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Search results for the GEO ID: GSE11040

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GSM279010

GPL1261

12.5 Valve Cells 1

Embryonic day (E)12.5 AV cushion, E17.5 AV valve and in vitro cultured MC3T3-E1 (subclone4) cells

Samples used for hybridization consisted of pooled RNA extracts from E12.5 AV cushion and E17.5 AV valve from wild-type FVB/N mice and in vitro cultured MC3T3 cells.

Sample_geo_accession	GSM279010
Sample_status	Public on Jul 11 2008
Sample_submission_date	Apr 03 2008
Sample_last_update_date	Jul 11 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	None
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Embryos were collected at E12.5 for isolation of AV cushion and E17.5 for isolation of AV valves. Dissected cushions and valves were washed in 1XPBS and collected in TRIzol Reagent (Invitrogen) for total RNA isolation.
Sample_extract_protocol_ch1	Quality control steps: Total RNA was purified using RNeasy Mini Kit (Qiagen) according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples used for hybridization consisted of pooled RNA extracts from the E12.5 AV cushion and E17.5 AV valve from wild-type FVB/N mice and in vitro cultured MC3T3 cells. Therefore, 6 hybridization experiments were performed in biological duplicates on pooled RNA extracts. The TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicenter) was used to make double-stranded cDNA from total RNA. An in vitro transcription reaction using the IVT Labeling Kit (Affymetrix) created biotin-labeled cRNA target. The cRNA target was chemically fragmented and then hybridized to an Affymetrix Mouse Genime 430 2.0 Genechip® Array400-500 ng of total RNA from each biological samples in duplicate was amplified twice with the Arcturus RiboAmp kit [Arcturus Bioscience, Inc., Mountain View, CA] and cRNA was labeled with biotin-UTP, CTP using T7 RNA polymerase [Enzo Life Sciences, Inc., Farmingdale, NY].
Sample_hyb_protocol	Create a hybridization cocktail for a single probe array that contains 0.034 ?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), 10% DMSO, and 1X Hybridization Buffer. Heat hybridization cocktail to 99?C for 5 minutes, to 45?C for 5 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 10 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 60 rpm.
Sample_hyb_protocol	Fluidics: Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.
Sample_scan_protocol	Images were scanned using a Genechip scanner 3000 [Affymetrix]
Sample_data_processing	Affymetrix murine MOE 430 2.0 gene chips were used. 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 quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and ?-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
Sample_data_processing	GeneSpring Gx 7.3 (Agilent technologies) was used to normalization, clustering and filtering. Individual clusters were then analyzed for functional relatedness of genes within the cluster using PANTHER gene classification system.
Sample_platform_id	GPL1261
Sample_contact_name	Katherine,E,Yutzey
Sample_contact_email	katherine.yutzey@cchmc.org
Sample_contact_phone	513-636-8340
Sample_contact_fax	513-636-5958
Sample_contact_department	Divison of Molecular Cardiovascular Biology
Sample_contact_institute	Cinicnnati Children's Hospital Medical Center
Sample_contact_address	240 Albert Sabin Way
Sample_contact_city	Cinicnnati
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/GSM279nnn/GSM279010/suppl/GSM279010.CEL.gz
Sample_series_id	GSE11040
Sample_data_row_count	45101

GSM279011

GPL1261

12.5 Valve Cells 2

Embryonic day (E)12.5 AV cushion, E17.5 AV valve and in vitro cultured MC3T3-E1 (subclone4) cells

Samples used for hybridization consisted of pooled RNA extracts from E12.5 AV cushion and E17.5 AV valve from wild-type FVB/N mice and in vitro cultured MC3T3 cells.

