Search results for the GEO ID: GSE20333  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM509547 | GPL201 |
|
Control, A44
|
Substantia nigra
|
age: 75
gender: M
|
Gene expression data from substantia nigra
|
| Sample_geo_accession | GSM509547
| | Sample_status | Public on Mar 10 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Mar 09 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2001, Affymetrix).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_hyb_protocol | Spike controls were added to 15 ug fragmented cRNA before overnight hybridisation. Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix GeneChip scanner. A complete description of these procedures is available at http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_scan_protocol | Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_data_processing | MAS 5 was used to read the CEL files. Genes were filtered using Mas 5 algorithm results. One expected difficulty when working with post mortem samples is the various degrees of degradation in the RNA preparations. Therefore, cRNA originating from these samples contain more 3' ends than 5' prime ends. Since the Affymetrix array probe sets are designed so that the 3' ends are selected whenever possible (http://www.affymetrix.com/support/technical/technotes/hgu133_design_technote.pdf ), the analysis of relatively high-3'content samples becomes feasible. Probe sets detected by MAS 5 as Present (P) have a signal with a p-value lower than 0.04 (determined from the probes contained in the probe set). This allows us to use present call with confidence. Samples that are partially degraded may hybridize to part of the probes in the probe sets leading to a high p-value (and detected as absent). If the probe set in at least four out of six samples was detected as present and all of the signals were greater than 20, we determined this probe set to be present. A list of 3517 probe sets representing genes with signals higher than 20 and detected as present (P) in all control samples, or with signals higher than 20 in all PD samples and detected as present in four out of the six samples was generated from the 8763 probe sets contained on the array.
| | Sample_platform_id | GPL201
| | Sample_contact_name | jasmine,,jacob
| | Sample_contact_email | j-jacob@sheba.health.gov.il
| | Sample_contact_phone | 97235302147
| | Sample_contact_institute | sheba medical center
| | Sample_contact_address | tel hashomer
| | Sample_contact_city | ramat gan
| | Sample_contact_state | Israel
| | Sample_contact_zip/postal_code | 78995
| | Sample_contact_country | Israel
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509547/suppl/GSM509547.CEL.gz
| | Sample_series_id | GSE20333
| | Sample_data_row_count | 8793
| | |
|
GSM509548 | GPL201 |
|
Control, A46
|
Substantia nigra
|
age: 85
gender: M
|
Gene expression data from substantia nigra
|
| Sample_geo_accession | GSM509548
| | Sample_status | Public on Mar 10 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Mar 09 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2001, Affymetrix).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_hyb_protocol | Spike controls were added to 15 ug fragmented cRNA before overnight hybridisation. Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix GeneChip scanner. A complete description of these procedures is available at http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_scan_protocol | Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_data_processing | MAS 5 was used to read the CEL files. Genes were filtered using Mas 5 algorithm results. One expected difficulty when working with post mortem samples is the various degrees of degradation in the RNA preparations. Therefore, cRNA originating from these samples contain more 3' ends than 5' prime ends. Since the Affymetrix array probe sets are designed so that the 3' ends are selected whenever possible (http://www.affymetrix.com/support/technical/technotes/hgu133_design_technote.pdf ), the analysis of relatively high-3'content samples becomes feasible. Probe sets detected by MAS 5 as Present (P) have a signal with a p-value lower than 0.04 (determined from the probes contained in the probe set). This allows us to use present call with confidence. Samples that are partially degraded may hybridize to part of the probes in the probe sets leading to a high p-value (and detected as absent). If the probe set in at least four out of six samples was detected as present and all of the signals were greater than 20, we determined this probe set to be present. A list of 3517 probe sets representing genes with signals higher than 20 and detected as present (P) in all control samples, or with signals higher than 20 in all PD samples and detected as present in four out of the six samples was generated from the 8763 probe sets contained on the array.
