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Search results for the GEO ID: GSE29995

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Description

Characteristics

GSM742289

GPL1261

NPS regions from 3 stage-matched Wnt3a null embryos (biological replicate 1)

Microdissect node and primitive streaks (NPS)

strain: C57BL/6 and 129/Sv mixed age: E7.75-8 embryos (0-2 somites) genotype/variation: Wnt3a null

Sample_geo_accession	GSM742289
Sample_status	Public on Jun 30 2011
Sample_submission_date	Jun 15 2011
Sample_last_update_date	Jun 30 2011
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	Total RNA was isolated with TRIzol reagent (Invitrogen) from dissected node and primitive streak regions of E7.75-E8 wildtype and Wnt3a mutant embryos as previously described (Dunty et al., 2008, Development Jan;135(1): 85-94).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Protocols for synthesis of cDNA and cRNA were performed using the Affymetrix Two-Cycle Target Labeling Kit (P/N 900494; Affymetrix, Santa Clara, CA) according to manufacturer’s recommendations (701025 Rev.6). Briefly, 30-50ng of total RNA from individual embryos was used as template for first cycle cDNA synthesis. For second cycle cDNA synthesis, equivalent amounts of cRNA from three stage-matched embryos per genotype were pooled (600ng total) to generate labeled-target per array. Following in-vitro transcription, biotin-labeled cRNA was hybridized to GeneChip® Mouse Genome 430 2.0 Arrays (Affymetrix).
Sample_hyb_protocol	Array hybridizations were performed per manufacturer's protocols (701027 Rev.5) in triplicate per genotype. Subsequent washing, staining, and array scanning were carried out according to manufacturer’s protocols (701028 Rev.5). Affymetrix GeneChips MOE430 2.0 39K microarrays were used for this study.
Sample_scan_protocol	Array scanning were carried out according to Affymetrix protocols (701028 Rev.5).
Sample_data_processing	Statistical analysis was performed on probe-intensity level data (CEL files) using BRB ArrayTools v.3.2. Initial filtering and preprocessing was achieved using the robust multi-array analysis (RMA) algorithm. Class comparison analysis was conducted using a random-variance F-test. Genes were considered statistically significant if their parametric p-value was less than 0.05. Moreover, a Multivariate Permutation Test was performed to control for false discoveries such that with 90% confidence the gene list so obtained had a false discovery rate of less than 10%. Hierarchical clustering was carried out for statistically-significant genes using normalized log base 2 of the signal values using BRB ArrayTools.
Sample_platform_id	GPL1261
Sample_contact_name	Terry. P,,Yamaguchi
Sample_contact_email	yamagute@mail.nih.gov
Sample_contact_phone	301-846-1732
Sample_contact_fax	301-846-7117
Sample_contact_laboratory	Cell Signaling in Vertebrate Development Section
Sample_contact_department	Cancer and Developmental Biology
Sample_contact_institute	National Cancer Institute-Frederick
Sample_contact_address	1050 Boyles St, Bldg 539,Rm218
Sample_contact_city	Frederick
Sample_contact_state	MD
Sample_contact_zip/postal_code	21702
Sample_contact_country	USA
Sample_contact_web_link	http://ccr.cancer.gov/staff/staff.asp?profileid=5411
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM742nnn/GSM742289/suppl/GSM742289.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM742nnn/GSM742289/suppl/GSM742289.CHP.gz
Sample_series_id	GSE29995
Sample_data_row_count	45101

GSM742290

GPL1261

NPS regions from 3 stage-matched Wnt3a null embryos (biological replicate 2)

Microdissect node and primitive streaks (NPS)

strain: C57BL/6 and 129/Sv mixed age: E7.75-8 embryos (0-2 somites) genotype/variation: Wnt3a null

