Result

Search results for the GEO ID: GSE15770

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Title

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Description

Characteristics

GSM394789

GPL1261

E18.5 Get1 +/- Bladder 2-4

bladder

age: Embryonic day 18.5 tissue: Bladder genotype: Get1 +/-

Get1 het E18.5 bladder

Sample_geo_accession	GSM394789
Sample_status	Public on May 20 2009
Sample_submission_date	Apr 20 2009
Sample_last_update_date	Jan 09 2013
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	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+mRNA present in the isolated total RNA (typically 100ng total RNA starting material each sample reaction) using the GeneChip WT cDNA synthesis Kit (Affymetrix, Inc., Santa Clara, CA) and random hexamers tagged with a T7 promoter sequence. The double-stranded cDNA is then used as a template to generate many copies of antisense cRNA from an in vitro transcription reaction (IVT) of 16hrs in the presence of T7 RNA Polymerase using the Affymetrix Genechip WT cDNA Amplification Kit. 10 ug of cRNA were input into the second cycle cDNA reaction with random hexamers that are used to reverse transcribe the cRNA from the first cycle to produce single-stranded DNA in the sense orientation.
Sample_label_protocol_ch1	The single-stranded DNA sample is fragmented (WT Terminal Labeling Kit, Affymetrix, Inc, Santa Clara, CA) to an average strand length of 60 bases (range 40-70bp) following prescribed protocols (Affymetrix GeneChip WT Sense Target Labeling Assay Manual). The fragmented single-stranded DNA is subsequently labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.
Sample_hyb_protocol	Following the recommended procedure, 0.54 ug of this fragmented target single-stranded cDNA was hybridized at 45c with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse Gene 1.0 ST array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fludics Station 450 (Fluidics protocol FS450_007).
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000 7G and GeneChip Operating Software v. 1.4 to produce .CEL intensity files.
Sample_data_processing	These probe cell intensity files (.CEL) were analyzed in Affymetrix Expression Console software v1.1 using the PLIER algorithm to generate probe level summarization files (.CHP).
Sample_data_processing	(Algorithm: PLIER v 2.0; Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile).
Sample_platform_id	GPL1261
Sample_contact_name	Amelia,Soto,Hopkin
Sample_contact_email	sotoa@uci.edu
Sample_contact_phone	9498249372
Sample_contact_laboratory	Bogi Andersen
Sample_contact_department	Biological Chemistry & Medicine
Sample_contact_institute	University of California Irvine
Sample_contact_address	250 Sprague Hall
Sample_contact_city	Irvine
Sample_contact_state	CA
Sample_contact_zip/postal_code	92617
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM394nnn/GSM394789/suppl/GSM394789.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM394nnn/GSM394789/suppl/GSM394789.CHP.gz
Sample_relation	Reanalyzed by: GSM1061787
Sample_series_id	GSE15768
Sample_series_id	GSE15770
Sample_series_id	GSE16150
Sample_data_row_count	45101

GSM395744

GPL1261

E18.5 Get1 +/- Bladder 2-5

bladder

age: Embryonic day 18.5 tissue: Bladder genotype: Get1 +/-

Get1 Het E18.5 bladder

Sample_geo_accession	GSM395744
Sample_status	Public on May 20 2009
Sample_submission_date	Apr 21 2009
Sample_last_update_date	Jan 09 2013
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	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+mRNA present in the isolated total RNA (typically 100ng total RNA starting material each sample reaction) using the GeneChip WT cDNA synthesis Kit (Affymetrix, Inc., Santa Clara, CA) and random hexamers tagged with a T7 promoter sequence. The double-stranded cDNA is then used as a template to generate many copies of antisense cRNA from an in vitro transcription reaction (IVT) of 16hrs in the presence of T7 RNA Polymerase using the Affymetrix Genechip WT cDNA Amplification Kit. 10 ug of cRNA were input into the second cycle cDNA reaction with random hexamers that are used to reverse transcribe the cRNA from the first cycle to produce single-stranded DNA in the sense orientation.
Sample_label_protocol_ch1	The single-stranded DNA sample is fragmented (WT Terminal Labeling Kit, Affymetrix, Inc, Santa Clara, CA) to an average strand length of 60 bases (range 40-70bp) following prescribed protocols (Affymetrix GeneChip WT Sense Target Labeling Assay Manual). The fragmented single-stranded DNA is subsequently labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.
Sample_hyb_protocol	Following the recommended procedure, 0.54 ug of this fragmented target single-stranded cDNA was hybridized at 45c with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse Gene 1.0 ST array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fludics Station 450 (Fluidics protocol FS450_007).
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000 7G and GeneChip Operating Software v. 1.4 to produce .CEL intensity files.
Sample_data_processing	These probe cell intensity files (.CEL) were analyzed in Affymetrix Expression Console software v1.1 using the PLIER algorithm to generate probe level summarization files (.CHP).
Sample_data_processing	(Algorithm: PLIER v 2.0; Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile).
Sample_platform_id	GPL1261
Sample_contact_name	Amelia,Soto,Hopkin
Sample_contact_email	sotoa@uci.edu
Sample_contact_phone	9498249372
Sample_contact_laboratory	Bogi Andersen
Sample_contact_department	Biological Chemistry & Medicine
Sample_contact_institute	University of California Irvine
Sample_contact_address	250 Sprague Hall
Sample_contact_city	Irvine
Sample_contact_state	CA
Sample_contact_zip/postal_code	92617
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM395nnn/GSM395744/suppl/GSM395744.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM395nnn/GSM395744/suppl/GSM395744.CHP.gz
Sample_relation	Reanalyzed by: GSM1061788
Sample_series_id	GSE15768
Sample_series_id	GSE15770
Sample_series_id	GSE16150
Sample_data_row_count	45101

