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Search results for the GEO ID: GSE19873

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GSM496702

GPL339

16-20 somites mid-foregut, biological rep1

Mouse embryonic mid-foregut at 16-20 somite developmental stage

genotype: wild type development stage/age: embryos containing between 16 and 20 somites, E8.5

Gene expression data from mouse mid-foregut tissue at 16-20 somite stage

Sample_geo_accession	GSM496702
Sample_status	Public on Jan 14 2010
Sample_submission_date	Jan 13 2010
Sample_last_update_date	Jan 13 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	To obtain mid-foregut tissue, the neural tube and heart were dissected away for the embryo to expose the foregut. The foregut tissue posterior to the pharyngeal arches and anterior to the liver was excised using tungsten needles. Collected tissues were placed immediately in RNeasyTM buffer (QIAGEN). Five to ten mid-foreguts were pooled for each of the three somite groups for RNA analysis.
Sample_extract_protocol_ch1	Total RNA was isolated from dissected tissues using RNeasyTM micropurification kit (QIAGEN) according to the manufacturer’s directions, followed by treatment on column with DNA-freeTM DNase (Ambion). RNA concentrations were measured in 1 μl (1/10 of the sample) in a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA (100 ng) was amplified using the RiboAmp HS kit (Arcturus Engineering, Inc) as described by the manufacturer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was labelled using biotinylated ribonucleotides during the second in vitro transcription step using ENZO kit (Affymetrix). After two rounds of amplification, 10-15 μg of amplified RNA (aRNA) were obtained. The quality of the amplification product was evaluated by examining the size distribution of the aRNA in an agarose gel stained with Sybr Gold (Molecular Probes).
Sample_hyb_protocol	10 μg of the fragmented, biotinylated aRNA, was added to a hybridization cocktail containing 50 fmol/mL control oligonucleotide B2, 1X eukaryotic hybridization controls, 0.1 mg/mL herring sperm DNA, and 0.5 mg/mL BSA in 1X hybridization buffer(100 mM MES, 1M [Na+], 20 mM EDTA, 0.01% Tween-20) for a total volume of 300 μL. The mixture was incubated to 99 °C for 5 min followed by 45 °C for 5 min. The mixture was then spun at 16,000xg for 5 min. 200 μL of hybridization mix was loaded on a chip that had been pre-incubated with 200 μL 1X hybridization buffer at 45 °C and 60 rpm for 10 min. The chip was hybridized for 16 hrs at 45°C and 60 rpm.Arrays were washed and stained according to the EukGE-WS2v4 Antibody Amplification for Eukaryotic Targets protocol on a Fluidics Station 450.This consists of a wash with non–stringent buffer (6X SSPE, 0.01% Tween-20), followed by a wash with stringent buffer (100 mM MES, 0.1M [Na+], 0.01% Tween-20), a stain with Strepavidin-Phycoerythrin (100 mM MES, 1M [Na+], 0.05% Tween-20, 2 mg/mL BSA, 10 μg/mL Streptavidin-Phycoerythrin), a wash with non-stringent buffer, a stain with biotinylated anti-strepavidin antibody (100 mM MES, 1M [Na+], 0.05% Tween-20, 2 mg/mL BSA, 0.1 mg/mL goat IgG, 3 μg/mLbiotinylated antibody), a stain again with Strepavidin-Phycoerythrin, and a final wash with non-stringent buffer.
Sample_scan_protocol	The stained arrays were scanned using an Affymetrix GeneChip Scanner 3000.
Sample_data_processing	The scanned images were quantified and scaled. The average signal intensity of each chip was scaled to 100. The normalization factor was set to 1. All other parameters were used at the default settings. A single weighted mean expression level for each gene was derived using Microarray Suite (MAS) 5.0 software. Using a one sided Wilconox signed rank test, the MAS5.0 software generated a detection p value.
Sample_platform_id	GPL339
Sample_contact_name	Maria,Isabel,Ramirez
Sample_contact_email	mramirez@bu.edu
Sample_contact_laboratory	Pulmonary Center
Sample_contact_department	Medicine
Sample_contact_institute	Boston University School of Medicine
Sample_contact_address	72 E. Concord St. E603
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02118
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM496nnn/GSM496702/suppl/GSM496702.CEL.gz
Sample_series_id	GSE19873
Sample_data_row_count	22690

GSM496703

GPL339

16-20 somites mid-foregut, biological rep2

Mouse embryonic mid-foregut at 16-20 somite developmental stage

genotype: wild type development stage/age: embryos containing between 16 and 20 somites, E8.5