Sample_geo_accession	GSM742290
Sample_status	Public on Jun 30 2011
Sample_submission_date	Jun 15 2011
Sample_last_update_date	Jun 30 2011
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	Total RNA was isolated with TRIzol reagent (Invitrogen) from dissected node and primitive streak regions of E7.75-E8 wildtype and Wnt3a mutant embryos as previously described (Dunty et al., 2008, Development Jan;135(1): 85-94).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Protocols for synthesis of cDNA and cRNA were performed using the Affymetrix Two-Cycle Target Labeling Kit (P/N 900494; Affymetrix, Santa Clara, CA) according to manufacturer’s recommendations (701025 Rev.6). Briefly, 30-50ng of total RNA from individual embryos was used as template for first cycle cDNA synthesis. For second cycle cDNA synthesis, equivalent amounts of cRNA from three stage-matched embryos per genotype were pooled (600ng total) to generate labeled-target per array. Following in-vitro transcription, biotin-labeled cRNA was hybridized to GeneChip® Mouse Genome 430 2.0 Arrays (Affymetrix).
Sample_hyb_protocol	Array hybridizations were performed per manufacturer's protocols (701027 Rev.5) in triplicate per genotype. Subsequent washing, staining, and array scanning were carried out according to manufacturer’s protocols (701028 Rev.5). Affymetrix GeneChips MOE430 2.0 39K microarrays were used for this study.
Sample_scan_protocol	Array scanning were carried out according to Affymetrix protocols (701028 Rev.5).
Sample_data_processing	Statistical analysis was performed on probe-intensity level data (CEL files) using BRB ArrayTools v.3.2. Initial filtering and preprocessing was achieved using the robust multi-array analysis (RMA) algorithm. Class comparison analysis was conducted using a random-variance F-test. Genes were considered statistically significant if their parametric p-value was less than 0.05. Moreover, a Multivariate Permutation Test was performed to control for false discoveries such that with 90% confidence the gene list so obtained had a false discovery rate of less than 10%. Hierarchical clustering was carried out for statistically-significant genes using normalized log base 2 of the signal values using BRB ArrayTools.
Sample_platform_id	GPL1261
Sample_contact_name	Terry. P,,Yamaguchi
Sample_contact_email	yamagute@mail.nih.gov
Sample_contact_phone	301-846-1732
Sample_contact_fax	301-846-7117
Sample_contact_laboratory	Cell Signaling in Vertebrate Development Section
Sample_contact_department	Cancer and Developmental Biology
Sample_contact_institute	National Cancer Institute-Frederick
Sample_contact_address	1050 Boyles St, Bldg 539,Rm218
Sample_contact_city	Frederick
Sample_contact_state	MD
Sample_contact_zip/postal_code	21702
Sample_contact_country	USA
Sample_contact_web_link	http://ccr.cancer.gov/staff/staff.asp?profileid=5411
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM742nnn/GSM742290/suppl/GSM742290.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM742nnn/GSM742290/suppl/GSM742290.CHP.gz
Sample_series_id	GSE29995
Sample_data_row_count	45101

GSM742291

GPL1261

NPS regions from 3 stage-matched Wnt3a null embryos (biological replicate 3)

Microdissect node and primitive streaks (NPS)

strain: C57BL/6 and 129/Sv mixed age: E7.75-8 embryos (0-2 somites) genotype/variation: Wnt3a null