Sample_geo_accession	GSM279011
Sample_status	Public on Jul 11 2008
Sample_submission_date	Apr 03 2008
Sample_last_update_date	Jul 11 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	None
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Embryos were collected at E12.5 for isolation of AV cushion and E17.5 for isolation of AV valves. Dissected cushions and valves were washed in 1XPBS and collected in TRIzol Reagent (Invitrogen) for total RNA isolation.
Sample_extract_protocol_ch1	Quality control steps: Total RNA was purified using RNeasy Mini Kit (Qiagen) according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples used for hybridization consisted of pooled RNA extracts from the E12.5 AV cushion and E17.5 AV valve from wild-type FVB/N mice and in vitro cultured MC3T3 cells. Therefore, 6 hybridization experiments were performed in biological duplicates on pooled RNA extracts. The TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicenter) was used to make double-stranded cDNA from total RNA. An in vitro transcription reaction using the IVT Labeling Kit (Affymetrix) created biotin-labeled cRNA target. The cRNA target was chemically fragmented and then hybridized to an Affymetrix Mouse Genime 430 2.0 Genechip® Array400-500 ng of total RNA from each biological samples in duplicate was amplified twice with the Arcturus RiboAmp kit [Arcturus Bioscience, Inc., Mountain View, CA] and cRNA was labeled with biotin-UTP, CTP using T7 RNA polymerase [Enzo Life Sciences, Inc., Farmingdale, NY].
Sample_hyb_protocol	Create a hybridization cocktail for a single probe array that contains 0.034 ?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), 10% DMSO, and 1X Hybridization Buffer. Heat hybridization cocktail to 99?C for 5 minutes, to 45?C for 5 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 10 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 60 rpm.
Sample_hyb_protocol	Fluidics: Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.
Sample_scan_protocol	Images were scanned using a Genechip scanner 3000 [Affymetrix]
Sample_data_processing	Affymetrix murine MOE 430 2.0 gene chips were used. 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 quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and ?-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
Sample_data_processing	GeneSpring Gx 7.3 (Agilent technologies) was used to normalization, clustering and filtering. Individual clusters were then analyzed for functional relatedness of genes within the cluster using PANTHER gene classification system.
Sample_platform_id	GPL1261
Sample_contact_name	Katherine,E,Yutzey
Sample_contact_email	katherine.yutzey@cchmc.org
Sample_contact_phone	513-636-8340
Sample_contact_fax	513-636-5958
Sample_contact_department	Divison of Molecular Cardiovascular Biology
Sample_contact_institute	Cinicnnati Children's Hospital Medical Center
Sample_contact_address	240 Albert Sabin Way
Sample_contact_city	Cinicnnati
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/GSM279nnn/GSM279011/suppl/GSM279011.CEL.gz
Sample_series_id	GSE11040
Sample_data_row_count	45101

GSM279012

GPL1261

17.5 Valve Cells 1

Embryonic day (E)12.5 AV cushion, E17.5 AV valve and in vitro cultured MC3T3-E1 (subclone4) cells

Samples used for hybridization consisted of pooled RNA extracts from E12.5 AV cushion and E17.5 AV valve from wild-type FVB/N mice and in vitro cultured MC3T3 cells.