| | Sample_platform_id | GPL201
| | Sample_contact_name | jasmine,,jacob
| | Sample_contact_email | j-jacob@sheba.health.gov.il
| | Sample_contact_phone | 97235302147
| | Sample_contact_institute | sheba medical center
| | Sample_contact_address | tel hashomer
| | Sample_contact_city | ramat gan
| | Sample_contact_state | Israel
| | Sample_contact_zip/postal_code | 78995
| | Sample_contact_country | Israel
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509548/suppl/GSM509548.CEL.gz
| | Sample_series_id | GSE20333
| | Sample_data_row_count | 8793
| | |
|
GSM509549 | GPL201 |
|
Control, A48
|
Substantia nigra
|
age: 68
gender: M
|
Gene expression data from substantia nigra
|
| Sample_geo_accession | GSM509549
| | Sample_status | Public on Mar 10 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Mar 09 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2001, Affymetrix).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_hyb_protocol | Spike controls were added to 15 ug fragmented cRNA before overnight hybridisation. Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix GeneChip scanner. A complete description of these procedures is available at http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_scan_protocol | Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_data_processing | MAS 5 was used to read the CEL files. Genes were filtered using Mas 5 algorithm results. One expected difficulty when working with post mortem samples is the various degrees of degradation in the RNA preparations. Therefore, cRNA originating from these samples contain more 3' ends than 5' prime ends. Since the Affymetrix array probe sets are designed so that the 3' ends are selected whenever possible (http://www.affymetrix.com/support/technical/technotes/hgu133_design_technote.pdf ), the analysis of relatively high-3'content samples becomes feasible. Probe sets detected by MAS 5 as Present (P) have a signal with a p-value lower than 0.04 (determined from the probes contained in the probe set). This allows us to use present call with confidence. Samples that are partially degraded may hybridize to part of the probes in the probe sets leading to a high p-value (and detected as absent). If the probe set in at least four out of six samples was detected as present and all of the signals were greater than 20, we determined this probe set to be present. A list of 3517 probe sets representing genes with signals higher than 20 and detected as present (P) in all control samples, or with signals higher than 20 in all PD samples and detected as present in four out of the six samples was generated from the 8763 probe sets contained on the array.
| | Sample_platform_id | GPL201
| | Sample_contact_name | jasmine,,jacob
| | Sample_contact_email | j-jacob@sheba.health.gov.il
| | Sample_contact_phone | 97235302147
| | Sample_contact_institute | sheba medical center
| | Sample_contact_address | tel hashomer
| | Sample_contact_city | ramat gan
| | Sample_contact_state | Israel
| | Sample_contact_zip/postal_code | 78995
| | Sample_contact_country | Israel
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509549/suppl/GSM509549.CEL.gz
| | Sample_series_id | GSE20333
| | Sample_data_row_count | 8793
| | |
|
GSM509550 | GPL201 |
|
Control, A49
|
Substantia nigra
|
age: 88
gender: M
|
Gene expression data from substantia nigra
|
| Sample_geo_accession | GSM509550
| | Sample_status | Public on Mar 10 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Mar 09 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2001, Affymetrix).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_hyb_protocol | Spike controls were added to 15 ug fragmented cRNA before overnight hybridisation. Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix GeneChip scanner. A complete description of these procedures is available at http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_scan_protocol | Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_data_processing | MAS 5 was used to read the CEL files. Genes were filtered using Mas 5 algorithm results. One expected difficulty when working with post mortem samples is the various degrees of degradation in the RNA preparations. Therefore, cRNA originating from these samples contain more 3' ends than 5' prime ends. Since the Affymetrix array probe sets are designed so that the 3' ends are selected whenever possible (http://www.affymetrix.com/support/technical/technotes/hgu133_design_technote.pdf ), the analysis of relatively high-3'content samples becomes feasible. Probe sets detected by MAS 5 as Present (P) have a signal with a p-value lower than 0.04 (determined from the probes contained in the probe set). This allows us to use present call with confidence. Samples that are partially degraded may hybridize to part of the probes in the probe sets leading to a high p-value (and detected as absent). If the probe set in at least four out of six samples was detected as present and all of the signals were greater than 20, we determined this probe set to be present. A list of 3517 probe sets representing genes with signals higher than 20 and detected as present (P) in all control samples, or with signals higher than 20 in all PD samples and detected as present in four out of the six samples was generated from the 8763 probe sets contained on the array.