Sample_geo_accession	GSM742291
Sample_status	Public on Jun 30 2011
Sample_submission_date	Jun 15 2011
Sample_last_update_date	Jun 30 2011
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	Total RNA was isolated with TRIzol reagent (Invitrogen) from dissected node and primitive streak regions of E7.75-E8 wildtype and Wnt3a mutant embryos as previously described (Dunty et al., 2008, Development Jan;135(1): 85-94).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Protocols for synthesis of cDNA and cRNA were performed using the Affymetrix Two-Cycle Target Labeling Kit (P/N 900494; Affymetrix, Santa Clara, CA) according to manufacturer’s recommendations (701025 Rev.6). Briefly, 30-50ng of total RNA from individual embryos was used as template for first cycle cDNA synthesis. For second cycle cDNA synthesis, equivalent amounts of cRNA from three stage-matched embryos per genotype were pooled (600ng total) to generate labeled-target per array. Following in-vitro transcription, biotin-labeled cRNA was hybridized to GeneChip® Mouse Genome 430 2.0 Arrays (Affymetrix).
Sample_hyb_protocol	Array hybridizations were performed per manufacturer's protocols (701027 Rev.5) in triplicate per genotype. Subsequent washing, staining, and array scanning were carried out according to manufacturer’s protocols (701028 Rev.5). Affymetrix GeneChips MOE430 2.0 39K microarrays were used for this study.
Sample_scan_protocol	Array scanning were carried out according to Affymetrix protocols (701028 Rev.5).
Sample_data_processing	Statistical analysis was performed on probe-intensity level data (CEL files) using BRB ArrayTools v.3.2. Initial filtering and preprocessing was achieved using the robust multi-array analysis (RMA) algorithm. Class comparison analysis was conducted using a random-variance F-test. Genes were considered statistically significant if their parametric p-value was less than 0.05. Moreover, a Multivariate Permutation Test was performed to control for false discoveries such that with 90% confidence the gene list so obtained had a false discovery rate of less than 10%. Hierarchical clustering was carried out for statistically-significant genes using normalized log base 2 of the signal values using BRB ArrayTools.
Sample_platform_id	GPL1261
Sample_contact_name	Terry. P,,Yamaguchi
Sample_contact_email	yamagute@mail.nih.gov
Sample_contact_phone	301-846-1732
Sample_contact_fax	301-846-7117
Sample_contact_laboratory	Cell Signaling in Vertebrate Development Section
Sample_contact_department	Cancer and Developmental Biology
Sample_contact_institute	National Cancer Institute-Frederick
Sample_contact_address	1050 Boyles St, Bldg 539,Rm218
Sample_contact_city	Frederick
Sample_contact_state	MD
Sample_contact_zip/postal_code	21702
Sample_contact_country	USA
Sample_contact_web_link	http://ccr.cancer.gov/staff/staff.asp?profileid=5411
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM742nnn/GSM742291/suppl/GSM742291.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM742nnn/GSM742291/suppl/GSM742291.CHP.gz
Sample_series_id	GSE29995
Sample_data_row_count	45101

GSM742292

GPL1261

NPS regions from 3 stage-matched Wnt3a wildtype embryos (biological replicate 1)

Microdissect node and primitive streaks (NPS)

strain: C57BL/6 and 129/Sv mixed age: E7.75-8 embryos (0-2 somites) genotype/variation: Wnt3a wild type

Sample_geo_accession	GSM742292
Sample_status	Public on Jun 30 2011
Sample_submission_date	Jun 15 2011
Sample_last_update_date	Jun 30 2011
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	Total RNA was isolated with TRIzol reagent (Invitrogen) from dissected node and primitive streak regions of E7.75-E8 wildtype and Wnt3a mutant embryos as previously described (Dunty et al., 2008, Development Jan;135(1): 85-94).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Protocols for synthesis of cDNA and cRNA were performed using the Affymetrix Two-Cycle Target Labeling Kit (P/N 900494; Affymetrix, Santa Clara, CA) according to manufacturer’s recommendations (701025 Rev.6). Briefly, 30-50ng of total RNA from individual embryos was used as template for first cycle cDNA synthesis. For second cycle cDNA synthesis, equivalent amounts of cRNA from three stage-matched embryos per genotype were pooled (600ng total) to generate labeled-target per array. Following in-vitro transcription, biotin-labeled cRNA was hybridized to GeneChip® Mouse Genome 430 2.0 Arrays (Affymetrix).
Sample_hyb_protocol	Array hybridizations were performed per manufacturer's protocols (701027 Rev.5) in triplicate per genotype. Subsequent washing, staining, and array scanning were carried out according to manufacturer’s protocols (701028 Rev.5). Affymetrix GeneChips MOE430 2.0 39K microarrays were used for this study.
Sample_scan_protocol	Array scanning were carried out according to Affymetrix protocols (701028 Rev.5).
Sample_data_processing	Statistical analysis was performed on probe-intensity level data (CEL files) using BRB ArrayTools v.3.2. Initial filtering and preprocessing was achieved using the robust multi-array analysis (RMA) algorithm. Class comparison analysis was conducted using a random-variance F-test. Genes were considered statistically significant if their parametric p-value was less than 0.05. Moreover, a Multivariate Permutation Test was performed to control for false discoveries such that with 90% confidence the gene list so obtained had a false discovery rate of less than 10%. Hierarchical clustering was carried out for statistically-significant genes using normalized log base 2 of the signal values using BRB ArrayTools.
Sample_platform_id	GPL1261
Sample_contact_name	Terry. P,,Yamaguchi
Sample_contact_email	yamagute@mail.nih.gov
Sample_contact_phone	301-846-1732
Sample_contact_fax	301-846-7117
Sample_contact_laboratory	Cell Signaling in Vertebrate Development Section
Sample_contact_department	Cancer and Developmental Biology
Sample_contact_institute	National Cancer Institute-Frederick
Sample_contact_address	1050 Boyles St, Bldg 539,Rm218
Sample_contact_city	Frederick
Sample_contact_state	MD
Sample_contact_zip/postal_code	21702
Sample_contact_country	USA
Sample_contact_web_link	http://ccr.cancer.gov/staff/staff.asp?profileid=5411
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM742nnn/GSM742292/suppl/GSM742292.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM742nnn/GSM742292/suppl/GSM742292.CHP.gz
Sample_series_id	GSE29995
Sample_data_row_count	45101

