Search results for the GEO ID: GSE12685  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM318211 | GPL96 |
|
Control 405
|
Frontal cortex synaptoneurosome
|
Synaptoneurosomes isolated from human brain frontal cortex of control patient with MMSE 29
|
The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
|
| Sample_geo_accession | GSM318211
| | Sample_status | Public on Jan 10 2009
| | Sample_submission_date | Sep 04 2008
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Alzheimer's Disease Research Center Neuropathology Core, NIA AG05142
| | Sample_treatment_protocol_ch1 | Synaptoneurosomes were prepared by a standard method (Banko et al., 2004; Johnson et al., 1997; Villasana et al., 2006; Westmark and Malter, 2007). with slight modifications. Frontal cortex (0.5gm-2.5gm) was thawed and homogenized with a Teflon-homogenizer (4 strokes at 1000 rpm) in buffer (1/10wt/vol), containing 0.35M sucrose pH7.4, 10mM HEPES, 1mM EDTA, 0.25mM dithiothreitol, 30U/ml RNAse inhibitor and a protease inhibitor cocktail (Pierce, Rockford, Il). Cell debris and nuclei were removed by centrifugation at 1000g for 10 min at 4°C yielding pellet P1 and supernatant S1. The S1 fraction was passed sequentially through a series of screens with decreasing pore sizes of 100, 80, 30 and 10m. The final filtrate was resuspended in 3 volumes of buffer without sucrose and centrifuged at 2000xg, for 15 minutes at 4°C to yield a pellet containing synaptoneurosomes. Total preparation time did not exceed 1 hour.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from synaptoneurosome preparations was extracted with Trizol LS and purified with RNeasy columns. The RNA was quantified and checked for purity by comparison of absorbance at 260 and 280nm in the Nanodrop Spectrophotometer. Total RNA and mRNA were analyzed for integrity and concentration by microanalysis in an Agilent bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation and amplification of cDNA was accomplished by the use of an Enzo BioArray High Yield RNA Transcript Labeling Kit followed by purification by absorption over an RNeasy column.
| | Sample_hyb_protocol | Hybridization to the HG-U133A (Affymetrix) was performed according to standard Affymetrix protocols. Probe-sets consist of 11 probe-pairs, distributed across the array, which are typically designed with bias towards the 3'-end of each gene and include a mismatched pair for quantification and subtraction of non-specific hybridization. Escherichia coli internal spike controls are also included to determine hybridization efficiency. The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner.
| | Sample_scan_protocol | The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner. Microarray Analysis Suite 5.0 (MAS 5.0) was used for the initial signal analysis which generates a signal detection value based on the difference between the perfect match (PM) and mismatch (MM) probes in a probe set. A ‘present’ or ‘absent’ call was assigned to each gene by MAS 5.0 according to certain threshold and the detection p-values. The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
| | Sample_data_processing | Model-Based Expression Index (dChip) (Li and Wong, 2001) implemented in Bioconductor, was used for signal normalization within an individual chip and across all samples. For high-level analysis, statistics tests were conducted to find significantly expressed genes, and this small set of genes was applied for clustering and pathway analysis. Probe sets that were differentially expressed among control and IAD were identified using ANOVA. Benjamini and Hochberg’s False Discovery Rate (FDR) was used for adjusting for multiple testing. The genes with significant change in expression were subject to hierarchical clustering using dChip.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Celia,,Williams
| | Sample_contact_email | celia@usc.edu
| | Sample_contact_phone | 3234421603
| | Sample_contact_fax | 3234421608
| | Sample_contact_laboratory | MCA348
| | Sample_contact_department | Pathology
| | Sample_contact_institute | Keck School of Medicine, USC
| | Sample_contact_address | 2011 Zonal Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90033
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318211/suppl/GSM318211.CEL.gz
| | Sample_series_id | GSE12685
| | Sample_data_row_count | 22283
| | |
|
GSM318212 | GPL96 |
|
Control 530
|
Frontal cortex synaptoneurosome
|
Synaptoneurosomes isolated from human brain frontal cortex of control patient with MMSE 28
|
The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
|
| Sample_geo_accession | GSM318212
| | Sample_status | Public on Jan 10 2009
| | Sample_submission_date | Sep 04 2008
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Alzheimer's Disease Research Center Neuropathology Core, NIA AG05142
| | Sample_treatment_protocol_ch1 | Synaptoneurosomes were prepared by a standard method (Banko et al., 2004; Johnson et al., 1997; Villasana et al., 2006; Westmark and Malter, 2007). with slight modifications. Frontal cortex (0.5gm-2.5gm) was thawed and homogenized with a Teflon-homogenizer (4 strokes at 1000 rpm) in buffer (1/10wt/vol), containing 0.35M sucrose pH7.4, 10mM HEPES, 1mM EDTA, 0.25mM dithiothreitol, 30U/ml RNAse inhibitor and a protease inhibitor cocktail (Pierce, Rockford, Il). Cell debris and nuclei were removed by centrifugation at 1000g for 10 min at 4°C yielding pellet P1 and supernatant S1. The S1 fraction was passed sequentially through a series of screens with decreasing pore sizes of 100, 80, 30 and 10m. The final filtrate was resuspended in 3 volumes of buffer without sucrose and centrifuged at 2000xg, for 15 minutes at 4°C to yield a pellet containing synaptoneurosomes. Total preparation time did not exceed 1 hour.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NA isolation
| | Sample_extract_protocol_ch1 | Total RNA from synaptoneurosome preparations was extracted with Trizol LS and purified with RNeasy columns. The RNA was quantified and checked for purity by comparison of absorbance at 260 and 280nm in the Nanodrop Spectrophotometer. Total RNA and mRNA were analyzed for integrity and concentration by microanalysis in an Agilent bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation and amplification of cDNA was accomplished by the use of an Enzo BioArray High Yield RNA Transcript Labeling Kit followed by purification by absorption over an RNeasy column.
| | Sample_hyb_protocol | Hybridization to the HG-U133A (Affymetrix) was performed according to standard Affymetrix protocols. Probe-sets consist of 11 probe-pairs, distributed across the array, which are typically designed with bias towards the 3'-end of each gene and include a mismatched pair for quantification and subtraction of non-specific hybridization. Escherichia coli internal spike controls are also included to determine hybridization efficiency. The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner.