Sample_geo_accession	GSM279012
Sample_status	Public on Jul 11 2008
Sample_submission_date	Apr 03 2008
Sample_last_update_date	Jul 11 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	None
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Embryos were collected at E12.5 for isolation of AV cushion and E17.5 for isolation of AV valves. Dissected cushions and valves were washed in 1XPBS and collected in TRIzol Reagent (Invitrogen) for total RNA isolation.
Sample_extract_protocol_ch1	Quality control steps: Total RNA was purified using RNeasy Mini Kit (Qiagen) according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples used for hybridization consisted of pooled RNA extracts from the E12.5 AV cushion and E17.5 AV valve from wild-type FVB/N mice and in vitro cultured MC3T3 cells. Therefore, 6 hybridization experiments were performed in biological duplicates on pooled RNA extracts. The TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicenter) was used to make double-stranded cDNA from total RNA. An in vitro transcription reaction using the IVT Labeling Kit (Affymetrix) created biotin-labeled cRNA target. The cRNA target was chemically fragmented and then hybridized to an Affymetrix Mouse Genime 430 2.0 Genechip® Array400-500 ng of total RNA from each biological samples in duplicate was amplified twice with the Arcturus RiboAmp kit [Arcturus Bioscience, Inc., Mountain View, CA] and cRNA was labeled with biotin-UTP, CTP using T7 RNA polymerase [Enzo Life Sciences, Inc., Farmingdale, NY].
Sample_hyb_protocol	Create a hybridization cocktail for a single probe array that contains 0.034 ?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), 10% DMSO, and 1X Hybridization Buffer. Heat hybridization cocktail to 99?C for 5 minutes, to 45?C for 5 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 10 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 60 rpm.
Sample_hyb_protocol	Fluidics: Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.
Sample_scan_protocol	Images were scanned using a Genechip scanner 3000 [Affymetrix]
Sample_data_processing	Affymetrix murine MOE 430 2.0 gene chips were used. 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 quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and ?-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
Sample_data_processing	GeneSpring Gx 7.3 (Agilent technologies) was used to normalization, clustering and filtering. Individual clusters were then analyzed for functional relatedness of genes within the cluster using PANTHER gene classification system.
Sample_platform_id	GPL1261
Sample_contact_name	Katherine,E,Yutzey
Sample_contact_email	katherine.yutzey@cchmc.org
Sample_contact_phone	513-636-8340
Sample_contact_fax	513-636-5958
Sample_contact_department	Divison of Molecular Cardiovascular Biology
Sample_contact_institute	Cinicnnati Children's Hospital Medical Center
Sample_contact_address	240 Albert Sabin Way
Sample_contact_city	Cinicnnati
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/GSM279nnn/GSM279012/suppl/GSM279012.CEL.gz
Sample_series_id	GSE11040
Sample_data_row_count	45101

GSM279013

GPL1261

17.5 Valve Cells 2

Embryonic day (E)12.5 AV cushion, E17.5 AV valve and in vitro cultured MC3T3-E1 (subclone4) cells

Samples used for hybridization consisted of pooled RNA extracts from E12.5 AV cushion and E17.5 AV valve from wild-type FVB/N mice and in vitro cultured MC3T3 cells.

Sample_geo_accession	GSM279013
Sample_status	Public on Jul 11 2008
Sample_submission_date	Apr 03 2008
Sample_last_update_date	Jul 11 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	None
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Embryos were collected at E12.5 for isolation of AV cushion and E17.5 for isolation of AV valves. Dissected cushions and valves were washed in 1XPBS and collected in TRIzol Reagent (Invitrogen) for total RNA isolation.
Sample_extract_protocol_ch1	Quality control steps: Total RNA was purified using RNeasy Mini Kit (Qiagen) according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples used for hybridization consisted of pooled RNA extracts from the E12.5 AV cushion and E17.5 AV valve from wild-type FVB/N mice and in vitro cultured MC3T3 cells. Therefore, 6 hybridization experiments were performed in biological duplicates on pooled RNA extracts. The TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicenter) was used to make double-stranded cDNA from total RNA. An in vitro transcription reaction using the IVT Labeling Kit (Affymetrix) created biotin-labeled cRNA target. The cRNA target was chemically fragmented and then hybridized to an Affymetrix Mouse Genime 430 2.0 Genechip® Array400-500 ng of total RNA from each biological samples in duplicate was amplified twice with the Arcturus RiboAmp kit [Arcturus Bioscience, Inc., Mountain View, CA] and cRNA was labeled with biotin-UTP, CTP using T7 RNA polymerase [Enzo Life Sciences, Inc., Farmingdale, NY].
Sample_hyb_protocol	Create a hybridization cocktail for a single probe array that contains 0.034 ?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), 10% DMSO, and 1X Hybridization Buffer. Heat hybridization cocktail to 99?C for 5 minutes, to 45?C for 5 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 10 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 60 rpm.
Sample_hyb_protocol	Fluidics: Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.
Sample_scan_protocol	Images were scanned using a Genechip scanner 3000 [Affymetrix]
Sample_data_processing	Affymetrix murine MOE 430 2.0 gene chips were used. 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 quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and ?-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
Sample_data_processing	GeneSpring Gx 7.3 (Agilent technologies) was used to normalization, clustering and filtering. Individual clusters were then analyzed for functional relatedness of genes within the cluster using PANTHER gene classification system.
Sample_platform_id	GPL1261
Sample_contact_name	Katherine,E,Yutzey
Sample_contact_email	katherine.yutzey@cchmc.org
Sample_contact_phone	513-636-8340
Sample_contact_fax	513-636-5958
Sample_contact_department	Divison of Molecular Cardiovascular Biology
Sample_contact_institute	Cinicnnati Children's Hospital Medical Center
Sample_contact_address	240 Albert Sabin Way
Sample_contact_city	Cinicnnati
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/GSM279nnn/GSM279013/suppl/GSM279013.CEL.gz
Sample_series_id	GSE11040
Sample_data_row_count	45101

