|
amplified RNA
|
| Sample_geo_accession | GSM318419
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318419/suppl/GSM318419.CEL.gz
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318420 | GPL570 |
|
endothelial_rep9
|
human endothelial cells isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: endothelial, age:19, gender:male, diagnostic group: schizophrenia, PMI:28h
|
amplified RNA
|
| Sample_geo_accession | GSM318420
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318420/suppl/GSM318420.CEL.gz
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318421 | GPL570 |
|
endothelial_rep10
|
human endothelial cells isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: endothelial, age:47, gender:female, diagnostic group: schizophrenia, PMI:35h
|
amplified RNA
|
| Sample_geo_accession | GSM318421
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318421/suppl/GSM318421.CEL.gz
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318422 | GPL570 |
|
endothelial_rep11
|
human endothelial cells isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: endothelial, age:54, gender:female, diagnostic group: schizophrenia, PMI:42h
|
amplified RNA
|
| Sample_geo_accession | GSM318422
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318422/suppl/GSM318422.CEL.gz
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318423 | GPL570 |
|
endothelial_rep12
|
human endothelial cells isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: endothelial, age:47, gender:female, diagnostic group: schizophrenia, PMI:30h
|
amplified RNA
|
| Sample_geo_accession | GSM318423
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318423/suppl/GSM318423.CEL.gz
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318424 | GPL570 |
|
endothelial_rep13
|
human endothelial cells isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: endothelial, age:42, gender:male, diagnostic group: schizophrenia, PMI:19h
|
amplified RNA
|
| Sample_geo_accession | GSM318424
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318424/suppl/GSM318424.CEL.gz
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318425 | GPL570 |
|
endothelial_rep14
|
human endothelial cells isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: endothelial, age:47, gender:male, diagnostic group: control, PMI:11h
|
amplified RNA
|
| Sample_geo_accession | GSM318425
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318425/suppl/GSM318425.CEL.gz
| | Sample_relation | Reanalysis of: GSM309048
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318426 | GPL570 |
|
endothelial_rep15
|
human endothelial cells isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: endothelial, age:55, gender:male, diagnostic group: control, PMI:31h
|
amplified RNA
|
| Sample_geo_accession | GSM318426
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318426/suppl/GSM318426.CEL.gz
| | Sample_relation | Reanalysis of: GSM309049
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318427 | GPL570 |
|
endothelial_rep16
|
human endothelial cells isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: endothelial, age:34, gender:male, diagnostic group: control, PMI:22h
|
amplified RNA
|
| Sample_geo_accession | GSM318427
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318427/suppl/GSM318427.CEL.gz
| | Sample_relation | Reanalysis of: GSM309050
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318428 | GPL570 |
|
neuron_rep3
|
human neurons isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: neuronal, age:47, gender:male, diagnostic group: control, PMI:11h
|
amplified RNA
|
| Sample_geo_accession | GSM318428
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318428/suppl/GSM318428.CEL.gz
| | Sample_relation | Reanalysis of: GSM309051
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318429 | GPL570 |
|
neuron_rep4
|
human neurons isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: neuronal, age:39, gender:female, diagnostic group: control, PMI:58h
|
amplified RNA
|
| Sample_geo_accession | GSM318429
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318429/suppl/GSM318429.CEL.gz
| | Sample_relation | Reanalysis of: GSM309052
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318430 | GPL570 |
|
neuron_rep5
|
human neurons isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: neuronal, age:44, gender:female, diagnostic group: schizophrenia, PMI:26h
|
amplified RNA
|
| Sample_geo_accession | GSM318430
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318430/suppl/GSM318430.CEL.gz
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318431 | GPL570 |
|
neuron_rep6
|
human neurons isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: neuronal, age:41, gender:female, diagnostic group: bipolar disorder, PMI:28h
|
amplified RNA
|
| Sample_geo_accession | GSM318431
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318431/suppl/GSM318431.CEL.gz
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318432 | GPL570 |
|
neuron_rep7
|
human neurons isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: neuronal, age:48, gender:male, diagnostic group: bipolar disorder, PMI:23h
|
amplified RNA
|
| Sample_geo_accession | GSM318432
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318432/suppl/GSM318432.CEL.gz
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318433 | GPL570 |
|
neuron_rep8
|
human neurons isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: neuronal, age:46, gender:male, diagnostic group: control, PMI:31h
|
amplified RNA
|
| Sample_geo_accession | GSM318433
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318433/suppl/GSM318433.CEL.gz
| | Sample_relation | Reanalysis of: GSM309045
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318434 | GPL570 |
|
neuron_rep9
|
human neurons isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: neuronal, age:35, gender:male, diagnostic group: bipolar disorder, PMI:35h
|