| | Sample_scan_protocol | The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner. Microarray Analysis Suite 5.0 (MAS 5.0) was used for the initial signal analysis which generates a signal detection value based on the difference between the perfect match (PM) and mismatch (MM) probes in a probe set. A ‘present’ or ‘absent’ call was assigned to each gene by MAS 5.0 according to certain threshold and the detection p-values. The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
| | Sample_data_processing | Model-Based Expression Index (dChip) (Li and Wong, 2001) implemented in Bioconductor, was used for signal normalization within an individual chip and across all samples. For high-level analysis, statistics tests were conducted to find significantly expressed genes, and this small set of genes was applied for clustering and pathway analysis. Probe sets that were differentially expressed among control and IAD were identified using ANOVA. Benjamini and Hochberg’s False Discovery Rate (FDR) was used for adjusting for multiple testing. The genes with significant change in expression were subject to hierarchical clustering using dChip.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Celia,,Williams
| | Sample_contact_email | celia@usc.edu
| | Sample_contact_phone | 3234421603
| | Sample_contact_fax | 3234421608
| | Sample_contact_laboratory | MCA348
| | Sample_contact_department | Pathology
| | Sample_contact_institute | Keck School of Medicine, USC
| | Sample_contact_address | 2011 Zonal Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90033
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318212/suppl/GSM318212.CEL.gz
| | Sample_series_id | GSE12685
| | Sample_data_row_count | 22283
| | |
|
GSM318213 | GPL96 |
|
Control 564
|
Frontal cortex synaptoneurosome
|
Synaptoneurosomes isolated from human brain frontal cortex of control patient with MMSE 27
|
The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
|
| Sample_geo_accession | GSM318213
| | Sample_status | Public on Jan 10 2009
| | Sample_submission_date | Sep 04 2008
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Alzheimer's Disease Research Center Neuropathology Core, NIA AG05142
| | Sample_treatment_protocol_ch1 | Synaptoneurosomes were prepared by a standard method (Banko et al., 2004; Johnson et al., 1997; Villasana et al., 2006; Westmark and Malter, 2007). with slight modifications. Frontal cortex (0.5gm-2.5gm) was thawed and homogenized with a Teflon-homogenizer (4 strokes at 1000 rpm) in buffer (1/10wt/vol), containing 0.35M sucrose pH7.4, 10mM HEPES, 1mM EDTA, 0.25mM dithiothreitol, 30U/ml RNAse inhibitor and a protease inhibitor cocktail (Pierce, Rockford, Il). Cell debris and nuclei were removed by centrifugation at 1000g for 10 min at 4°C yielding pellet P1 and supernatant S1. The S1 fraction was passed sequentially through a series of screens with decreasing pore sizes of 100, 80, 30 and 10m. The final filtrate was resuspended in 3 volumes of buffer without sucrose and centrifuged at 2000xg, for 15 minutes at 4°C to yield a pellet containing synaptoneurosomes. Total preparation time did not exceed 1 hour.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | NA isolation
| | Sample_extract_protocol_ch1 | Total RNA from synaptoneurosome preparations was extracted with Trizol LS and purified with RNeasy columns. The RNA was quantified and checked for purity by comparison of absorbance at 260 and 280nm in the Nanodrop Spectrophotometer. Total RNA and mRNA were analyzed for integrity and concentration by microanalysis in an Agilent bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation and amplification of cDNA was accomplished by the use of an Enzo BioArray High Yield RNA Transcript Labeling Kit followed by purification by absorption over an RNeasy column.
| | Sample_hyb_protocol | Hybridization to the HG-U133A (Affymetrix) was performed according to standard Affymetrix protocols. Probe-sets consist of 11 probe-pairs, distributed across the array, which are typically designed with bias towards the 3'-end of each gene and include a mismatched pair for quantification and subtraction of non-specific hybridization. Escherichia coli internal spike controls are also included to determine hybridization efficiency. The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner.
| | Sample_scan_protocol | The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner. Microarray Analysis Suite 5.0 (MAS 5.0) was used for the initial signal analysis which generates a signal detection value based on the difference between the perfect match (PM) and mismatch (MM) probes in a probe set. A ‘present’ or ‘absent’ call was assigned to each gene by MAS 5.0 according to certain threshold and the detection p-values. The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
| | Sample_data_processing | Model-Based Expression Index (dChip) (Li and Wong, 2001) implemented in Bioconductor, was used for signal normalization within an individual chip and across all samples. For high-level analysis, statistics tests were conducted to find significantly expressed genes, and this small set of genes was applied for clustering and pathway analysis. Probe sets that were differentially expressed among control and IAD were identified using ANOVA. Benjamini and Hochberg’s False Discovery Rate (FDR) was used for adjusting for multiple testing. The genes with significant change in expression were subject to hierarchical clustering using dChip.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Celia,,Williams
| | Sample_contact_email | celia@usc.edu
| | Sample_contact_phone | 3234421603
| | Sample_contact_fax | 3234421608
| | Sample_contact_laboratory | MCA348
| | Sample_contact_department | Pathology
| | Sample_contact_institute | Keck School of Medicine, USC
| | Sample_contact_address | 2011 Zonal Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90033
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318213/suppl/GSM318213.CEL.gz
| | Sample_series_id | GSE12685
| | Sample_data_row_count | 22283
| | |
|
GSM318310 | GPL96 |
|
Control 585
|
Frontal cortex synaptoneurosome
|
Synaptoneurosomes isolated from human brain frontal cortex of control patient with MMSE 29
|
The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
|
| Sample_geo_accession | GSM318310
| | Sample_status | Public on Jan 10 2009
| | Sample_submission_date | Sep 04 2008
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Alzheimer's Disease Research Center Neuropathology Core, NIA AG05142
| | Sample_treatment_protocol_ch1 | Synaptoneurosomes were prepared by a standard method (Banko et al., 2004; Johnson et al., 1997; Villasana et al., 2006; Westmark and Malter, 2007). with slight modifications. Frontal cortex (0.5gm-2.5gm) was thawed and homogenized with a Teflon-homogenizer (4 strokes at 1000 rpm) in buffer (1/10wt/vol), containing 0.35M sucrose pH7.4, 10mM HEPES, 1mM EDTA, 0.25mM dithiothreitol, 30U/ml RNAse inhibitor and a protease inhibitor cocktail (Pierce, Rockford, Il). Cell debris and nuclei were removed by centrifugation at 1000g for 10 min at 4°C yielding pellet P1 and supernatant S1. The S1 fraction was passed sequentially through a series of screens with decreasing pore sizes of 100, 80, 30 and 10m. The final filtrate was resuspended in 3 volumes of buffer without sucrose and centrifuged at 2000xg, for 15 minutes at 4°C to yield a pellet containing synaptoneurosomes. Total preparation time did not exceed 1 hour.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from synaptoneurosome preparations was extracted with Trizol LS and purified with RNeasy columns. The RNA was quantified and checked for purity by comparison of absorbance at 260 and 280nm in the Nanodrop Spectrophotometer. Total RNA and mRNA were analyzed for integrity and concentration by microanalysis in an Agilent bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation and amplification of cDNA was accomplished by the use of an Enzo BioArray High Yield RNA Transcript Labeling Kit followed by purification by absorption over an RNeasy column.