GSM395745

GPL1261

E18.5 Get1 +/- Bladder 2-6

bladder

age: Embryonic day 18.5 tissue: Bladder genotype: Get1 +/-

Get1 Het E18.5 bladder

Sample_geo_accession	GSM395745
Sample_status	Public on May 20 2009
Sample_submission_date	Apr 21 2009
Sample_last_update_date	Jan 09 2013
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	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+mRNA present in the isolated total RNA (typically 100ng total RNA starting material each sample reaction) using the GeneChip WT cDNA synthesis Kit (Affymetrix, Inc., Santa Clara, CA) and random hexamers tagged with a T7 promoter sequence. The double-stranded cDNA is then used as a template to generate many copies of antisense cRNA from an in vitro transcription reaction (IVT) of 16hrs in the presence of T7 RNA Polymerase using the Affymetrix Genechip WT cDNA Amplification Kit. 10 ug of cRNA were input into the second cycle cDNA reaction with random hexamers that are used to reverse transcribe the cRNA from the first cycle to produce single-stranded DNA in the sense orientation.
Sample_label_protocol_ch1	The single-stranded DNA sample is fragmented (WT Terminal Labeling Kit, Affymetrix, Inc, Santa Clara, CA) to an average strand length of 60 bases (range 40-70bp) following prescribed protocols (Affymetrix GeneChip WT Sense Target Labeling Assay Manual). The fragmented single-stranded DNA is subsequently labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.
Sample_hyb_protocol	Following the recommended procedure, 0.54 ug of this fragmented target single-stranded cDNA was hybridized at 45c with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse Gene 1.0 ST array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fludics Station 450 (Fluidics protocol FS450_007).
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000 7G and GeneChip Operating Software v. 1.4 to produce .CEL intensity files.
Sample_data_processing	These probe cell intensity files (.CEL) were analyzed in Affymetrix Expression Console software v1.1 using the PLIER algorithm to generate probe level summarization files (.CHP).
Sample_data_processing	(Algorithm: PLIER v 2.0; Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile).
Sample_platform_id	GPL1261
Sample_contact_name	Amelia,Soto,Hopkin
Sample_contact_email	sotoa@uci.edu
Sample_contact_phone	9498249372
Sample_contact_laboratory	Bogi Andersen
Sample_contact_department	Biological Chemistry & Medicine
Sample_contact_institute	University of California Irvine
Sample_contact_address	250 Sprague Hall
Sample_contact_city	Irvine
Sample_contact_state	CA
Sample_contact_zip/postal_code	92617
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM395nnn/GSM395745/suppl/GSM395745.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM395nnn/GSM395745/suppl/GSM395745.CHP.gz
Sample_relation	Reanalyzed by: GSM1061789
Sample_series_id	GSE15768
Sample_series_id	GSE15770
Sample_series_id	GSE16150
Sample_data_row_count	45101