GSM279014

GPL1261

MC3T3 Cell Line 1

Embryonic day (E)12.5 AV cushion, E17.5 AV valve and in vitro cultured MC3T3-E1 (subclone4) cells

Samples used for hybridization consisted of pooled RNA extracts from E12.5 AV cushion and E17.5 AV valve from wild-type FVB/N mice and in vitro cultured MC3T3 cells.

Sample_geo_accession	GSM279014
Sample_status	Public on Jul 11 2008
Sample_submission_date	Apr 03 2008
Sample_last_update_date	Jul 11 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	None
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Embryos were collected at E12.5 for isolation of AV cushion and E17.5 for isolation of AV valves. Dissected cushions and valves were washed in 1XPBS and collected in TRIzol Reagent (Invitrogen) for total RNA isolation.
Sample_extract_protocol_ch1	Quality control steps: Total RNA was purified using RNeasy Mini Kit (Qiagen) according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples used for hybridization consisted of pooled RNA extracts from the E12.5 AV cushion and E17.5 AV valve from wild-type FVB/N mice and in vitro cultured MC3T3 cells. Therefore, 6 hybridization experiments were performed in biological duplicates on pooled RNA extracts. The TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicenter) was used to make double-stranded cDNA from total RNA. An in vitro transcription reaction using the IVT Labeling Kit (Affymetrix) created biotin-labeled cRNA target. The cRNA target was chemically fragmented and then hybridized to an Affymetrix Mouse Genime 430 2.0 Genechip® Array400-500 ng of total RNA from each biological samples in duplicate was amplified twice with the Arcturus RiboAmp kit [Arcturus Bioscience, Inc., Mountain View, CA] and cRNA was labeled with biotin-UTP, CTP using T7 RNA polymerase [Enzo Life Sciences, Inc., Farmingdale, NY].
Sample_hyb_protocol	Create a hybridization cocktail for a single probe array that contains 0.034 ?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), 10% DMSO, and 1X Hybridization Buffer. Heat hybridization cocktail to 99?C for 5 minutes, to 45?C for 5 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 10 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 60 rpm.
Sample_hyb_protocol	Fluidics: Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.
Sample_scan_protocol	Images were scanned using a Genechip scanner 3000 [Affymetrix]
Sample_data_processing	Affymetrix murine MOE 430 2.0 gene chips were used. 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 quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and ?-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
Sample_data_processing	GeneSpring Gx 7.3 (Agilent technologies) was used to normalization, clustering and filtering. Individual clusters were then analyzed for functional relatedness of genes within the cluster using PANTHER gene classification system.
Sample_platform_id	GPL1261
Sample_contact_name	Katherine,E,Yutzey
Sample_contact_email	katherine.yutzey@cchmc.org
Sample_contact_phone	513-636-8340
Sample_contact_fax	513-636-5958
Sample_contact_department	Divison of Molecular Cardiovascular Biology
Sample_contact_institute	Cinicnnati Children's Hospital Medical Center
Sample_contact_address	240 Albert Sabin Way
Sample_contact_city	Cinicnnati
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/GSM279nnn/GSM279014/suppl/GSM279014.CEL.gz
Sample_series_id	GSE11040
Sample_data_row_count	45101