| | Sample_hyb_protocol | Hybridization to the HG-U133A (Affymetrix) was performed according to standard Affymetrix protocols. Probe-sets consist of 11 probe-pairs, distributed across the array, which are typically designed with bias towards the 3'-end of each gene and include a mismatched pair for quantification and subtraction of non-specific hybridization. Escherichia coli internal spike controls are also included to determine hybridization efficiency. The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner.
| | Sample_scan_protocol | The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner. Microarray Analysis Suite 5.0 (MAS 5.0) was used for the initial signal analysis which generates a signal detection value based on the difference between the perfect match (PM) and mismatch (MM) probes in a probe set. A ‘present’ or ‘absent’ call was assigned to each gene by MAS 5.0 according to certain threshold and the detection p-values. The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
| | Sample_data_processing | Model-Based Expression Index (dChip) (Li and Wong, 2001) implemented in Bioconductor, was used for signal normalization within an individual chip and across all samples. For high-level analysis, statistics tests were conducted to find significantly expressed genes, and this small set of genes was applied for clustering and pathway analysis. Probe sets that were differentially expressed among control and IAD were identified using ANOVA. Benjamini and Hochberg’s False Discovery Rate (FDR) was used for adjusting for multiple testing. The genes with significant change in expression were subject to hierarchical clustering using dChip.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Celia,,Williams
| | Sample_contact_email | celia@usc.edu
| | Sample_contact_phone | 3234421603
| | Sample_contact_fax | 3234421608
| | Sample_contact_laboratory | MCA348
| | Sample_contact_department | Pathology
| | Sample_contact_institute | Keck School of Medicine, USC
| | Sample_contact_address | 2011 Zonal Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90033
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318310/suppl/GSM318310.CEL.gz
| | Sample_series_id | GSE12685
| | Sample_data_row_count | 22283
| | |
|
GSM318311 | GPL96 |
|
Control 632
|
Frontal cortex synaptoneurosome
|
Synaptoneurosomes isolated from human brain frontal cortex of control patient with MMSE 29
|
The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
|
| Sample_geo_accession | GSM318311
| | Sample_status | Public on Jan 10 2009
| | Sample_submission_date | Sep 04 2008
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Alzheimer's Disease Research Center Neuropathology Core, NIA AG05142
| | Sample_treatment_protocol_ch1 | Synaptoneurosomes were prepared by a standard method (Banko et al., 2004; Johnson et al., 1997; Villasana et al., 2006; Westmark and Malter, 2007). with slight modifications. Frontal cortex (0.5gm-2.5gm) was thawed and homogenized with a Teflon-homogenizer (4 strokes at 1000 rpm) in buffer (1/10wt/vol), containing 0.35M sucrose pH7.4, 10mM HEPES, 1mM EDTA, 0.25mM dithiothreitol, 30U/ml RNAse inhibitor and a protease inhibitor cocktail (Pierce, Rockford, Il). Cell debris and nuclei were removed by centrifugation at 1000g for 10 min at 4°C yielding pellet P1 and supernatant S1. The S1 fraction was passed sequentially through a series of screens with decreasing pore sizes of 100, 80, 30 and 10m. The final filtrate was resuspended in 3 volumes of buffer without sucrose and centrifuged at 2000xg, for 15 minutes at 4°C to yield a pellet containing synaptoneurosomes. Total preparation time did not exceed 1 hour.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from synaptoneurosome preparations was extracted with Trizol LS and purified with RNeasy columns. The RNA was quantified and checked for purity by comparison of absorbance at 260 and 280nm in the Nanodrop Spectrophotometer. Total RNA and mRNA were analyzed for integrity and concentration by microanalysis in an Agilent bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation and amplification of cDNA was accomplished by the use of an Enzo BioArray High Yield RNA Transcript Labeling Kit followed by purification by absorption over an RNeasy column.
| | Sample_hyb_protocol | Hybridization to the HG-U133A (Affymetrix) was performed according to standard Affymetrix protocols. Probe-sets consist of 11 probe-pairs, distributed across the array, which are typically designed with bias towards the 3'-end of each gene and include a mismatched pair for quantification and subtraction of non-specific hybridization. Escherichia coli internal spike controls are also included to determine hybridization efficiency. The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner.
| | Sample_scan_protocol | The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner. Microarray Analysis Suite 5.0 (MAS 5.0) was used for the initial signal analysis which generates a signal detection value based on the difference between the perfect match (PM) and mismatch (MM) probes in a probe set. A ‘present’ or ‘absent’ call was assigned to each gene by MAS 5.0 according to certain threshold and the detection p-values. The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
| | Sample_data_processing | Model-Based Expression Index (dChip) (Li and Wong, 2001) implemented in Bioconductor, was used for signal normalization within an individual chip and across all samples. For high-level analysis, statistics tests were conducted to find significantly expressed genes, and this small set of genes was applied for clustering and pathway analysis. Probe sets that were differentially expressed among control and IAD were identified using ANOVA. Benjamini and Hochberg’s False Discovery Rate (FDR) was used for adjusting for multiple testing. The genes with significant change in expression were subject to hierarchical clustering using dChip.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Celia,,Williams
| | Sample_contact_email | celia@usc.edu
| | Sample_contact_phone | 3234421603
| | Sample_contact_fax | 3234421608
| | Sample_contact_laboratory | MCA348
| | Sample_contact_department | Pathology
| | Sample_contact_institute | Keck School of Medicine, USC
| | Sample_contact_address | 2011 Zonal Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90033
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318311/suppl/GSM318311.CEL.gz
| | Sample_series_id | GSE12685
| | Sample_data_row_count | 22283
| | |
|
GSM318312 | GPL96 |
|
Control 679
|
Frontal cortex synaptoneurosome
|
Synaptoneurosomes isolated from human brain frontal cortex of control patient with MMSE 28
|
The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
|
| Sample_geo_accession | GSM318312
| | Sample_status | Public on Jan 10 2009
| | Sample_submission_date | Sep 04 2008
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Alzheimer's Disease Research Center Neuropathology Core, NIA AG05142
| | Sample_treatment_protocol_ch1 | Synaptoneurosomes were prepared by a standard method (Banko et al., 2004; Johnson et al., 1997; Villasana et al., 2006; Westmark and Malter, 2007). with slight modifications. Frontal cortex (0.5gm-2.5gm) was thawed and homogenized with a Teflon-homogenizer (4 strokes at 1000 rpm) in buffer (1/10wt/vol), containing 0.35M sucrose pH7.4, 10mM HEPES, 1mM EDTA, 0.25mM dithiothreitol, 30U/ml RNAse inhibitor and a protease inhibitor cocktail (Pierce, Rockford, Il). Cell debris and nuclei were removed by centrifugation at 1000g for 10 min at 4°C yielding pellet P1 and supernatant S1. The S1 fraction was passed sequentially through a series of screens with decreasing pore sizes of 100, 80, 30 and 10m. The final filtrate was resuspended in 3 volumes of buffer without sucrose and centrifuged at 2000xg, for 15 minutes at 4°C to yield a pellet containing synaptoneurosomes. Total preparation time did not exceed 1 hour.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from synaptoneurosome preparations was extracted with Trizol LS and purified with RNeasy columns. The RNA was quantified and checked for purity by comparison of absorbance at 260 and 280nm in the Nanodrop Spectrophotometer. Total RNA and mRNA were analyzed for integrity and concentration by microanalysis in an Agilent bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation and amplification of cDNA was accomplished by the use of an Enzo BioArray High Yield RNA Transcript Labeling Kit followed by purification by absorption over an RNeasy column.