| | Sample_platform_id | GPL201
| | Sample_contact_name | jasmine,,jacob
| | Sample_contact_email | j-jacob@sheba.health.gov.il
| | Sample_contact_phone | 97235302147
| | Sample_contact_institute | sheba medical center
| | Sample_contact_address | tel hashomer
| | Sample_contact_city | ramat gan
| | Sample_contact_state | Israel
| | Sample_contact_zip/postal_code | 78995
| | Sample_contact_country | Israel
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509550/suppl/GSM509550.CEL.gz
| | Sample_series_id | GSE20333
| | Sample_data_row_count | 8793
| | |
|
GSM509551 | GPL201 |
|
Control, A11
|
Substantia nigra
|
age: 72
gender: M
|
Gene expression data from substantia nigra
|
| Sample_geo_accession | GSM509551
| | Sample_status | Public on Mar 10 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Mar 09 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2001, Affymetrix).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_hyb_protocol | Spike controls were added to 15 ug fragmented cRNA before overnight hybridisation. Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix GeneChip scanner. A complete description of these procedures is available at http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_scan_protocol | Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_data_processing | MAS 5 was used to read the CEL files. Genes were filtered using Mas 5 algorithm results. One expected difficulty when working with post mortem samples is the various degrees of degradation in the RNA preparations. Therefore, cRNA originating from these samples contain more 3' ends than 5' prime ends. Since the Affymetrix array probe sets are designed so that the 3' ends are selected whenever possible (http://www.affymetrix.com/support/technical/technotes/hgu133_design_technote.pdf ), the analysis of relatively high-3'content samples becomes feasible. Probe sets detected by MAS 5 as Present (P) have a signal with a p-value lower than 0.04 (determined from the probes contained in the probe set). This allows us to use present call with confidence. Samples that are partially degraded may hybridize to part of the probes in the probe sets leading to a high p-value (and detected as absent). If the probe set in at least four out of six samples was detected as present and all of the signals were greater than 20, we determined this probe set to be present. A list of 3517 probe sets representing genes with signals higher than 20 and detected as present (P) in all control samples, or with signals higher than 20 in all PD samples and detected as present in four out of the six samples was generated from the 8763 probe sets contained on the array.
| | Sample_platform_id | GPL201
| | Sample_contact_name | jasmine,,jacob
| | Sample_contact_email | j-jacob@sheba.health.gov.il
| | Sample_contact_phone | 97235302147
| | Sample_contact_institute | sheba medical center
| | Sample_contact_address | tel hashomer
| | Sample_contact_city | ramat gan
| | Sample_contact_state | Israel
| | Sample_contact_zip/postal_code | 78995
| | Sample_contact_country | Israel
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509551/suppl/GSM509551.CEL.gz
| | Sample_series_id | GSE20333
| | Sample_data_row_count | 8793
| | |
|
GSM509552 | GPL201 |
|
Control, A12
|
Substantia nigra
|
age: 86
gender: F
|
Gene expression data from substantia nigra
|
| Sample_geo_accession | GSM509552
| | Sample_status | Public on Mar 10 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Mar 09 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2001, Affymetrix).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_hyb_protocol | Spike controls were added to 15 ug fragmented cRNA before overnight hybridisation. Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix GeneChip scanner. A complete description of these procedures is available at http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_scan_protocol | Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_data_processing | MAS 5 was used to read the CEL files. Genes were filtered using Mas 5 algorithm results. One expected difficulty when working with post mortem samples is the various degrees of degradation in the RNA preparations. Therefore, cRNA originating from these samples contain more 3' ends than 5' prime ends. Since the Affymetrix array probe sets are designed so that the 3' ends are selected whenever possible (http://www.affymetrix.com/support/technical/technotes/hgu133_design_technote.pdf ), the analysis of relatively high-3'content samples becomes feasible. Probe sets detected by MAS 5 as Present (P) have a signal with a p-value lower than 0.04 (determined from the probes contained in the probe set). This allows us to use present call with confidence. Samples that are partially degraded may hybridize to part of the probes in the probe sets leading to a high p-value (and detected as absent). If the probe set in at least four out of six samples was detected as present and all of the signals were greater than 20, we determined this probe set to be present. A list of 3517 probe sets representing genes with signals higher than 20 and detected as present (P) in all control samples, or with signals higher than 20 in all PD samples and detected as present in four out of the six samples was generated from the 8763 probe sets contained on the array.
