Search results for the GEO ID: GSE8717  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM215800 | GPL570 |
|
8814_Mock_1
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
8814_Mock_1
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215800
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215800/suppl/GSM215800.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215801 | GPL570 |
|
90-8_Infect_1
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
90-8_Infect_1
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215801
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215801/suppl/GSM215801.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215802 | GPL570 |
|
90-8_Mock_2
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
90-8_Mock_2
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215802
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215802/suppl/GSM215802.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215803 | GPL570 |
|
S462_Infect_2
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
S462_Infect_2
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215803
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215803/suppl/GSM215803.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215804 | GPL570 |
|
S462_Mock_2
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
S462_Mock_2
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215804
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215804/suppl/GSM215804.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215805 | GPL570 |
|
T265_Mock_2
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
T265_Mock_2
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215805
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215805/suppl/GSM215805.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215806 | GPL570 |
|
26T_Infect_1
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
26T_Infect_1
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215806
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215806/suppl/GSM215806.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215807 | GPL570 |
|
26T_Infect_2
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
26T_Infect_2
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215807
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215807/suppl/GSM215807.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215808 | GPL570 |
|
26T_Mock_1
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
26T_Mock_1
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215808
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215808/suppl/GSM215808.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215809 | GPL570 |
|
26T_Mock_2
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
26T_Mock_2
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215809
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215809/suppl/GSM215809.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215810 | GPL570 |
|
S462_Infect_3
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
S462_Infect_3
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215810
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215810/suppl/GSM215810.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215811 | GPL570 |
|
S462_Mock_3
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
S462_Mock_3
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215811
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215811/suppl/GSM215811.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215812 | GPL570 |
|
90-8_Mock_1
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
90-8_Mock_1
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215812
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215812/suppl/GSM215812.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215813 | GPL570 |
|
T265_Infect_2
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
T265_Infect_2
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215813
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215813/suppl/GSM215813.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215814 | GPL570 |
|
T265_Mock_3
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
T265_Mock_3
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215814
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215814/suppl/GSM215814.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215815 | GPL570 |
|
S462_Infect_1
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
S462_Infect_1
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215815
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215815/suppl/GSM215815.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215816 | GPL570 |
|
S462_Mock_1
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
S462_Mock_1
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215816
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215816/suppl/GSM215816.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215817 | GPL570 |
|
T265_Mock_1
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
T265_Mock_1
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215817
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215817/suppl/GSM215817.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215818 | GPL570 |
|
T265_Infect_1
|
MPNST cancer cells infected with G207 and oncolytic HSV.
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T265_Infect_1
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Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215818
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215818/suppl/GSM215818.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215819 | GPL570 |
|
8814_Infect_1
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
8814_Infect_1
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215819
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215819/suppl/GSM215819.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215820 | GPL570 |
|
8814_Mock_2
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
8814_Mock_2
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215820
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215820/suppl/GSM215820.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
|
GSM215821 | GPL570 |
|
90-8_Infect_2
|
MPNST cancer cells infected with G207 and oncolytic HSV.
|
90-8_Infect_2
|
Five different human MPNST cell lines, mock treated or infected with G207.
|
| Sample_geo_accession | GSM215821
| | Sample_status | Public on Aug 08 2007
| | Sample_submission_date | Aug 07 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Samples were mock treated or infected with G207.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from uninfected or G207 infected MPNST cancer cells. RNA was collected at 6 hours post infection. RNA was hybridized to the Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA).
| | Sample_extract_protocol_ch1 | Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was extracted from cells using Trizol (Invitrogen, Carlsbad, CA) followed by RNeasy purification (Qiagen, Valencia, CA) according the manufacturer’s specifications. Labeling involved an in vitro transcription reaction using the ENZO BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY) according to manufacturer’s instructions.
| | Sample_hyb_protocol | Create a hybridization cocktail for a single probe array that contains 0.05 ?g/?L fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 95°C for 5 minutes, to 45°C for 10 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 ?L of 1X Hybridization Buffer. Incubate at 45°C for 5 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 ?L of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization oven rotating at 30 rpm. Hybridized arrays were washed, labeled with phycoerythrin conjugated streptavidin (Molecular Probes, Eugene, OR) and scanned on the Affymetrix scanner.
| | Sample_scan_protocol | Images were scanned using a Genechip scanner 3000 [Affymetrix]
| | Sample_data_processing | Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.3.
| | Sample_data_processing | Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
| | Sample_data_processing | GeneSpring 7.3 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. Raw expression data in .cel files were imported into Genespring (Silicon Genetics) and RMA processed using quantile normalization. Data were normalized in Genespring via data transformation, per chip normalization to the 50th percentile and per gene normalization to the average of the corresponding time-matched mock infected samples. For statistical analysis, we performed a 1-way ANOVA with non-parametric analysis with a false discovery rate of 0.025 with multiple testing correction by Benjamin and Hochberg FDR. The number of probe-sets passing these criteria was 7,817. This list was filtered on expression level for <0.7 and >1.3 giving 7,351 probe-sets. K-means clustering was performed for maximum of 5 clusters.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Bruce,J,Aronow
| | Sample_contact_email | bruce.aronow@chmcc.org
| | Sample_contact_phone | 513-636-4865
| | Sample_contact_institute | Cincinnati Children's Hospital Medical Center
| | Sample_contact_address |
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45229
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM215nnn/GSM215821/suppl/GSM215821.CEL.gz
| | Sample_series_id | GSE8717
| | Sample_data_row_count | 54675
| | |
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