| | Sample_hyb_protocol | Hybridization to the HG-U133A (Affymetrix) was performed according to standard Affymetrix protocols. Probe-sets consist of 11 probe-pairs, distributed across the array, which are typically designed with bias towards the 3'-end of each gene and include a mismatched pair for quantification and subtraction of non-specific hybridization. Escherichia coli internal spike controls are also included to determine hybridization efficiency. The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner.
| | Sample_scan_protocol | The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner. Microarray Analysis Suite 5.0 (MAS 5.0) was used for the initial signal analysis which generates a signal detection value based on the difference between the perfect match (PM) and mismatch (MM) probes in a probe set. A ‘present’ or ‘absent’ call was assigned to each gene by MAS 5.0 according to certain threshold and the detection p-values. The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
| | Sample_data_processing | Model-Based Expression Index (dChip) (Li and Wong, 2001) implemented in Bioconductor, was used for signal normalization within an individual chip and across all samples. For high-level analysis, statistics tests were conducted to find significantly expressed genes, and this small set of genes was applied for clustering and pathway analysis. Probe sets that were differentially expressed among control and IAD were identified using ANOVA. Benjamini and Hochberg’s False Discovery Rate (FDR) was used for adjusting for multiple testing. The genes with significant change in expression were subject to hierarchical clustering using dChip.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Celia,,Williams
| | Sample_contact_email | celia@usc.edu
| | Sample_contact_phone | 3234421603
| | Sample_contact_fax | 3234421608
| | Sample_contact_laboratory | MCA348
| | Sample_contact_department | Pathology
| | Sample_contact_institute | Keck School of Medicine, USC
| | Sample_contact_address | 2011 Zonal Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90033
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318312/suppl/GSM318312.CEL.gz
| | Sample_series_id | GSE12685
| | Sample_data_row_count | 22283
| | |
|
GSM318313 | GPL96 |
|
Control 688
|
Frontal cortex synaptoneurosome
|
Synaptoneurosomes isolated from human brain frontal cortex of control patient with MMSE 25
|
The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
|
| Sample_geo_accession | GSM318313
| | Sample_status | Public on Jan 10 2009
| | Sample_submission_date | Sep 04 2008
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Alzheimer's Disease Research Center Neuropathology Core, NIA AG05142
| | Sample_treatment_protocol_ch1 | Synaptoneurosomes were prepared by a standard method (Banko et al., 2004; Johnson et al., 1997; Villasana et al., 2006; Westmark and Malter, 2007). with slight modifications. Frontal cortex (0.5gm-2.5gm) was thawed and homogenized with a Teflon-homogenizer (4 strokes at 1000 rpm) in buffer (1/10wt/vol), containing 0.35M sucrose pH7.4, 10mM HEPES, 1mM EDTA, 0.25mM dithiothreitol, 30U/ml RNAse inhibitor and a protease inhibitor cocktail (Pierce, Rockford, Il). Cell debris and nuclei were removed by centrifugation at 1000g for 10 min at 4°C yielding pellet P1 and supernatant S1. The S1 fraction was passed sequentially through a series of screens with decreasing pore sizes of 100, 80, 30 and 10m. The final filtrate was resuspended in 3 volumes of buffer without sucrose and centrifuged at 2000xg, for 15 minutes at 4°C to yield a pellet containing synaptoneurosomes. Total preparation time did not exceed 1 hour.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from synaptoneurosome preparations was extracted with Trizol LS and purified with RNeasy columns. The RNA was quantified and checked for purity by comparison of absorbance at 260 and 280nm in the Nanodrop Spectrophotometer. Total RNA and mRNA were analyzed for integrity and concentration by microanalysis in an Agilent bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation and amplification of cDNA was accomplished by the use of an Enzo BioArray High Yield RNA Transcript Labeling Kit followed by purification by absorption over an RNeasy column.
| | Sample_hyb_protocol | Hybridization to the HG-U133A (Affymetrix) was performed according to standard Affymetrix protocols. Probe-sets consist of 11 probe-pairs, distributed across the array, which are typically designed with bias towards the 3'-end of each gene and include a mismatched pair for quantification and subtraction of non-specific hybridization. Escherichia coli internal spike controls are also included to determine hybridization efficiency. The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner.