GSM395746

GPL1261

E14.5 WT Bladder 1-3

Bladder

age: Embryonic day 14.5 tissue: Bladder genotype: wild-type

E14.5 WT bladder

Sample_geo_accession	GSM395746
Sample_status	Public on May 20 2009
Sample_submission_date	Apr 21 2009
Sample_last_update_date	Jan 09 2013
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	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+mRNA present in the isolated total RNA (typically 100ng total RNA starting material each sample reaction) using the GeneChip WT cDNA synthesis Kit (Affymetrix, Inc., Santa Clara, CA) and random hexamers tagged with a T7 promoter sequence. The double-stranded cDNA is then used as a template to generate many copies of antisense cRNA from an in vitro transcription reaction (IVT) of 16hrs in the presence of T7 RNA Polymerase using the Affymetrix Genechip WT cDNA Amplification Kit. 10 ug of cRNA were input into the second cycle cDNA reaction with random hexamers that are used to reverse transcribe the cRNA from the first cycle to produce single-stranded DNA in the sense orientation.
Sample_label_protocol_ch1	The single-stranded DNA sample is fragmented (WT Terminal Labeling Kit, Affymetrix, Inc, Santa Clara, CA) to an average strand length of 60 bases (range 40-70bp) following prescribed protocols (Affymetrix GeneChip WT Sense Target Labeling Assay Manual). The fragmented single-stranded DNA is subsequently labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.
Sample_hyb_protocol	Following the recommended procedure, 0.54 ug of this fragmented target single-stranded cDNA was hybridized at 45c with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse Gene 1.0 ST array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fludics Station 450 (Fluidics protocol FS450_007).
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000 7G and GeneChip Operating Software v. 1.4 to produce .CEL intensity files.
Sample_data_processing	These probe cell intensity files (.CEL) were analyzed in Affymetrix Expression Console software v1.1 using the PLIER algorithm to generate probe level summarization files (.CHP).
Sample_data_processing	(Algorithm: PLIER v 2.0; Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile).
Sample_platform_id	GPL1261
Sample_contact_name	Amelia,Soto,Hopkin
Sample_contact_email	sotoa@uci.edu
Sample_contact_phone	9498249372
Sample_contact_laboratory	Bogi Andersen
Sample_contact_department	Biological Chemistry & Medicine
Sample_contact_institute	University of California Irvine
Sample_contact_address	250 Sprague Hall
Sample_contact_city	Irvine
Sample_contact_state	CA
Sample_contact_zip/postal_code	92617
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM395nnn/GSM395746/suppl/GSM395746.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM395nnn/GSM395746/suppl/GSM395746.CHP.gz
Sample_relation	Reanalyzed by: GSM1061782
Sample_series_id	GSE15770
Sample_series_id	GSE16150
Sample_data_row_count	45101

GSM395757

GPL1261

E16.5 WT Bladder 1-1

Bladder

age: Embryonic day 16.5 tissue: Bladder genotype: wild-type

E16.5 WT bladder

Sample_geo_accession	GSM395757
Sample_status	Public on May 20 2009
Sample_submission_date	Apr 21 2009
Sample_last_update_date	Jan 09 2013
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	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+mRNA present in the isolated total RNA (typically 100ng total RNA starting material each sample reaction) using the GeneChip WT cDNA synthesis Kit (Affymetrix, Inc., Santa Clara, CA) and random hexamers tagged with a T7 promoter sequence. The double-stranded cDNA is then used as a template to generate many copies of antisense cRNA from an in vitro transcription reaction (IVT) of 16hrs in the presence of T7 RNA Polymerase using the Affymetrix Genechip WT cDNA Amplification Kit. 10 ug of cRNA were input into the second cycle cDNA reaction with random hexamers that are used to reverse transcribe the cRNA from the first cycle to produce single-stranded DNA in the sense orientation.
Sample_label_protocol_ch1	The single-stranded DNA sample is fragmented (WT Terminal Labeling Kit, Affymetrix, Inc, Santa Clara, CA) to an average strand length of 60 bases (range 40-70bp) following prescribed protocols (Affymetrix GeneChip WT Sense Target Labeling Assay Manual). The fragmented single-stranded DNA is subsequently labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.
Sample_hyb_protocol	Following the recommended procedure, 0.54 ug of this fragmented target single-stranded cDNA was hybridized at 45c with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse Gene 1.0 ST array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fludics Station 450 (Fluidics protocol FS450_007).
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000 7G and GeneChip Operating Software v. 1.4 to produce .CEL intensity files.
Sample_data_processing	These probe cell intensity files (.CEL) were analyzed in Affymetrix Expression Console software v1.1 using the PLIER algorithm to generate probe level summarization files (.CHP).
Sample_data_processing	(Algorithm: PLIER v 2.0; Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile).
Sample_platform_id	GPL1261
Sample_contact_name	Amelia,Soto,Hopkin
Sample_contact_email	sotoa@uci.edu
Sample_contact_phone	9498249372
Sample_contact_laboratory	Bogi Andersen
Sample_contact_department	Biological Chemistry & Medicine
Sample_contact_institute	University of California Irvine
Sample_contact_address	250 Sprague Hall
Sample_contact_city	Irvine
Sample_contact_state	CA
Sample_contact_zip/postal_code	92617
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM395nnn/GSM395757/suppl/GSM395757.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM395nnn/GSM395757/suppl/GSM395757.CHP.gz
Sample_relation	Reanalyzed by: GSM1061784
Sample_series_id	GSE15770
Sample_series_id	GSE16150
Sample_data_row_count	45101