| | Sample_platform_id | GPL201
| | Sample_contact_name | jasmine,,jacob
| | Sample_contact_email | j-jacob@sheba.health.gov.il
| | Sample_contact_phone | 97235302147
| | Sample_contact_institute | sheba medical center
| | Sample_contact_address | tel hashomer
| | Sample_contact_city | ramat gan
| | Sample_contact_state | Israel
| | Sample_contact_zip/postal_code | 78995
| | Sample_contact_country | Israel
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509552/suppl/GSM509552.CEL.gz
| | Sample_series_id | GSE20333
| | Sample_data_row_count | 8793
| | |
|
GSM509553 | GPL201 |
|
Parkinson's disease, A9
|
Substantia nigra
|
age: 73
gender: F
|
Gene expression data from substantia nigra
|
| Sample_geo_accession | GSM509553
| | Sample_status | Public on Mar 10 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Mar 09 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2001, Affymetrix).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_hyb_protocol | Spike controls were added to 15 ug fragmented cRNA before overnight hybridisation. Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix GeneChip scanner. A complete description of these procedures is available at http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_scan_protocol | Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_data_processing | MAS 5 was used to read the CEL files. Genes were filtered using Mas 5 algorithm results. One expected difficulty when working with post mortem samples is the various degrees of degradation in the RNA preparations. Therefore, cRNA originating from these samples contain more 3' ends than 5' prime ends. Since the Affymetrix array probe sets are designed so that the 3' ends are selected whenever possible (http://www.affymetrix.com/support/technical/technotes/hgu133_design_technote.pdf ), the analysis of relatively high-3'content samples becomes feasible. Probe sets detected by MAS 5 as Present (P) have a signal with a p-value lower than 0.04 (determined from the probes contained in the probe set). This allows us to use present call with confidence. Samples that are partially degraded may hybridize to part of the probes in the probe sets leading to a high p-value (and detected as absent). If the probe set in at least four out of six samples was detected as present and all of the signals were greater than 20, we determined this probe set to be present. A list of 3517 probe sets representing genes with signals higher than 20 and detected as present (P) in all control samples, or with signals higher than 20 in all PD samples and detected as present in four out of the six samples was generated from the 8763 probe sets contained on the array.
| | Sample_platform_id | GPL201
| | Sample_contact_name | jasmine,,jacob
| | Sample_contact_email | j-jacob@sheba.health.gov.il
| | Sample_contact_phone | 97235302147
| | Sample_contact_institute | sheba medical center
| | Sample_contact_address | tel hashomer
| | Sample_contact_city | ramat gan
| | Sample_contact_state | Israel
| | Sample_contact_zip/postal_code | 78995
| | Sample_contact_country | Israel
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509553/suppl/GSM509553.CEL.gz
| | Sample_series_id | GSE20333
| | Sample_data_row_count | 8793
| | |
|
GSM509554 | GPL201 |
|
Parkinson's disease, A10
|
Substantia nigra
|
age: 79
gender: F
|
Gene expression data from substantia nigra
|
| Sample_geo_accession | GSM509554
| | Sample_status | Public on Mar 10 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Mar 09 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2001, Affymetrix).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_hyb_protocol | Spike controls were added to 15 ug fragmented cRNA before overnight hybridisation. Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix GeneChip scanner. A complete description of these procedures is available at http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_scan_protocol | Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_data_processing | MAS 5 was used to read the CEL files. Genes were filtered using Mas 5 algorithm results. One expected difficulty when working with post mortem samples is the various degrees of degradation in the RNA preparations. Therefore, cRNA originating from these samples contain more 3' ends than 5' prime ends. Since the Affymetrix array probe sets are designed so that the 3' ends are selected whenever possible (http://www.affymetrix.com/support/technical/technotes/hgu133_design_technote.pdf ), the analysis of relatively high-3'content samples becomes feasible. Probe sets detected by MAS 5 as Present (P) have a signal with a p-value lower than 0.04 (determined from the probes contained in the probe set). This allows us to use present call with confidence. Samples that are partially degraded may hybridize to part of the probes in the probe sets leading to a high p-value (and detected as absent). If the probe set in at least four out of six samples was detected as present and all of the signals were greater than 20, we determined this probe set to be present. A list of 3517 probe sets representing genes with signals higher than 20 and detected as present (P) in all control samples, or with signals higher than 20 in all PD samples and detected as present in four out of the six samples was generated from the 8763 probe sets contained on the array.