Gene expression data from mouse mid-foregut tissue at 16-20 somite stage

Sample_geo_accession	GSM496703
Sample_status	Public on Jan 14 2010
Sample_submission_date	Jan 13 2010
Sample_last_update_date	Jan 13 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	To obtain mid-foregut tissue, the neural tube and heart were dissected away for the embryo to expose the foregut. The foregut tissue posterior to the pharyngeal arches and anterior to the liver was excised using tungsten needles. Collected tissues were placed immediately in RNeasyTM buffer (QIAGEN). Five to ten mid-foreguts were pooled for each of the three somite groups for RNA analysis.
Sample_extract_protocol_ch1	Total RNA was isolated from dissected tissues using RNeasyTM micropurification kit (QIAGEN) according to the manufacturer’s directions, followed by treatment on column with DNA-freeTM DNase (Ambion). RNA concentrations were measured in 1 μl (1/10 of the sample) in a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA (100 ng) was amplified using the RiboAmp HS kit (Arcturus Engineering, Inc) as described by the manufacturer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was labelled using biotinylated ribonucleotides during the second in vitro transcription step using ENZO kit (Affymetrix). After two rounds of amplification, 10-15 μg of amplified RNA (aRNA) were obtained. The quality of the amplification product was evaluated by examining the size distribution of the aRNA in an agarose gel stained with Sybr Gold (Molecular Probes).
Sample_hyb_protocol	10 μg of the fragmented, biotinylated aRNA, was added to a hybridization cocktail containing 50 fmol/mL control oligonucleotide B2, 1X eukaryotic hybridization controls, 0.1 mg/mL herring sperm DNA, and 0.5 mg/mL BSA in 1X hybridization buffer(100 mM MES, 1M [Na+], 20 mM EDTA, 0.01% Tween-20) for a total volume of 300 μL. The mixture was incubated to 99 °C for 5 min followed by 45 °C for 5 min. The mixture was then spun at 16,000xg for 5 min. 200 μL of hybridization mix was loaded on a chip that had been pre-incubated with 200 μL 1X hybridization buffer at 45 °C and 60 rpm for 10 min. The chip was hybridized for 16 hrs at 45°C and 60 rpm.Arrays were washed and stained according to the EukGE-WS2v4 Antibody Amplification for Eukaryotic Targets protocol on a Fluidics Station 450.This consists of a wash with non–stringent buffer (6X SSPE, 0.01% Tween-20), followed by a wash with stringent buffer (100 mM MES, 0.1M [Na+], 0.01% Tween-20), a stain with Strepavidin-Phycoerythrin (100 mM MES, 1M [Na+], 0.05% Tween-20, 2 mg/mL BSA, 10 μg/mL Streptavidin-Phycoerythrin), a wash with non-stringent buffer, a stain with biotinylated anti-strepavidin antibody (100 mM MES, 1M [Na+], 0.05% Tween-20, 2 mg/mL BSA, 0.1 mg/mL goat IgG, 3 μg/mLbiotinylated antibody), a stain again with Strepavidin-Phycoerythrin, and a final wash with non-stringent buffer.
Sample_scan_protocol	The stained arrays were scanned using an Affymetrix GeneChip Scanner 3000.
Sample_data_processing	The scanned images were quantified and scaled. The average signal intensity of each chip was scaled to 100. The normalization factor was set to 1. All other parameters were used at the default settings. A single weighted mean expression level for each gene was derived using Microarray Suite (MAS) 5.0 software. Using a one sided Wilconox signed rank test, the MAS5.0 software generated a detection p value.
Sample_platform_id	GPL339
Sample_contact_name	Maria,Isabel,Ramirez
Sample_contact_email	mramirez@bu.edu
Sample_contact_laboratory	Pulmonary Center
Sample_contact_department	Medicine
Sample_contact_institute	Boston University School of Medicine
Sample_contact_address	72 E. Concord St. E603
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02118
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM496nnn/GSM496703/suppl/GSM496703.CEL.gz
Sample_series_id	GSE19873
Sample_data_row_count	22690

GSM496704

GPL339

16-20 somites mid-foregut, biological rep3

Mouse embryonic mid-foregut at 16-20 somite developmental stage

genotype: wild type development stage/age: embryos containing between 16 and 20 somites, E8.5