GSM395758

GPL1261

E16.5 WT Bladder 1-2

Bladder

age: Embryonic day 16.5 tissue: Bladder genotype: wild-type

E16.5 WT bladder

Sample_geo_accession	GSM395758
Sample_status	Public on May 20 2009
Sample_submission_date	Apr 21 2009
Sample_last_update_date	Jan 09 2013
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	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+mRNA present in the isolated total RNA (typically 100ng total RNA starting material each sample reaction) using the GeneChip WT cDNA synthesis Kit (Affymetrix, Inc., Santa Clara, CA) and random hexamers tagged with a T7 promoter sequence. The double-stranded cDNA is then used as a template to generate many copies of antisense cRNA from an in vitro transcription reaction (IVT) of 16hrs in the presence of T7 RNA Polymerase using the Affymetrix Genechip WT cDNA Amplification Kit. 10 ug of cRNA were input into the second cycle cDNA reaction with random hexamers that are used to reverse transcribe the cRNA from the first cycle to produce single-stranded DNA in the sense orientation.
Sample_label_protocol_ch1	The single-stranded DNA sample is fragmented (WT Terminal Labeling Kit, Affymetrix, Inc, Santa Clara, CA) to an average strand length of 60 bases (range 40-70bp) following prescribed protocols (Affymetrix GeneChip WT Sense Target Labeling Assay Manual). The fragmented single-stranded DNA is subsequently labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.
Sample_hyb_protocol	Following the recommended procedure, 0.54 ug of this fragmented target single-stranded cDNA was hybridized at 45c with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse Gene 1.0 ST array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fludics Station 450 (Fluidics protocol FS450_007).
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000 7G and GeneChip Operating Software v. 1.4 to produce .CEL intensity files.
Sample_data_processing	These probe cell intensity files (.CEL) were analyzed in Affymetrix Expression Console software v1.1 using the PLIER algorithm to generate probe level summarization files (.CHP).
Sample_data_processing	(Algorithm: PLIER v 2.0; Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile).
Sample_platform_id	GPL1261
Sample_contact_name	Amelia,Soto,Hopkin
Sample_contact_email	sotoa@uci.edu
Sample_contact_phone	9498249372
Sample_contact_laboratory	Bogi Andersen
Sample_contact_department	Biological Chemistry & Medicine
Sample_contact_institute	University of California Irvine
Sample_contact_address	250 Sprague Hall
Sample_contact_city	Irvine
Sample_contact_state	CA
Sample_contact_zip/postal_code	92617
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM395nnn/GSM395758/suppl/GSM395758.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM395nnn/GSM395758/suppl/GSM395758.CHP.gz
Sample_relation	Reanalyzed by: GSM1061785
Sample_series_id	GSE15770
Sample_series_id	GSE16150
Sample_data_row_count	45101