| | Sample_scan_protocol | The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner. Microarray Analysis Suite 5.0 (MAS 5.0) was used for the initial signal analysis which generates a signal detection value based on the difference between the perfect match (PM) and mismatch (MM) probes in a probe set. A ‘present’ or ‘absent’ call was assigned to each gene by MAS 5.0 according to certain threshold and the detection p-values. The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
| | Sample_data_processing | Model-Based Expression Index (dChip) (Li and Wong, 2001) implemented in Bioconductor, was used for signal normalization within an individual chip and across all samples. For high-level analysis, statistics tests were conducted to find significantly expressed genes, and this small set of genes was applied for clustering and pathway analysis. Probe sets that were differentially expressed among control and IAD were identified using ANOVA. Benjamini and Hochberg’s False Discovery Rate (FDR) was used for adjusting for multiple testing. The genes with significant change in expression were subject to hierarchical clustering using dChip.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Celia,,Williams
| | Sample_contact_email | celia@usc.edu
| | Sample_contact_phone | 3234421603
| | Sample_contact_fax | 3234421608
| | Sample_contact_laboratory | MCA348
| | Sample_contact_department | Pathology
| | Sample_contact_institute | Keck School of Medicine, USC
| | Sample_contact_address | 2011 Zonal Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90033
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318313/suppl/GSM318313.CEL.gz
| | Sample_series_id | GSE12685
| | Sample_data_row_count | 22283
| | |
|
GSM318314 | GPL96 |
|
Control 715
|
Frontal cortex synaptoneurosome
|
Synaptoneurosomes isolated from human brain frontal cortex of control patient with MMSE 28
|
The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
|
| Sample_geo_accession | GSM318314
| | Sample_status | Public on Jan 10 2009
| | Sample_submission_date | Sep 04 2008
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Alzheimer's Disease Research Center Neuropathology Core, NIA AG05142
| | Sample_treatment_protocol_ch1 | Synaptoneurosomes were prepared by a standard method (Banko et al., 2004; Johnson et al., 1997; Villasana et al., 2006; Westmark and Malter, 2007). with slight modifications. Frontal cortex (0.5gm-2.5gm) was thawed and homogenized with a Teflon-homogenizer (4 strokes at 1000 rpm) in buffer (1/10wt/vol), containing 0.35M sucrose pH7.4, 10mM HEPES, 1mM EDTA, 0.25mM dithiothreitol, 30U/ml RNAse inhibitor and a protease inhibitor cocktail (Pierce, Rockford, Il). Cell debris and nuclei were removed by centrifugation at 1000g for 10 min at 4°C yielding pellet P1 and supernatant S1. The S1 fraction was passed sequentially through a series of screens with decreasing pore sizes of 100, 80, 30 and 10m. The final filtrate was resuspended in 3 volumes of buffer without sucrose and centrifuged at 2000xg, for 15 minutes at 4°C to yield a pellet containing synaptoneurosomes. Total preparation time did not exceed 1 hour.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from synaptoneurosome preparations was extracted with Trizol LS and purified with RNeasy columns. The RNA was quantified and checked for purity by comparison of absorbance at 260 and 280nm in the Nanodrop Spectrophotometer. Total RNA and mRNA were analyzed for integrity and concentration by microanalysis in an Agilent bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation and amplification of cDNA was accomplished by the use of an Enzo BioArray High Yield RNA Transcript Labeling Kit followed by purification by absorption over an RNeasy column.
| | Sample_hyb_protocol | Hybridization to the HG-U133A (Affymetrix) was performed according to standard Affymetrix protocols. Probe-sets consist of 11 probe-pairs, distributed across the array, which are typically designed with bias towards the 3'-end of each gene and include a mismatched pair for quantification and subtraction of non-specific hybridization. Escherichia coli internal spike controls are also included to determine hybridization efficiency. The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner.
| | Sample_scan_protocol | The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner. Microarray Analysis Suite 5.0 (MAS 5.0) was used for the initial signal analysis which generates a signal detection value based on the difference between the perfect match (PM) and mismatch (MM) probes in a probe set. A ‘present’ or ‘absent’ call was assigned to each gene by MAS 5.0 according to certain threshold and the detection p-values. The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
| | Sample_data_processing | Model-Based Expression Index (dChip) (Li and Wong, 2001) implemented in Bioconductor, was used for signal normalization within an individual chip and across all samples. For high-level analysis, statistics tests were conducted to find significantly expressed genes, and this small set of genes was applied for clustering and pathway analysis. Probe sets that were differentially expressed among control and IAD were identified using ANOVA. Benjamini and Hochberg’s False Discovery Rate (FDR) was used for adjusting for multiple testing. The genes with significant change in expression were subject to hierarchical clustering using dChip.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Celia,,Williams
| | Sample_contact_email | celia@usc.edu
| | Sample_contact_phone | 3234421603
| | Sample_contact_fax | 3234421608
| | Sample_contact_laboratory | MCA348
| | Sample_contact_department | Pathology
| | Sample_contact_institute | Keck School of Medicine, USC
| | Sample_contact_address | 2011 Zonal Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90033
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318314/suppl/GSM318314.CEL.gz
| | Sample_series_id | GSE12685
| | Sample_data_row_count | 22283
| | |
|
GSM318317 | GPL96 |
|
Incipient AD 224
|
Frontal cortex synaptoneurosome
|
Synaptoneurosomes isolated from human brain frontal cortex of a patient with incipient Alzheimer's Disease with MMSE 26
|
The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
|
| Sample_geo_accession | GSM318317
| | Sample_status | Public on Jan 10 2009
| | Sample_submission_date | Sep 04 2008
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Alzheimer's Disease Research Center Neuropathology Core, NIA AG05142
| | Sample_treatment_protocol_ch1 | Synaptoneurosomes were prepared by a standard method (Banko et al., 2004; Johnson et al., 1997; Villasana et al., 2006; Westmark and Malter, 2007). with slight modifications. Frontal cortex (0.5gm-2.5gm) was thawed and homogenized with a Teflon-homogenizer (4 strokes at 1000 rpm) in buffer (1/10wt/vol), containing 0.35M sucrose pH7.4, 10mM HEPES, 1mM EDTA, 0.25mM dithiothreitol, 30U/ml RNAse inhibitor and a protease inhibitor cocktail (Pierce, Rockford, Il). Cell debris and nuclei were removed by centrifugation at 1000g for 10 min at 4°C yielding pellet P1 and supernatant S1. The S1 fraction was passed sequentially through a series of screens with decreasing pore sizes of 100, 80, 30 and 10m. The final filtrate was resuspended in 3 volumes of buffer without sucrose and centrifuged at 2000xg, for 15 minutes at 4°C to yield a pellet containing synaptoneurosomes. Total preparation time did not exceed 1 hour.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from synaptoneurosome preparations was extracted with Trizol LS and purified with RNeasy columns. The RNA was quantified and checked for purity by comparison of absorbance at 260 and 280nm in the Nanodrop Spectrophotometer. Total RNA and mRNA were analyzed for integrity and concentration by microanalysis in an Agilent bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation and amplification of cDNA was accomplished by the use of an Enzo BioArray High Yield RNA Transcript Labeling Kit followed by purification by absorption over an RNeasy column.
| | Sample_hyb_protocol | Hybridization to the HG-U133A (Affymetrix) was performed according to standard Affymetrix protocols. Probe-sets consist of 11 probe-pairs, distributed across the array, which are typically designed with bias towards the 3'-end of each gene and include a mismatched pair for quantification and subtraction of non-specific hybridization. Escherichia coli internal spike controls are also included to determine hybridization efficiency. The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner.