Gene expression data from mouse mid-foregut tissue at 16-20 somite stage

Sample_geo_accession	GSM496704
Sample_status	Public on Jan 14 2010
Sample_submission_date	Jan 13 2010
Sample_last_update_date	Jan 13 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	To obtain mid-foregut tissue, the neural tube and heart were dissected away for the embryo to expose the foregut. The foregut tissue posterior to the pharyngeal arches and anterior to the liver was excised using tungsten needles. Collected tissues were placed immediately in RNeasyTM buffer (QIAGEN). Five to ten mid-foreguts were pooled for each of the three somite groups for RNA analysis.
Sample_extract_protocol_ch1	Total RNA was isolated from dissected tissues using RNeasyTM micropurification kit (QIAGEN) according to the manufacturer’s directions, followed by treatment on column with DNA-freeTM DNase (Ambion). RNA concentrations were measured in 1 μl (1/10 of the sample) in a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA (100 ng) was amplified using the RiboAmp HS kit (Arcturus Engineering, Inc) as described by the manufacturer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was labelled using biotinylated ribonucleotides during the second in vitro transcription step using ENZO kit (Affymetrix). After two rounds of amplification, 10-15 μg of amplified RNA (aRNA) were obtained. The quality of the amplification product was evaluated by examining the size distribution of the aRNA in an agarose gel stained with Sybr Gold (Molecular Probes).
Sample_hyb_protocol	10 μg of the fragmented, biotinylated aRNA, was added to a hybridization cocktail containing 50 fmol/mL control oligonucleotide B2, 1X eukaryotic hybridization controls, 0.1 mg/mL herring sperm DNA, and 0.5 mg/mL BSA in 1X hybridization buffer(100 mM MES, 1M [Na+], 20 mM EDTA, 0.01% Tween-20) for a total volume of 300 μL. The mixture was incubated to 99 °C for 5 min followed by 45 °C for 5 min. The mixture was then spun at 16,000xg for 5 min. 200 μL of hybridization mix was loaded on a chip that had been pre-incubated with 200 μL 1X hybridization buffer at 45 °C and 60 rpm for 10 min. The chip was hybridized for 16 hrs at 45°C and 60 rpm.Arrays were washed and stained according to the EukGE-WS2v4 Antibody Amplification for Eukaryotic Targets protocol on a Fluidics Station 450.This consists of a wash with non–stringent buffer (6X SSPE, 0.01% Tween-20), followed by a wash with stringent buffer (100 mM MES, 0.1M [Na+], 0.01% Tween-20), a stain with Strepavidin-Phycoerythrin (100 mM MES, 1M [Na+], 0.05% Tween-20, 2 mg/mL BSA, 10 μg/mL Streptavidin-Phycoerythrin), a wash with non-stringent buffer, a stain with biotinylated anti-strepavidin antibody (100 mM MES, 1M [Na+], 0.05% Tween-20, 2 mg/mL BSA, 0.1 mg/mL goat IgG, 3 μg/mLbiotinylated antibody), a stain again with Strepavidin-Phycoerythrin, and a final wash with non-stringent buffer.
Sample_scan_protocol	The stained arrays were scanned using an Affymetrix GeneChip Scanner 3000.
Sample_data_processing	The scanned images were quantified and scaled. The average signal intensity of each chip was scaled to 100. The normalization factor was set to 1. All other parameters were used at the default settings. A single weighted mean expression level for each gene was derived using Microarray Suite (MAS) 5.0 software. Using a one sided Wilconox signed rank test, the MAS5.0 software generated a detection p value.
Sample_platform_id	GPL339
Sample_contact_name	Maria,Isabel,Ramirez
Sample_contact_email	mramirez@bu.edu
Sample_contact_laboratory	Pulmonary Center
Sample_contact_department	Medicine
Sample_contact_institute	Boston University School of Medicine
Sample_contact_address	72 E. Concord St. E603
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02118
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM496nnn/GSM496704/suppl/GSM496704.CEL.gz
Sample_series_id	GSE19873
Sample_data_row_count	22690

GSM496705

GPL339

21-25 somites mid-foregut, biological rep1

Mouse embryonic mid-foregut at 21-25 somite developmental stage

genotype: wild type development stage/age: embryos containing between 21 and 25 somites, E9.0