GSM395763

GPL1261

E16.5 WT Bladder 1-3

Bladder

age: Embryonic day 16.5 tissue: Bladder genotype: wild-type

E16.5 WT bladder

Sample_geo_accession	GSM395763
Sample_status	Public on May 20 2009
Sample_submission_date	Apr 21 2009
Sample_last_update_date	Jan 09 2013
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	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+mRNA present in the isolated total RNA (typically 100ng total RNA starting material each sample reaction) using the GeneChip WT cDNA synthesis Kit (Affymetrix, Inc., Santa Clara, CA) and random hexamers tagged with a T7 promoter sequence. The double-stranded cDNA is then used as a template to generate many copies of antisense cRNA from an in vitro transcription reaction (IVT) of 16hrs in the presence of T7 RNA Polymerase using the Affymetrix Genechip WT cDNA Amplification Kit. 10 ug of cRNA were input into the second cycle cDNA reaction with random hexamers that are used to reverse transcribe the cRNA from the first cycle to produce single-stranded DNA in the sense orientation.
Sample_label_protocol_ch1	The single-stranded DNA sample is fragmented (WT Terminal Labeling Kit, Affymetrix, Inc, Santa Clara, CA) to an average strand length of 60 bases (range 40-70bp) following prescribed protocols (Affymetrix GeneChip WT Sense Target Labeling Assay Manual). The fragmented single-stranded DNA is subsequently labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.
Sample_hyb_protocol	Following the recommended procedure, 0.54 ug of this fragmented target single-stranded cDNA was hybridized at 45c with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse Gene 1.0 ST array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fludics Station 450 (Fluidics protocol FS450_007).
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000 7G and GeneChip Operating Software v. 1.4 to produce .CEL intensity files.
Sample_data_processing	These probe cell intensity files (.CEL) were analyzed in Affymetrix Expression Console software v1.1 using the PLIER algorithm to generate probe level summarization files (.CHP).
Sample_data_processing	(Algorithm: PLIER v 2.0; Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile).
Sample_platform_id	GPL1261
Sample_contact_name	Amelia,Soto,Hopkin
Sample_contact_email	sotoa@uci.edu
Sample_contact_phone	9498249372
Sample_contact_laboratory	Bogi Andersen
Sample_contact_department	Biological Chemistry & Medicine
Sample_contact_institute	University of California Irvine
Sample_contact_address	250 Sprague Hall
Sample_contact_city	Irvine
Sample_contact_state	CA
Sample_contact_zip/postal_code	92617
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM395nnn/GSM395763/suppl/GSM395763.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM395nnn/GSM395763/suppl/GSM395763.CHP.gz
Sample_relation	Reanalyzed by: GSM1061786
Sample_series_id	GSE15770
Sample_series_id	GSE16150
Sample_data_row_count	45101

GSM395765

GPL1261

E14.5 WT Bladder 1-6

Bladder

age: Embryonic day 14.5 tissue: Bladder genotype: wild-type

E14.5 WT bladder

Sample_geo_accession	GSM395765
Sample_status	Public on May 20 2009
Sample_submission_date	Apr 21 2009
Sample_last_update_date	Jan 09 2013
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	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+mRNA present in the isolated total RNA (typically 100ng total RNA starting material each sample reaction) using the GeneChip WT cDNA synthesis Kit (Affymetrix, Inc., Santa Clara, CA) and random hexamers tagged with a T7 promoter sequence. The double-stranded cDNA is then used as a template to generate many copies of antisense cRNA from an in vitro transcription reaction (IVT) of 16hrs in the presence of T7 RNA Polymerase using the Affymetrix Genechip WT cDNA Amplification Kit. 10 ug of cRNA were input into the second cycle cDNA reaction with random hexamers that are used to reverse transcribe the cRNA from the first cycle to produce single-stranded DNA in the sense orientation.
Sample_label_protocol_ch1	The single-stranded DNA sample is fragmented (WT Terminal Labeling Kit, Affymetrix, Inc, Santa Clara, CA) to an average strand length of 60 bases (range 40-70bp) following prescribed protocols (Affymetrix GeneChip WT Sense Target Labeling Assay Manual). The fragmented single-stranded DNA is subsequently labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.
Sample_hyb_protocol	Following the recommended procedure, 0.54 ug of this fragmented target single-stranded cDNA was hybridized at 45c with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix Mouse Gene 1.0 ST array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fludics Station 450 (Fluidics protocol FS450_007).
Sample_scan_protocol	Arrays were scanned using the GeneChip Scanner 3000 7G and GeneChip Operating Software v. 1.4 to produce .CEL intensity files.
Sample_data_processing	These probe cell intensity files (.CEL) were analyzed in Affymetrix Expression Console software v1.1 using the PLIER algorithm to generate probe level summarization files (.CHP).
Sample_data_processing	(Algorithm: PLIER v 2.0; Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile).
Sample_data_processing
Sample_data_processing
Sample_platform_id	GPL1261
Sample_contact_name	Amelia,Soto,Hopkin
Sample_contact_email	sotoa@uci.edu
Sample_contact_phone	9498249372
Sample_contact_laboratory	Bogi Andersen
Sample_contact_department	Biological Chemistry & Medicine
Sample_contact_institute	University of California Irvine
Sample_contact_address	250 Sprague Hall
Sample_contact_city	Irvine
Sample_contact_state	CA
Sample_contact_zip/postal_code	92617
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM395nnn/GSM395765/suppl/GSM395765.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM395nnn/GSM395765/suppl/GSM395765.CHP.gz
Sample_relation	Reanalyzed by: GSM1061783
Sample_series_id	GSE15770
Sample_series_id	GSE16150
Sample_data_row_count	45101

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