| | Sample_scan_protocol | The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner. Microarray Analysis Suite 5.0 (MAS 5.0) was used for the initial signal analysis which generates a signal detection value based on the difference between the perfect match (PM) and mismatch (MM) probes in a probe set. A ‘present’ or ‘absent’ call was assigned to each gene by MAS 5.0 according to certain threshold and the detection p-values. The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
| | Sample_data_processing | Model-Based Expression Index (dChip) (Li and Wong, 2001) implemented in Bioconductor, was used for signal normalization within an individual chip and across all samples. For high-level analysis, statistics tests were conducted to find significantly expressed genes, and this small set of genes was applied for clustering and pathway analysis. Probe sets that were differentially expressed among control and IAD were identified using ANOVA. Benjamini and Hochberg’s False Discovery Rate (FDR) was used for adjusting for multiple testing. The genes with significant change in expression were subject to hierarchical clustering using dChip.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Celia,,Williams
| | Sample_contact_email | celia@usc.edu
| | Sample_contact_phone | 3234421603
| | Sample_contact_fax | 3234421608
| | Sample_contact_laboratory | MCA348
| | Sample_contact_department | Pathology
| | Sample_contact_institute | Keck School of Medicine, USC
| | Sample_contact_address | 2011 Zonal Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90033
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318317/suppl/GSM318317.CEL.gz
| | Sample_series_id | GSE12685
| | Sample_data_row_count | 22283
| | |
|
GSM318320 | GPL96 |
|
Incipient AD 385
|
Frontal cortex synaptoneurosome
|
Synaptoneurosomes isolated from human brain frontal cortex of a patient with incipient Alzheimer's Disease with MMSE 21
|
The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
|
| Sample_geo_accession | GSM318320
| | Sample_status | Public on Jan 10 2009
| | Sample_submission_date | Sep 04 2008
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Alzheimer's Disease Research Center Neuropathology Core, NIA AG05142
| | Sample_treatment_protocol_ch1 | Synaptoneurosomes were prepared by a standard method (Banko et al., 2004; Johnson et al., 1997; Villasana et al., 2006; Westmark and Malter, 2007). with slight modifications. Frontal cortex (0.5gm-2.5gm) was thawed and homogenized with a Teflon-homogenizer (4 strokes at 1000 rpm) in buffer (1/10wt/vol), containing 0.35M sucrose pH7.4, 10mM HEPES, 1mM EDTA, 0.25mM dithiothreitol, 30U/ml RNAse inhibitor and a protease inhibitor cocktail (Pierce, Rockford, Il). Cell debris and nuclei were removed by centrifugation at 1000g for 10 min at 4°C yielding pellet P1 and supernatant S1. The S1 fraction was passed sequentially through a series of screens with decreasing pore sizes of 100, 80, 30 and 10m. The final filtrate was resuspended in 3 volumes of buffer without sucrose and centrifuged at 2000xg, for 15 minutes at 4°C to yield a pellet containing synaptoneurosomes. Total preparation time did not exceed 1 hour.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from synaptoneurosome preparations was extracted with Trizol LS and purified with RNeasy columns. The RNA was quantified and checked for purity by comparison of absorbance at 260 and 280nm in the Nanodrop Spectrophotometer. Total RNA and mRNA were analyzed for integrity and concentration by microanalysis in an Agilent bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation and amplification of cDNA was accomplished by the use of an Enzo BioArray High Yield RNA Transcript Labeling Kit followed by purification by absorption over an RNeasy column.
| | Sample_hyb_protocol | Hybridization to the HG-U133A (Affymetrix) was performed according to standard Affymetrix protocols. Probe-sets consist of 11 probe-pairs, distributed across the array, which are typically designed with bias towards the 3'-end of each gene and include a mismatched pair for quantification and subtraction of non-specific hybridization. Escherichia coli internal spike controls are also included to determine hybridization efficiency. The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner.
| | Sample_scan_protocol | The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner. Microarray Analysis Suite 5.0 (MAS 5.0) was used for the initial signal analysis which generates a signal detection value based on the difference between the perfect match (PM) and mismatch (MM) probes in a probe set. A ‘present’ or ‘absent’ call was assigned to each gene by MAS 5.0 according to certain threshold and the detection p-values. The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
| | Sample_data_processing | Model-Based Expression Index (dChip) (Li and Wong, 2001) implemented in Bioconductor, was used for signal normalization within an individual chip and across all samples. For high-level analysis, statistics tests were conducted to find significantly expressed genes, and this small set of genes was applied for clustering and pathway analysis. Probe sets that were differentially expressed among control and IAD were identified using ANOVA. Benjamini and Hochberg’s False Discovery Rate (FDR) was used for adjusting for multiple testing. The genes with significant change in expression were subject to hierarchical clustering using dChip.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Celia,,Williams
| | Sample_contact_email | celia@usc.edu
| | Sample_contact_phone | 3234421603
| | Sample_contact_fax | 3234421608
| | Sample_contact_laboratory | MCA348
| | Sample_contact_department | Pathology
| | Sample_contact_institute | Keck School of Medicine, USC
| | Sample_contact_address | 2011 Zonal Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90033
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318320/suppl/GSM318320.CEL.gz
| | Sample_series_id | GSE12685
| | Sample_data_row_count | 22283
| | |
|
GSM318321 | GPL96 |
|
Incipient AD 606
|
Frontal cortex synaptoneurosome
|
Synaptoneurosomes isolated from human brain frontal cortex of a patient with incipient Alzheimer's Disease with MMSE 26
|
The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
|
| Sample_geo_accession | GSM318321
| | Sample_status | Public on Jan 10 2009
| | Sample_submission_date | Sep 04 2008
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Alzheimer's Disease Research Center Neuropathology Core, NIA AG05142
| | Sample_treatment_protocol_ch1 | Synaptoneurosomes were prepared by a standard method (Banko et al., 2004; Johnson et al., 1997; Villasana et al., 2006; Westmark and Malter, 2007). with slight modifications. Frontal cortex (0.5gm-2.5gm) was thawed and homogenized with a Teflon-homogenizer (4 strokes at 1000 rpm) in buffer (1/10wt/vol), containing 0.35M sucrose pH7.4, 10mM HEPES, 1mM EDTA, 0.25mM dithiothreitol, 30U/ml RNAse inhibitor and a protease inhibitor cocktail (Pierce, Rockford, Il). Cell debris and nuclei were removed by centrifugation at 1000g for 10 min at 4°C yielding pellet P1 and supernatant S1. The S1 fraction was passed sequentially through a series of screens with decreasing pore sizes of 100, 80, 30 and 10m. The final filtrate was resuspended in 3 volumes of buffer without sucrose and centrifuged at 2000xg, for 15 minutes at 4°C to yield a pellet containing synaptoneurosomes. Total preparation time did not exceed 1 hour.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from synaptoneurosome preparations was extracted with Trizol LS and purified with RNeasy columns. The RNA was quantified and checked for purity by comparison of absorbance at 260 and 280nm in the Nanodrop Spectrophotometer. Total RNA and mRNA were analyzed for integrity and concentration by microanalysis in an Agilent bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation and amplification of cDNA was accomplished by the use of an Enzo BioArray High Yield RNA Transcript Labeling Kit followed by purification by absorption over an RNeasy column.