Gene expression data from mouse mid-foregut tissue at 21-25 somite stage

Sample_geo_accession	GSM496705
Sample_status	Public on Jan 14 2010
Sample_submission_date	Jan 13 2010
Sample_last_update_date	Jan 13 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	To obtain mid-foregut tissue, the neural tube and heart were dissected away for the embryo to expose the foregut. The foregut tissue posterior to the pharyngeal arches and anterior to the liver was excised using tungsten needles. Collected tissues were placed immediately in RNeasyTM buffer (QIAGEN). Five to ten mid-foreguts were pooled for each of the three somite groups for RNA analysis.
Sample_extract_protocol_ch1	Total RNA was isolated from dissected tissues using RNeasyTM micropurification kit (QIAGEN) according to the manufacturer’s directions, followed by treatment on column with DNA-freeTM DNase (Ambion). RNA concentrations were measured in 1 μl (1/10 of the sample) in a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA (100 ng) was amplified using the RiboAmp HS kit (Arcturus Engineering, Inc) as described by the manufacturer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was labelled using biotinylated ribonucleotides during the second in vitro transcription step using ENZO kit (Affymetrix). After two rounds of amplification, 10-15 μg of amplified RNA (aRNA) were obtained. The quality of the amplification product was evaluated by examining the size distribution of the aRNA in an agarose gel stained with Sybr Gold (Molecular Probes).
Sample_hyb_protocol	10 μg of the fragmented, biotinylated aRNA, was added to a hybridization cocktail containing 50 fmol/mL control oligonucleotide B2, 1X eukaryotic hybridization controls, 0.1 mg/mL herring sperm DNA, and 0.5 mg/mL BSA in 1X hybridization buffer(100 mM MES, 1M [Na+], 20 mM EDTA, 0.01% Tween-20) for a total volume of 300 μL. The mixture was incubated to 99 °C for 5 min followed by 45 °C for 5 min. The mixture was then spun at 16,000xg for 5 min. 200 μL of hybridization mix was loaded on a chip that had been pre-incubated with 200 μL 1X hybridization buffer at 45 °C and 60 rpm for 10 min. The chip was hybridized for 16 hrs at 45°C and 60 rpm.Arrays were washed and stained according to the EukGE-WS2v4 Antibody Amplification for Eukaryotic Targets protocol on a Fluidics Station 450.This consists of a wash with non–stringent buffer (6X SSPE, 0.01% Tween-20), followed by a wash with stringent buffer (100 mM MES, 0.1M [Na+], 0.01% Tween-20), a stain with Strepavidin-Phycoerythrin (100 mM MES, 1M [Na+], 0.05% Tween-20, 2 mg/mL BSA, 10 μg/mL Streptavidin-Phycoerythrin), a wash with non-stringent buffer, a stain with biotinylated anti-strepavidin antibody (100 mM MES, 1M [Na+], 0.05% Tween-20, 2 mg/mL BSA, 0.1 mg/mL goat IgG, 3 μg/mLbiotinylated antibody), a stain again with Strepavidin-Phycoerythrin, and a final wash with non-stringent buffer.
Sample_scan_protocol	The stained arrays were scanned using an Affymetrix GeneChip Scanner 3000.
Sample_data_processing	The scanned images were quantified and scaled. The average signal intensity of each chip was scaled to 100. The normalization factor was set to 1. All other parameters were used at the default settings. A single weighted mean expression level for each gene was derived using Microarray Suite (MAS) 5.0 software. Using a one sided Wilconox signed rank test, the MAS5.0 software generated a detection p value.
Sample_platform_id	GPL339
Sample_contact_name	Maria,Isabel,Ramirez
Sample_contact_email	mramirez@bu.edu
Sample_contact_laboratory	Pulmonary Center
Sample_contact_department	Medicine
Sample_contact_institute	Boston University School of Medicine
Sample_contact_address	72 E. Concord St. E603
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02118
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM496nnn/GSM496705/suppl/GSM496705.CEL.gz
Sample_series_id	GSE19873
Sample_data_row_count	22690

GSM496706

GPL339

21-25 somites mid-foregut, biological rep2

Mouse embryonic mid-foregut at 21-25 somite developmental stage

genotype: wild type development stage/age: embryos containing between 21 and 25 somites, E9.0