GSM279015

GPL1261

MC3T3 Cell Line 2

Embryonic day (E)12.5 AV cushion, E17.5 AV valve and in vitro cultured MC3T3-E1 (subclone4) cells

Samples used for hybridization consisted of pooled RNA extracts from E12.5 AV cushion and E17.5 AV valve from wild-type FVB/N mice and in vitro cultured MC3T3 cells.

Sample_geo_accession	GSM279015
Sample_status	Public on Jul 11 2008
Sample_submission_date	Apr 03 2008
Sample_last_update_date	Jul 11 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	None
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Embryos were collected at E12.5 for isolation of AV cushion and E17.5 for isolation of AV valves. Dissected cushions and valves were washed in 1XPBS and collected in TRIzol Reagent (Invitrogen) for total RNA isolation.
Sample_extract_protocol_ch1	Quality control steps: Total RNA was purified using RNeasy Mini Kit (Qiagen) according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Samples used for hybridization consisted of pooled RNA extracts from the E12.5 AV cushion and E17.5 AV valve from wild-type FVB/N mice and in vitro cultured MC3T3 cells. Therefore, 6 hybridization experiments were performed in biological duplicates on pooled RNA extracts. The TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicenter) was used to make double-stranded cDNA from total RNA. An in vitro transcription reaction using the IVT Labeling Kit (Affymetrix) created biotin-labeled cRNA target. The cRNA target was chemically fragmented and then hybridized to an Affymetrix Mouse Genime 430 2.0 Genechip® Array400-500 ng of total RNA from each biological samples in duplicate was amplified twice with the Arcturus RiboAmp kit [Arcturus Bioscience, Inc., Mountain View, CA] and cRNA was labeled with biotin-UTP, CTP using T7 RNA polymerase [Enzo Life Sciences, Inc., Farmingdale, NY].
Sample_hyb_protocol	Create a hybridization cocktail for a single probe array that contains 0.034 ?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), 10% DMSO, and 1X Hybridization Buffer. Heat hybridization cocktail to 99?C for 5 minutes, to 45?C for 5 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 10 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 60 rpm.
Sample_hyb_protocol	Fluidics: Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.
Sample_scan_protocol	Images were scanned using a Genechip scanner 3000 [Affymetrix]
Sample_data_processing	Affymetrix murine MOE 430 2.0 gene chips were used. 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 quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and ?-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
Sample_data_processing	GeneSpring Gx 7.3 (Agilent technologies) was used to normalization, clustering and filtering. Individual clusters were then analyzed for functional relatedness of genes within the cluster using PANTHER gene classification system.
Sample_platform_id	GPL1261
Sample_contact_name	Katherine,E,Yutzey
Sample_contact_email	katherine.yutzey@cchmc.org
Sample_contact_phone	513-636-8340
Sample_contact_fax	513-636-5958
Sample_contact_department	Divison of Molecular Cardiovascular Biology
Sample_contact_institute	Cinicnnati Children's Hospital Medical Center
Sample_contact_address	240 Albert Sabin Way
Sample_contact_city	Cinicnnati
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/GSM279nnn/GSM279015/suppl/GSM279015.CEL.gz
Sample_series_id	GSE11040
Sample_data_row_count	45101

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Transcripts profile based on;

A. Differential status (Up/Down regulation)

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