| | Sample_hyb_protocol | Hybridization to the HG-U133A (Affymetrix) was performed according to standard Affymetrix protocols. Probe-sets consist of 11 probe-pairs, distributed across the array, which are typically designed with bias towards the 3'-end of each gene and include a mismatched pair for quantification and subtraction of non-specific hybridization. Escherichia coli internal spike controls are also included to determine hybridization efficiency. The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner.
| | Sample_scan_protocol | The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner. Microarray Analysis Suite 5.0 (MAS 5.0) was used for the initial signal analysis which generates a signal detection value based on the difference between the perfect match (PM) and mismatch (MM) probes in a probe set. A ‘present’ or ‘absent’ call was assigned to each gene by MAS 5.0 according to certain threshold and the detection p-values. The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
| | Sample_data_processing | Model-Based Expression Index (dChip) (Li and Wong, 2001) implemented in Bioconductor, was used for signal normalization within an individual chip and across all samples. For high-level analysis, statistics tests were conducted to find significantly expressed genes, and this small set of genes was applied for clustering and pathway analysis. Probe sets that were differentially expressed among control and IAD were identified using ANOVA. Benjamini and Hochberg’s False Discovery Rate (FDR) was used for adjusting for multiple testing. The genes with significant change in expression were subject to hierarchical clustering using dChip.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Celia,,Williams
| | Sample_contact_email | celia@usc.edu
| | Sample_contact_phone | 3234421603
| | Sample_contact_fax | 3234421608
| | Sample_contact_laboratory | MCA348
| | Sample_contact_department | Pathology
| | Sample_contact_institute | Keck School of Medicine, USC
| | Sample_contact_address | 2011 Zonal Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90033
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318321/suppl/GSM318321.CEL.gz
| | Sample_series_id | GSE12685
| | Sample_data_row_count | 22283
| | |
|
GSM318442 | GPL96 |
|
Incipient AD 678
|
Frontal cortex synaptoneurosome
|
Synaptoneurosomes isolated from human brain frontal cortex of a patient with incipient Alzheimer's Disease with MMSE 25
|
The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
|
| Sample_geo_accession | GSM318442
| | Sample_status | Public on Jan 10 2009
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Alzheimer's Disease Research Center Neuropathology Core, NIA AG05142
| | Sample_treatment_protocol_ch1 | Synaptoneurosomes were prepared by a standard method (Banko et al., 2004; Johnson et al., 1997; Villasana et al., 2006; Westmark and Malter, 2007). with slight modifications. Frontal cortex (0.5gm-2.5gm) was thawed and homogenized with a Teflon-homogenizer (4 strokes at 1000 rpm) in buffer (1/10wt/vol), containing 0.35M sucrose pH7.4, 10mM HEPES, 1mM EDTA, 0.25mM dithiothreitol, 30U/ml RNAse inhibitor and a protease inhibitor cocktail (Pierce, Rockford, Il). Cell debris and nuclei were removed by centrifugation at 1000g for 10 min at 4°C yielding pellet P1 and supernatant S1. The S1 fraction was passed sequentially through a series of screens with decreasing pore sizes of 100, 80, 30 and 10m. The final filtrate was resuspended in 3 volumes of buffer without sucrose and centrifuged at 2000xg, for 15 minutes at 4°C to yield a pellet containing synaptoneurosomes. Total preparation time did not exceed 1 hour.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from synaptoneurosome preparations was extracted with Trizol LS and purified with RNeasy columns. The RNA was quantified and checked for purity by comparison of absorbance at 260 and 280nm in the Nanodrop Spectrophotometer. Total RNA and mRNA were analyzed for integrity and concentration by microanalysis in an Agilent bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation and amplification of cDNA was accomplished by the use of an Enzo BioArray High Yield RNA Transcript Labeling Kit followed by purification by absorption over an RNeasy column.
| | Sample_hyb_protocol | Hybridization to the HG-U133A (Affymetrix) was performed according to standard Affymetrix protocols. Probe-sets consist of 11 probe-pairs, distributed across the array, which are typically designed with bias towards the 3'-end of each gene and include a mismatched pair for quantification and subtraction of non-specific hybridization. Escherichia coli internal spike controls are also included to determine hybridization efficiency. The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner.
| | Sample_scan_protocol | The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner. Microarray Analysis Suite 5.0 (MAS 5.0) was used for the initial signal analysis which generates a signal detection value based on the difference between the perfect match (PM) and mismatch (MM) probes in a probe set. A ‘present’ or ‘absent’ call was assigned to each gene by MAS 5.0 according to certain threshold and the detection p-values. The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
| | Sample_data_processing | Model-Based Expression Index (dChip) (Li and Wong, 2001) implemented in Bioconductor, was used for signal normalization within an individual chip and across all samples. For high-level analysis, statistics tests were conducted to find significantly expressed genes, and this small set of genes was applied for clustering and pathway analysis. Probe sets that were differentially expressed among control and IAD were identified using ANOVA. Benjamini and Hochberg’s False Discovery Rate (FDR) was used for adjusting for multiple testing. The genes with significant change in expression were subject to hierarchical clustering using dChip.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Celia,,Williams
| | Sample_contact_email | celia@usc.edu
| | Sample_contact_phone | 3234421603
| | Sample_contact_fax | 3234421608
| | Sample_contact_laboratory | MCA348
| | Sample_contact_department | Pathology
| | Sample_contact_institute | Keck School of Medicine, USC
| | Sample_contact_address | 2011 Zonal Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90033
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318442/suppl/GSM318442.CEL.gz
| | Sample_series_id | GSE12685
| | Sample_data_row_count | 22283
| | |
|
GSM318443 | GPL96 |
|
Incipient AD 702
|
Frontal cortex synaptoneurosome
|
Synaptoneurosomes isolated from human brain frontal cortex of a patient with incipient Alzheimer's Disease with MMSE 26
|
The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
|
| Sample_geo_accession | GSM318443
| | Sample_status | Public on Jan 10 2009
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Alzheimer's Disease Research Center Neuropathology Core, NIA AG05142
| | Sample_treatment_protocol_ch1 | Synaptoneurosomes were prepared by a standard method (Banko et al., 2004; Johnson et al., 1997; Villasana et al., 2006; Westmark and Malter, 2007). with slight modifications. Frontal cortex (0.5gm-2.5gm) was thawed and homogenized with a Teflon-homogenizer (4 strokes at 1000 rpm) in buffer (1/10wt/vol), containing 0.35M sucrose pH7.4, 10mM HEPES, 1mM EDTA, 0.25mM dithiothreitol, 30U/ml RNAse inhibitor and a protease inhibitor cocktail (Pierce, Rockford, Il). Cell debris and nuclei were removed by centrifugation at 1000g for 10 min at 4°C yielding pellet P1 and supernatant S1. The S1 fraction was passed sequentially through a series of screens with decreasing pore sizes of 100, 80, 30 and 10m. The final filtrate was resuspended in 3 volumes of buffer without sucrose and centrifuged at 2000xg, for 15 minutes at 4°C to yield a pellet containing synaptoneurosomes. Total preparation time did not exceed 1 hour.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from synaptoneurosome preparations was extracted with Trizol LS and purified with RNeasy columns. The RNA was quantified and checked for purity by comparison of absorbance at 260 and 280nm in the Nanodrop Spectrophotometer. Total RNA and mRNA were analyzed for integrity and concentration by microanalysis in an Agilent bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation and amplification of cDNA was accomplished by the use of an Enzo BioArray High Yield RNA Transcript Labeling Kit followed by purification by absorption over an RNeasy column.