| | Sample_platform_id | GPL201
| | Sample_contact_name | jasmine,,jacob
| | Sample_contact_email | j-jacob@sheba.health.gov.il
| | Sample_contact_phone | 97235302147
| | Sample_contact_institute | sheba medical center
| | Sample_contact_address | tel hashomer
| | Sample_contact_city | ramat gan
| | Sample_contact_state | Israel
| | Sample_contact_zip/postal_code | 78995
| | Sample_contact_country | Israel
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509554/suppl/GSM509554.CEL.gz
| | Sample_series_id | GSE20333
| | Sample_data_row_count | 8793
| | |
|
GSM509555 | GPL201 |
|
Parkinson's disease, A39
|
Substantia nigra
|
age: 87
gender: F
|
Gene expression data from substantia nigra
|
| Sample_geo_accession | GSM509555
| | Sample_status | Public on Mar 10 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Mar 09 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2001, Affymetrix).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_hyb_protocol | Spike controls were added to 15 ug fragmented cRNA before overnight hybridisation. Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix GeneChip scanner. A complete description of these procedures is available at http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_scan_protocol | Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_data_processing | MAS 5 was used to read the CEL files. Genes were filtered using Mas 5 algorithm results. One expected difficulty when working with post mortem samples is the various degrees of degradation in the RNA preparations. Therefore, cRNA originating from these samples contain more 3' ends than 5' prime ends. Since the Affymetrix array probe sets are designed so that the 3' ends are selected whenever possible (http://www.affymetrix.com/support/technical/technotes/hgu133_design_technote.pdf ), the analysis of relatively high-3'content samples becomes feasible. Probe sets detected by MAS 5 as Present (P) have a signal with a p-value lower than 0.04 (determined from the probes contained in the probe set). This allows us to use present call with confidence. Samples that are partially degraded may hybridize to part of the probes in the probe sets leading to a high p-value (and detected as absent). If the probe set in at least four out of six samples was detected as present and all of the signals were greater than 20, we determined this probe set to be present. A list of 3517 probe sets representing genes with signals higher than 20 and detected as present (P) in all control samples, or with signals higher than 20 in all PD samples and detected as present in four out of the six samples was generated from the 8763 probe sets contained on the array.
| | Sample_platform_id | GPL201
| | Sample_contact_name | jasmine,,jacob
| | Sample_contact_email | j-jacob@sheba.health.gov.il
| | Sample_contact_phone | 97235302147
| | Sample_contact_institute | sheba medical center
| | Sample_contact_address | tel hashomer
| | Sample_contact_city | ramat gan
| | Sample_contact_state | Israel
| | Sample_contact_zip/postal_code | 78995
| | Sample_contact_country | Israel
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509555/suppl/GSM509555.CEL.gz
| | Sample_series_id | GSE20333
| | Sample_data_row_count | 8793
| | |
|
GSM509556 | GPL201 |
|
Parkinson's disease, A41
|
Substantia nigra
|
age: 75
gender: M
|
Gene expression data from substantia nigra
|
| Sample_geo_accession | GSM509556
| | Sample_status | Public on Mar 10 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Mar 09 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2001, Affymetrix).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_hyb_protocol | Spike controls were added to 15 ug fragmented cRNA before overnight hybridisation. Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix GeneChip scanner. A complete description of these procedures is available at http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_scan_protocol | Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_data_processing | MAS 5 was used to read the CEL files. Genes were filtered using Mas 5 algorithm results. One expected difficulty when working with post mortem samples is the various degrees of degradation in the RNA preparations. Therefore, cRNA originating from these samples contain more 3' ends than 5' prime ends. Since the Affymetrix array probe sets are designed so that the 3' ends are selected whenever possible (http://www.affymetrix.com/support/technical/technotes/hgu133_design_technote.pdf ), the analysis of relatively high-3'content samples becomes feasible. Probe sets detected by MAS 5 as Present (P) have a signal with a p-value lower than 0.04 (determined from the probes contained in the probe set). This allows us to use present call with confidence. Samples that are partially degraded may hybridize to part of the probes in the probe sets leading to a high p-value (and detected as absent). If the probe set in at least four out of six samples was detected as present and all of the signals were greater than 20, we determined this probe set to be present. A list of 3517 probe sets representing genes with signals higher than 20 and detected as present (P) in all control samples, or with signals higher than 20 in all PD samples and detected as present in four out of the six samples was generated from the 8763 probe sets contained on the array.