Gene expression data from mouse mid-foregut tissue at 21-25 somite stage

Sample_geo_accession	GSM496706
Sample_status	Public on Jan 14 2010
Sample_submission_date	Jan 13 2010
Sample_last_update_date	Jan 13 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	To obtain mid-foregut tissue, the neural tube and heart were dissected away for the embryo to expose the foregut. The foregut tissue posterior to the pharyngeal arches and anterior to the liver was excised using tungsten needles. Collected tissues were placed immediately in RNeasyTM buffer (QIAGEN). Five to ten mid-foreguts were pooled for each of the three somite groups for RNA analysis.
Sample_extract_protocol_ch1	Total RNA was isolated from dissected tissues using RNeasyTM micropurification kit (QIAGEN) according to the manufacturer’s directions, followed by treatment on column with DNA-freeTM DNase (Ambion). RNA concentrations were measured in 1 μl (1/10 of the sample) in a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA (100 ng) was amplified using the RiboAmp HS kit (Arcturus Engineering, Inc) as described by the manufacturer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was labelled using biotinylated ribonucleotides during the second in vitro transcription step using ENZO kit (Affymetrix). After two rounds of amplification, 10-15 μg of amplified RNA (aRNA) were obtained. The quality of the amplification product was evaluated by examining the size distribution of the aRNA in an agarose gel stained with Sybr Gold (Molecular Probes).
Sample_hyb_protocol	10 μg of the fragmented, biotinylated aRNA, was added to a hybridization cocktail containing 50 fmol/mL control oligonucleotide B2, 1X eukaryotic hybridization controls, 0.1 mg/mL herring sperm DNA, and 0.5 mg/mL BSA in 1X hybridization buffer(100 mM MES, 1M [Na+], 20 mM EDTA, 0.01% Tween-20) for a total volume of 300 μL. The mixture was incubated to 99 °C for 5 min followed by 45 °C for 5 min. The mixture was then spun at 16,000xg for 5 min. 200 μL of hybridization mix was loaded on a chip that had been pre-incubated with 200 μL 1X hybridization buffer at 45 °C and 60 rpm for 10 min. The chip was hybridized for 16 hrs at 45°C and 60 rpm.Arrays were washed and stained according to the EukGE-WS2v4 Antibody Amplification for Eukaryotic Targets protocol on a Fluidics Station 450.This consists of a wash with non–stringent buffer (6X SSPE, 0.01% Tween-20), followed by a wash with stringent buffer (100 mM MES, 0.1M [Na+], 0.01% Tween-20), a stain with Strepavidin-Phycoerythrin (100 mM MES, 1M [Na+], 0.05% Tween-20, 2 mg/mL BSA, 10 μg/mL Streptavidin-Phycoerythrin), a wash with non-stringent buffer, a stain with biotinylated anti-strepavidin antibody (100 mM MES, 1M [Na+], 0.05% Tween-20, 2 mg/mL BSA, 0.1 mg/mL goat IgG, 3 μg/mLbiotinylated antibody), a stain again with Strepavidin-Phycoerythrin, and a final wash with non-stringent buffer.
Sample_scan_protocol	The stained arrays were scanned using an Affymetrix GeneChip Scanner 3000.
Sample_data_processing	The scanned images were quantified and scaled. The average signal intensity of each chip was scaled to 100. The normalization factor was set to 1. All other parameters were used at the default settings. A single weighted mean expression level for each gene was derived using Microarray Suite (MAS) 5.0 software. Using a one sided Wilconox signed rank test, the MAS5.0 software generated a detection p value.
Sample_platform_id	GPL339
Sample_contact_name	Maria,Isabel,Ramirez
Sample_contact_email	mramirez@bu.edu
Sample_contact_laboratory	Pulmonary Center
Sample_contact_department	Medicine
Sample_contact_institute	Boston University School of Medicine
Sample_contact_address	72 E. Concord St. E603
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02118
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM496nnn/GSM496706/suppl/GSM496706.CEL.gz
Sample_series_id	GSE19873
Sample_data_row_count	22690

GSM496707

GPL339

21-25 somites mid-foregut, biological rep3

Mouse embryonic mid-foregut at 21-25 somite developmental stage

genotype: wild type development stage/age: embryos containing between 21 and 25 somites, E9.0

Gene expression data from mouse mid-foregut tissue at 21-25 somite stage

Sample_geo_accession	GSM496707
Sample_status	Public on Jan 14 2010
Sample_submission_date	Jan 13 2010
Sample_last_update_date	Jan 13 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	To obtain mid-foregut tissue, the neural tube and heart were dissected away for the embryo to expose the foregut. The foregut tissue posterior to the pharyngeal arches and anterior to the liver was excised using tungsten needles. Collected tissues were placed immediately in RNeasyTM buffer (QIAGEN). Five to ten mid-foreguts were pooled for each of the three somite groups for RNA analysis.
Sample_extract_protocol_ch1	Total RNA was isolated from dissected tissues using RNeasyTM micropurification kit (QIAGEN) according to the manufacturer’s directions, followed by treatment on column with DNA-freeTM DNase (Ambion). RNA concentrations were measured in 1 μl (1/10 of the sample) in a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA (100 ng) was amplified using the RiboAmp HS kit (Arcturus Engineering, Inc) as described by the manufacturer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was labelled using biotinylated ribonucleotides during the second in vitro transcription step using ENZO kit (Affymetrix). After two rounds of amplification, 10-15 μg of amplified RNA (aRNA) were obtained. The quality of the amplification product was evaluated by examining the size distribution of the aRNA in an agarose gel stained with Sybr Gold (Molecular Probes).
Sample_hyb_protocol	10 μg of the fragmented, biotinylated aRNA, was added to a hybridization cocktail containing 50 fmol/mL control oligonucleotide B2, 1X eukaryotic hybridization controls, 0.1 mg/mL herring sperm DNA, and 0.5 mg/mL BSA in 1X hybridization buffer(100 mM MES, 1M [Na+], 20 mM EDTA, 0.01% Tween-20) for a total volume of 300 μL. The mixture was incubated to 99 °C for 5 min followed by 45 °C for 5 min. The mixture was then spun at 16,000xg for 5 min. 200 μL of hybridization mix was loaded on a chip that had been pre-incubated with 200 μL 1X hybridization buffer at 45 °C and 60 rpm for 10 min. The chip was hybridized for 16 hrs at 45°C and 60 rpm.Arrays were washed and stained according to the EukGE-WS2v4 Antibody Amplification for Eukaryotic Targets protocol on a Fluidics Station 450.This consists of a wash with non–stringent buffer (6X SSPE, 0.01% Tween-20), followed by a wash with stringent buffer (100 mM MES, 0.1M [Na+], 0.01% Tween-20), a stain with Strepavidin-Phycoerythrin (100 mM MES, 1M [Na+], 0.05% Tween-20, 2 mg/mL BSA, 10 μg/mL Streptavidin-Phycoerythrin), a wash with non-stringent buffer, a stain with biotinylated anti-strepavidin antibody (100 mM MES, 1M [Na+], 0.05% Tween-20, 2 mg/mL BSA, 0.1 mg/mL goat IgG, 3 μg/mLbiotinylated antibody), a stain again with Strepavidin-Phycoerythrin, and a final wash with non-stringent buffer.
Sample_scan_protocol	The stained arrays were scanned using an Affymetrix GeneChip Scanner 3000.
Sample_data_processing	The scanned images were quantified and scaled. The average signal intensity of each chip was scaled to 100. The normalization factor was set to 1. All other parameters were used at the default settings. A single weighted mean expression level for each gene was derived using Microarray Suite (MAS) 5.0 software. Using a one sided Wilconox signed rank test, the MAS5.0 software generated a detection p value.
Sample_platform_id	GPL339
Sample_contact_name	Maria,Isabel,Ramirez
Sample_contact_email	mramirez@bu.edu
Sample_contact_laboratory	Pulmonary Center
Sample_contact_department	Medicine
Sample_contact_institute	Boston University School of Medicine
Sample_contact_address	72 E. Concord St. E603
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02118
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM496nnn/GSM496707/suppl/GSM496707.CEL.gz
Sample_series_id	GSE19873
Sample_data_row_count	22690