| | Sample_hyb_protocol | Hybridization to the HG-U133A (Affymetrix) was performed according to standard Affymetrix protocols. Probe-sets consist of 11 probe-pairs, distributed across the array, which are typically designed with bias towards the 3'-end of each gene and include a mismatched pair for quantification and subtraction of non-specific hybridization. Escherichia coli internal spike controls are also included to determine hybridization efficiency. The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner.
| | Sample_scan_protocol | The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner. Microarray Analysis Suite 5.0 (MAS 5.0) was used for the initial signal analysis which generates a signal detection value based on the difference between the perfect match (PM) and mismatch (MM) probes in a probe set. A ‘present’ or ‘absent’ call was assigned to each gene by MAS 5.0 according to certain threshold and the detection p-values. The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
| | Sample_data_processing | Model-Based Expression Index (dChip) (Li and Wong, 2001) implemented in Bioconductor, was used for signal normalization within an individual chip and across all samples. For high-level analysis, statistics tests were conducted to find significantly expressed genes, and this small set of genes was applied for clustering and pathway analysis. Probe sets that were differentially expressed among control and IAD were identified using ANOVA. Benjamini and Hochberg’s False Discovery Rate (FDR) was used for adjusting for multiple testing. The genes with significant change in expression were subject to hierarchical clustering using dChip.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Celia,,Williams
| | Sample_contact_email | celia@usc.edu
| | Sample_contact_phone | 3234421603
| | Sample_contact_fax | 3234421608
| | Sample_contact_laboratory | MCA348
| | Sample_contact_department | Pathology
| | Sample_contact_institute | Keck School of Medicine, USC
| | Sample_contact_address | 2011 Zonal Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90033
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318443/suppl/GSM318443.CEL.gz
| | Sample_series_id | GSE12685
| | Sample_data_row_count | 22283
| | |
|
GSM318445 | GPL96 |
|
Incipient AD 733
|
Frontal cortex synaptoneurosome
|
Synaptoneurosomes isolated from human brain frontal cortex of a patient with incipient Alzheimer's Disease with MMSE 27
|
The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
|
| Sample_geo_accession | GSM318445
| | Sample_status | Public on Jan 10 2009
| | Sample_submission_date | Sep 05 2008
| | Sample_last_update_date | Jan 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Alzheimer's Disease Research Center Neuropathology Core, NIA AG05142
| | Sample_treatment_protocol_ch1 | Synaptoneurosomes were prepared by a standard method (Banko et al., 2004; Johnson et al., 1997; Villasana et al., 2006; Westmark and Malter, 2007). with slight modifications. Frontal cortex (0.5gm-2.5gm) was thawed and homogenized with a Teflon-homogenizer (4 strokes at 1000 rpm) in buffer (1/10wt/vol), containing 0.35M sucrose pH7.4, 10mM HEPES, 1mM EDTA, 0.25mM dithiothreitol, 30U/ml RNAse inhibitor and a protease inhibitor cocktail (Pierce, Rockford, Il). Cell debris and nuclei were removed by centrifugation at 1000g for 10 min at 4°C yielding pellet P1 and supernatant S1. The S1 fraction was passed sequentially through a series of screens with decreasing pore sizes of 100, 80, 30 and 10m. The final filtrate was resuspended in 3 volumes of buffer without sucrose and centrifuged at 2000xg, for 15 minutes at 4°C to yield a pellet containing synaptoneurosomes. Total preparation time did not exceed 1 hour.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from synaptoneurosome preparations was extracted with Trizol LS and purified with RNeasy columns. The RNA was quantified and checked for purity by comparison of absorbance at 260 and 280nm in the Nanodrop Spectrophotometer. Total RNA and mRNA were analyzed for integrity and concentration by microanalysis in an Agilent bioanalyzer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation and amplification of cDNA was accomplished by the use of an Enzo BioArray High Yield RNA Transcript Labeling Kit followed by purification by absorption over an RNeasy column.
| | Sample_hyb_protocol | Hybridization to the HG-U133A (Affymetrix) was performed according to standard Affymetrix protocols. Probe-sets consist of 11 probe-pairs, distributed across the array, which are typically designed with bias towards the 3'-end of each gene and include a mismatched pair for quantification and subtraction of non-specific hybridization. Escherichia coli internal spike controls are also included to determine hybridization efficiency. The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner.
| | Sample_scan_protocol | The hybridized array was washed, labeled with phycoerythrin-conjugated streptavidin and scanned in the Affymetrix scanner. Microarray Analysis Suite 5.0 (MAS 5.0) was used for the initial signal analysis which generates a signal detection value based on the difference between the perfect match (PM) and mismatch (MM) probes in a probe set. A ‘present’ or ‘absent’ call was assigned to each gene by MAS 5.0 according to certain threshold and the detection p-values. The microarray data was checked for RNA degradation, visible defects in images, and Affymetrix hybridization control by Bioconductor Affymetrix package (http://www.bioconductor.org/)
| | Sample_data_processing | Model-Based Expression Index (dChip) (Li and Wong, 2001) implemented in Bioconductor, was used for signal normalization within an individual chip and across all samples. For high-level analysis, statistics tests were conducted to find significantly expressed genes, and this small set of genes was applied for clustering and pathway analysis. Probe sets that were differentially expressed among control and IAD were identified using ANOVA. Benjamini and Hochberg’s False Discovery Rate (FDR) was used for adjusting for multiple testing. The genes with significant change in expression were subject to hierarchical clustering using dChip.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Celia,,Williams
| | Sample_contact_email | celia@usc.edu
| | Sample_contact_phone | 3234421603
| | Sample_contact_fax | 3234421608
| | Sample_contact_laboratory | MCA348
| | Sample_contact_department | Pathology
| | Sample_contact_institute | Keck School of Medicine, USC
| | Sample_contact_address | 2011 Zonal Ave
| | Sample_contact_city | Los Angeles
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 90033
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM318nnn/GSM318445/suppl/GSM318445.CEL.gz
| | Sample_series_id | GSE12685
| | Sample_data_row_count | 22283
| | |
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