amplified RNA
|
| Sample_geo_accession | GSM318434
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318434/suppl/GSM318434.CEL.gz
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318435 | GPL570 |
|
neuron_rep10
|
human neurons isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: neuronal, age:51, gender:male, diagnostic group: bipolar disorder, PMI:23h
|
amplified RNA
|
| Sample_geo_accession | GSM318435
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318435/suppl/GSM318435.CEL.gz
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318436 | GPL570 |
|
neuron_rep11
|
human neurons isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: neuronal, age:32, gender:male, diagnostic group: control, PMI:13h
|
amplified RNA
|
| Sample_geo_accession | GSM318436
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318436/suppl/GSM318436.CEL.gz
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318437 | GPL570 |
|
neuron_rep12
|
human neurons isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: neuronal, age:42, gender:male, diagnostic group: bipolar disorder, PMI:32h
|
amplified RNA
|
| Sample_geo_accession | GSM318437
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318437/suppl/GSM318437.CEL.gz
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318438 | GPL570 |
|
neuron_rep13
|
human neurons isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: neuronal, age:52, gender:male, diagnostic group: schizophrenia, PMI:16h
|
amplified RNA
|
| Sample_geo_accession | GSM318438
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318438/suppl/GSM318438.CEL.gz
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318439 | GPL570 |
|
neuron_rep14
|
human neurons isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: neuronal, age:47, gender:female, diagnostic group: schizophrenia, PMI:35h
|
amplified RNA
|
| Sample_geo_accession | GSM318439
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318439/suppl/GSM318439.CEL.gz
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318440 | GPL570 |
|
neuron_rep15
|
human neurons isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: neuronal, age:34, gender:male, diagnostic group: control, PMI:22h
|
amplified RNA
|
| Sample_geo_accession | GSM318440
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318440/suppl/GSM318440.CEL.gz
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
GSM318441 | GPL570 |
|
neuron_rep16
|
human neurons isolated from postmortem dorsolateral prefrontal cortex
|
Cell type: neuronal, age:49, gender:female, diagnostic group: control, PMI:45h
|
amplified RNA
|
| Sample_geo_accession | GSM318441
| | Sample_status | Public on Dec 18 2008
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Dec 18 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Stanley Medical Research Institute
| | Sample_treatment_protocol_ch1 | 15um tissue sections were cut onto polyethylene naphthalate membrane slides (Zeiss) and fixed for 10 minutes in acetone. After air drying, sections were incubated with either rabbit anti-von Willebrand factor (Chemicon) or mouse anti-neurofilament-160/200kD for 5 minutes, followed by brief washing in RNase-free phosphate buffered saline (PBS) and incubation in secondary antibody for 5 minutes (Cy3-conjugated goat anti-rabbit IgG or Cy2-conjugated goat anti-mouse IgG (Jackson Immunoresearch). All antibodies were used at 1:20 dilution with 1unit/ml RNase inhibitor (GE Healthcare) in RNase-free PBS (Ambion). These incubation conditions were found to give the best staining for cell identification together with optimal RNA preservation. Following antibody incubation and brief washing in PBS, sections were then dehydrated through ethanol series and cell capture was initiated immediately. Laser capture microdissection was carried out using the PALM microlaser system [22]. 1000 neurons were captured from each subject, in two batches of 500, or an equivalent area of vascular endothelium (approximately 40 0000 m2). Pyramidal neurons were selected based on staining and morphology.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using PALM extraction kit (Zeiss) according to instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was amplified through 2 rounds using the RiboAmp HS kit (Arcturus) according to instructions. Amplified RNA was converted to cDNA using Round 2 components of the RiboAmp HS kit, labelled by in vitro transcription in the presence of biotinylated UTP (Codelink Expression Assay kit, GE Healthcare), and purified using YM-30 columns (Microcon).
| | Sample_hyb_protocol | Hybridisation (16 hours), washing and staining were done by following the instructions of the chip manufacturer..
| | Sample_scan_protocol | The chips were scanned with a GeneChip scanner system. Microarray image data was analyzed with the GeneChip® Operating Software
| | Sample_data_processing | Expression measures were computed for each of the probesets on each of the GeneChips in the dataset using the robust multichip average (RMA) method, which is implemented in the BioConductor package ‘Affy’. RNA digestion plots were also generated using Affy package. A linear regression of expression values on the logarithm (base 2) of slope of the RNA digestion plots for each probeset was performed and the residuals from the regression were assigned as expression values for further analysis.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Laura,Wiseman,Harris
| | Sample_contact_department | Insitute of Chemical Engineering and Biotechnology
| | Sample_contact_institute | University of Cambridge
| | Sample_contact_address | Tennis Court Road
| | Sample_contact_city | Cambridge
| | Sample_contact_zip/postal_code | CB22 4RA
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318441/suppl/GSM318441.CEL.gz
| | Sample_series_id | GSE12679
| | Sample_data_row_count | 54675
| | |
|
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