GSM496708

GPL339

26-30 somites mid-foregut, biological rep1

Mouse embryonic mid-foregut at 26-30 somite developmental stage

genotype: wild type development stage/age: embryos containing between 26 and 30 somites, E9.5

Gene expression data from mouse mid-foregut tissue at 26-30 somite stage

Sample_geo_accession	GSM496708
Sample_status	Public on Jan 14 2010
Sample_submission_date	Jan 13 2010
Sample_last_update_date	Jan 13 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	To obtain mid-foregut tissue, the neural tube and heart were dissected away for the embryo to expose the foregut. The foregut tissue posterior to the pharyngeal arches and anterior to the liver was excised using tungsten needles. Collected tissues were placed immediately in RNeasyTM buffer (QIAGEN). Five to ten mid-foreguts were pooled for each of the three somite groups for RNA analysis.
Sample_extract_protocol_ch1	Total RNA was isolated from dissected tissues using RNeasyTM micropurification kit (QIAGEN) according to the manufacturer’s directions, followed by treatment on column with DNA-freeTM DNase (Ambion). RNA concentrations were measured in 1 μl (1/10 of the sample) in a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA (100 ng) was amplified using the RiboAmp HS kit (Arcturus Engineering, Inc) as described by the manufacturer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was labelled using biotinylated ribonucleotides during the second in vitro transcription step using ENZO kit (Affymetrix). After two rounds of amplification, 10-15 μg of amplified RNA (aRNA) were obtained. The quality of the amplification product was evaluated by examining the size distribution of the aRNA in an agarose gel stained with Sybr Gold (Molecular Probes).
Sample_hyb_protocol	10 μg of the fragmented, biotinylated aRNA, was added to a hybridization cocktail containing 50 fmol/mL control oligonucleotide B2, 1X eukaryotic hybridization controls, 0.1 mg/mL herring sperm DNA, and 0.5 mg/mL BSA in 1X hybridization buffer(100 mM MES, 1M [Na+], 20 mM EDTA, 0.01% Tween-20) for a total volume of 300 μL. The mixture was incubated to 99 °C for 5 min followed by 45 °C for 5 min. The mixture was then spun at 16,000xg for 5 min. 200 μL of hybridization mix was loaded on a chip that had been pre-incubated with 200 μL 1X hybridization buffer at 45 °C and 60 rpm for 10 min. The chip was hybridized for 16 hrs at 45°C and 60 rpm.Arrays were washed and stained according to the EukGE-WS2v4 Antibody Amplification for Eukaryotic Targets protocol on a Fluidics Station 450.This consists of a wash with non–stringent buffer (6X SSPE, 0.01% Tween-20), followed by a wash with stringent buffer (100 mM MES, 0.1M [Na+], 0.01% Tween-20), a stain with Strepavidin-Phycoerythrin (100 mM MES, 1M [Na+], 0.05% Tween-20, 2 mg/mL BSA, 10 μg/mL Streptavidin-Phycoerythrin), a wash with non-stringent buffer, a stain with biotinylated anti-strepavidin antibody (100 mM MES, 1M [Na+], 0.05% Tween-20, 2 mg/mL BSA, 0.1 mg/mL goat IgG, 3 μg/mLbiotinylated antibody), a stain again with Strepavidin-Phycoerythrin, and a final wash with non-stringent buffer.
Sample_scan_protocol	The stained arrays were scanned using an Affymetrix GeneChip Scanner 3000.
Sample_data_processing	The scanned images were quantified and scaled. The average signal intensity of each chip was scaled to 100. The normalization factor was set to 1. All other parameters were used at the default settings. A single weighted mean expression level for each gene was derived using Microarray Suite (MAS) 5.0 software. Using a one sided Wilconox signed rank test, the MAS5.0 software generated a detection p value.
Sample_platform_id	GPL339
Sample_contact_name	Maria,Isabel,Ramirez
Sample_contact_email	mramirez@bu.edu
Sample_contact_laboratory	Pulmonary Center
Sample_contact_department	Medicine
Sample_contact_institute	Boston University School of Medicine
Sample_contact_address	72 E. Concord St. E603
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02118
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM496nnn/GSM496708/suppl/GSM496708.CEL.gz
Sample_series_id	GSE19873
Sample_data_row_count	22690