| | Sample_platform_id | GPL201
| | Sample_contact_name | jasmine,,jacob
| | Sample_contact_email | j-jacob@sheba.health.gov.il
| | Sample_contact_phone | 97235302147
| | Sample_contact_institute | sheba medical center
| | Sample_contact_address | tel hashomer
| | Sample_contact_city | ramat gan
| | Sample_contact_state | Israel
| | Sample_contact_zip/postal_code | 78995
| | Sample_contact_country | Israel
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509556/suppl/GSM509556.CEL.gz
| | Sample_series_id | GSE20333
| | Sample_data_row_count | 8793
| | |
|
GSM509557 | GPL201 |
|
Parkinson's disease, A42
|
Substantia nigra
|
age: 78
gender: F
|
Gene expression data from substantia nigra
|
| Sample_geo_accession | GSM509557
| | Sample_status | Public on Mar 10 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Mar 09 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2001, Affymetrix).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_hyb_protocol | Spike controls were added to 15 ug fragmented cRNA before overnight hybridisation. Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix GeneChip scanner. A complete description of these procedures is available at http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_scan_protocol | Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_data_processing | MAS 5 was used to read the CEL files. Genes were filtered using Mas 5 algorithm results. One expected difficulty when working with post mortem samples is the various degrees of degradation in the RNA preparations. Therefore, cRNA originating from these samples contain more 3' ends than 5' prime ends. Since the Affymetrix array probe sets are designed so that the 3' ends are selected whenever possible (http://www.affymetrix.com/support/technical/technotes/hgu133_design_technote.pdf ), the analysis of relatively high-3'content samples becomes feasible. Probe sets detected by MAS 5 as Present (P) have a signal with a p-value lower than 0.04 (determined from the probes contained in the probe set). This allows us to use present call with confidence. Samples that are partially degraded may hybridize to part of the probes in the probe sets leading to a high p-value (and detected as absent). If the probe set in at least four out of six samples was detected as present and all of the signals were greater than 20, we determined this probe set to be present. A list of 3517 probe sets representing genes with signals higher than 20 and detected as present (P) in all control samples, or with signals higher than 20 in all PD samples and detected as present in four out of the six samples was generated from the 8763 probe sets contained on the array.
| | Sample_platform_id | GPL201
| | Sample_contact_name | jasmine,,jacob
| | Sample_contact_email | j-jacob@sheba.health.gov.il
| | Sample_contact_phone | 97235302147
| | Sample_contact_institute | sheba medical center
| | Sample_contact_address | tel hashomer
| | Sample_contact_city | ramat gan
| | Sample_contact_state | Israel
| | Sample_contact_zip/postal_code | 78995
| | Sample_contact_country | Israel
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509557/suppl/GSM509557.CEL.gz
| | Sample_series_id | GSE20333
| | Sample_data_row_count | 8793
| | |
|
GSM509558 | GPL201 |
|
Parkinson's disease, A43
|
Substantia nigra
|
age: 70
gender: M
|
Gene expression data from substantia nigra
|
| Sample_geo_accession | GSM509558
| | Sample_status | Public on Mar 10 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Mar 09 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2001, Affymetrix).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_hyb_protocol | Spike controls were added to 15 ug fragmented cRNA before overnight hybridisation. Arrays were then washed and stained with streptavidin-phycoerythrin, before being scanned on an Affymetrix GeneChip scanner. A complete description of these procedures is available at http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_scan_protocol | Standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2001).http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf
| | Sample_data_processing | MAS 5 was used to read the CEL files. Genes were filtered using Mas 5 algorithm results. One expected difficulty when working with post mortem samples is the various degrees of degradation in the RNA preparations. Therefore, cRNA originating from these samples contain more 3' ends than 5' prime ends. Since the Affymetrix array probe sets are designed so that the 3' ends are selected whenever possible (http://www.affymetrix.com/support/technical/technotes/hgu133_design_technote.pdf ), the analysis of relatively high-3'content samples becomes feasible. Probe sets detected by MAS 5 as Present (P) have a signal with a p-value lower than 0.04 (determined from the probes contained in the probe set). This allows us to use present call with confidence. Samples that are partially degraded may hybridize to part of the probes in the probe sets leading to a high p-value (and detected as absent). If the probe set in at least four out of six samples was detected as present and all of the signals were greater than 20, we determined this probe set to be present. A list of 3517 probe sets representing genes with signals higher than 20 and detected as present (P) in all control samples, or with signals higher than 20 in all PD samples and detected as present in four out of the six samples was generated from the 8763 probe sets contained on the array.
| | Sample_platform_id | GPL201
| | Sample_contact_name | jasmine,,jacob
| | Sample_contact_email | j-jacob@sheba.health.gov.il
| | Sample_contact_phone | 97235302147
| | Sample_contact_institute | sheba medical center
| | Sample_contact_address | tel hashomer
| | Sample_contact_city | ramat gan
| | Sample_contact_state | Israel
| | Sample_contact_zip/postal_code | 78995
| | Sample_contact_country | Israel
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509558/suppl/GSM509558.CEL.gz
| | Sample_series_id | GSE20333
| | Sample_data_row_count | 8793
| | |
|
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
Enter the group name here: |
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