GSM496709

GPL339

26-30 somites mid-foregut, biological rep2

Mouse embryonic mid-foregut at 26-30 somite developmental stage

genotype: wild type development stage/age: embryos containing between 26 and 30 somites, E9.5

Gene expression data from mouse mid-foregut tissue at 26-30 somite stage

Sample_geo_accession	GSM496709
Sample_status	Public on Jan 14 2010
Sample_submission_date	Jan 13 2010
Sample_last_update_date	Jan 13 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	To obtain mid-foregut tissue, the neural tube and heart were dissected away for the embryo to expose the foregut. The foregut tissue posterior to the pharyngeal arches and anterior to the liver was excised using tungsten needles. Collected tissues were placed immediately in RNeasyTM buffer (QIAGEN). Five to ten mid-foreguts were pooled for each of the three somite groups for RNA analysis.
Sample_extract_protocol_ch1	Total RNA was isolated from dissected tissues using RNeasyTM micropurification kit (QIAGEN) according to the manufacturer’s directions, followed by treatment on column with DNA-freeTM DNase (Ambion). RNA concentrations were measured in 1 μl (1/10 of the sample) in a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA (100 ng) was amplified using the RiboAmp HS kit (Arcturus Engineering, Inc) as described by the manufacturer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was labelled using biotinylated ribonucleotides during the second in vitro transcription step using ENZO kit (Affymetrix). After two rounds of amplification, 10-15 μg of amplified RNA (aRNA) were obtained. The quality of the amplification product was evaluated by examining the size distribution of the aRNA in an agarose gel stained with Sybr Gold (Molecular Probes).
Sample_hyb_protocol	10 μg of the fragmented, biotinylated aRNA, was added to a hybridization cocktail containing 50 fmol/mL control oligonucleotide B2, 1X eukaryotic hybridization controls, 0.1 mg/mL herring sperm DNA, and 0.5 mg/mL BSA in 1X hybridization buffer(100 mM MES, 1M [Na+], 20 mM EDTA, 0.01% Tween-20) for a total volume of 300 μL. The mixture was incubated to 99 °C for 5 min followed by 45 °C for 5 min. The mixture was then spun at 16,000xg for 5 min. 200 μL of hybridization mix was loaded on a chip that had been pre-incubated with 200 μL 1X hybridization buffer at 45 °C and 60 rpm for 10 min. The chip was hybridized for 16 hrs at 45°C and 60 rpm.Arrays were washed and stained according to the EukGE-WS2v4 Antibody Amplification for Eukaryotic Targets protocol on a Fluidics Station 450.This consists of a wash with non–stringent buffer (6X SSPE, 0.01% Tween-20), followed by a wash with stringent buffer (100 mM MES, 0.1M [Na+], 0.01% Tween-20), a stain with Strepavidin-Phycoerythrin (100 mM MES, 1M [Na+], 0.05% Tween-20, 2 mg/mL BSA, 10 μg/mL Streptavidin-Phycoerythrin), a wash with non-stringent buffer, a stain with biotinylated anti-strepavidin antibody (100 mM MES, 1M [Na+], 0.05% Tween-20, 2 mg/mL BSA, 0.1 mg/mL goat IgG, 3 μg/mLbiotinylated antibody), a stain again with Strepavidin-Phycoerythrin, and a final wash with non-stringent buffer.
Sample_scan_protocol	The stained arrays were scanned using an Affymetrix GeneChip Scanner 3000.
Sample_data_processing	The scanned images were quantified and scaled. The average signal intensity of each chip was scaled to 100. The normalization factor was set to 1. All other parameters were used at the default settings. A single weighted mean expression level for each gene was derived using Microarray Suite (MAS) 5.0 software. Using a one sided Wilconox signed rank test, the MAS5.0 software generated a detection p value.
Sample_platform_id	GPL339
Sample_contact_name	Maria,Isabel,Ramirez
Sample_contact_email	mramirez@bu.edu
Sample_contact_laboratory	Pulmonary Center
Sample_contact_department	Medicine
Sample_contact_institute	Boston University School of Medicine
Sample_contact_address	72 E. Concord St. E603
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02118
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM496nnn/GSM496709/suppl/GSM496709.CEL.gz
Sample_series_id	GSE19873
Sample_data_row_count	22690

GSM496710

GPL339

26-30 somites mid-foregut, biological rep3

Mouse embryonic mid-foregut at 26-30 somite developmental stage

genotype: wild type development stage/age: embryos containing between 26 and 30 somites, E9.5

Gene expression data from mouse mid-foregut tissue at 26-30 somite stage

Sample_geo_accession	GSM496710
Sample_status	Public on Jan 14 2010
Sample_submission_date	Jan 13 2010
Sample_last_update_date	Jan 13 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	To obtain mid-foregut tissue, the neural tube and heart were dissected away for the embryo to expose the foregut. The foregut tissue posterior to the pharyngeal arches and anterior to the liver was excised using tungsten needles. Collected tissues were placed immediately in RNeasyTM buffer (QIAGEN). Five to ten mid-foreguts were pooled for each of the three somite groups for RNA analysis.
Sample_extract_protocol_ch1	Total RNA was isolated from dissected tissues using RNeasyTM micropurification kit (QIAGEN) according to the manufacturer’s directions, followed by treatment on column with DNA-freeTM DNase (Ambion). RNA concentrations were measured in 1 μl (1/10 of the sample) in a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). RNA (100 ng) was amplified using the RiboAmp HS kit (Arcturus Engineering, Inc) as described by the manufacturer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA was labelled using biotinylated ribonucleotides during the second in vitro transcription step using ENZO kit (Affymetrix). After two rounds of amplification, 10-15 μg of amplified RNA (aRNA) were obtained. The quality of the amplification product was evaluated by examining the size distribution of the aRNA in an agarose gel stained with Sybr Gold (Molecular Probes).
Sample_hyb_protocol	10 μg of the fragmented, biotinylated aRNA, was added to a hybridization cocktail containing 50 fmol/mL control oligonucleotide B2, 1X eukaryotic hybridization controls, 0.1 mg/mL herring sperm DNA, and 0.5 mg/mL BSA in 1X hybridization buffer(100 mM MES, 1M [Na+], 20 mM EDTA, 0.01% Tween-20) for a total volume of 300 μL. The mixture was incubated to 99 °C for 5 min followed by 45 °C for 5 min. The mixture was then spun at 16,000xg for 5 min. 200 μL of hybridization mix was loaded on a chip that had been pre-incubated with 200 μL 1X hybridization buffer at 45 °C and 60 rpm for 10 min. The chip was hybridized for 16 hrs at 45°C and 60 rpm.Arrays were washed and stained according to the EukGE-WS2v4 Antibody Amplification for Eukaryotic Targets protocol on a Fluidics Station 450.This consists of a wash with non–stringent buffer (6X SSPE, 0.01% Tween-20), followed by a wash with stringent buffer (100 mM MES, 0.1M [Na+], 0.01% Tween-20), a stain with Strepavidin-Phycoerythrin (100 mM MES, 1M [Na+], 0.05% Tween-20, 2 mg/mL BSA, 10 μg/mL Streptavidin-Phycoerythrin), a wash with non-stringent buffer, a stain with biotinylated anti-strepavidin antibody (100 mM MES, 1M [Na+], 0.05% Tween-20, 2 mg/mL BSA, 0.1 mg/mL goat IgG, 3 μg/mLbiotinylated antibody), a stain again with Strepavidin-Phycoerythrin, and a final wash with non-stringent buffer.
Sample_scan_protocol	The stained arrays were scanned using an Affymetrix GeneChip Scanner 3000.
Sample_data_processing	The scanned images were quantified and scaled. The average signal intensity of each chip was scaled to 100. The normalization factor was set to 1. All other parameters were used at the default settings. A single weighted mean expression level for each gene was derived using Microarray Suite (MAS) 5.0 software. Using a one sided Wilconox signed rank test, the MAS5.0 software generated a detection p value.
Sample_platform_id	GPL339
Sample_contact_name	Maria,Isabel,Ramirez
Sample_contact_email	mramirez@bu.edu
Sample_contact_laboratory	Pulmonary Center
Sample_contact_department	Medicine
Sample_contact_institute	Boston University School of Medicine
Sample_contact_address	72 E. Concord St. E603
Sample_contact_city	Boston
Sample_contact_state	MA
Sample_contact_zip/postal_code	02118
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM496nnn/GSM496710/suppl/GSM496710.CEL.gz
Sample_series_id	GSE19873
Sample_data_row_count	22690

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