GSM742293

GPL1261

NPS regions from 3 stage-matched Wnt3a wildtype embryos (biological replicate 2)

Microdissect node and primitive streaks (NPS)

strain: C57BL/6 and 129/Sv mixed age: E7.75-8 embryos (0-2 somites) genotype/variation: Wnt3a wild type

Sample_geo_accession	GSM742293
Sample_status	Public on Jun 30 2011
Sample_submission_date	Jun 15 2011
Sample_last_update_date	Jun 30 2011
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	Total RNA was isolated with TRIzol reagent (Invitrogen) from dissected node and primitive streak regions of E7.75-E8 wildtype and Wnt3a mutant embryos as previously described (Dunty et al., 2008, Development Jan;135(1): 85-94).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Protocols for synthesis of cDNA and cRNA were performed using the Affymetrix Two-Cycle Target Labeling Kit (P/N 900494; Affymetrix, Santa Clara, CA) according to manufacturer’s recommendations (701025 Rev.6). Briefly, 30-50ng of total RNA from individual embryos was used as template for first cycle cDNA synthesis. For second cycle cDNA synthesis, equivalent amounts of cRNA from three stage-matched embryos per genotype were pooled (600ng total) to generate labeled-target per array. Following in-vitro transcription, biotin-labeled cRNA was hybridized to GeneChip® Mouse Genome 430 2.0 Arrays (Affymetrix).
Sample_hyb_protocol	Array hybridizations were performed per manufacturer's protocols (701027 Rev.5) in triplicate per genotype. Subsequent washing, staining, and array scanning were carried out according to manufacturer’s protocols (701028 Rev.5). Affymetrix GeneChips MOE430 2.0 39K microarrays were used for this study.
Sample_scan_protocol	Array scanning were carried out according to Affymetrix protocols (701028 Rev.5).
Sample_data_processing	Statistical analysis was performed on probe-intensity level data (CEL files) using BRB ArrayTools v.3.2. Initial filtering and preprocessing was achieved using the robust multi-array analysis (RMA) algorithm. Class comparison analysis was conducted using a random-variance F-test. Genes were considered statistically significant if their parametric p-value was less than 0.05. Moreover, a Multivariate Permutation Test was performed to control for false discoveries such that with 90% confidence the gene list so obtained had a false discovery rate of less than 10%. Hierarchical clustering was carried out for statistically-significant genes using normalized log base 2 of the signal values using BRB ArrayTools.
Sample_platform_id	GPL1261
Sample_contact_name	Terry. P,,Yamaguchi
Sample_contact_email	yamagute@mail.nih.gov
Sample_contact_phone	301-846-1732
Sample_contact_fax	301-846-7117
Sample_contact_laboratory	Cell Signaling in Vertebrate Development Section
Sample_contact_department	Cancer and Developmental Biology
Sample_contact_institute	National Cancer Institute-Frederick
Sample_contact_address	1050 Boyles St, Bldg 539,Rm218
Sample_contact_city	Frederick
Sample_contact_state	MD
Sample_contact_zip/postal_code	21702
Sample_contact_country	USA
Sample_contact_web_link	http://ccr.cancer.gov/staff/staff.asp?profileid=5411
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM742nnn/GSM742293/suppl/GSM742293.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM742nnn/GSM742293/suppl/GSM742293.CHP.gz
Sample_series_id	GSE29995
Sample_data_row_count	45101

GSM742294

GPL1261

NPS regions from 3 stage-matched Wnt3a wildtype embryos (biological replicate 3)

Microdissect node and primitive streaks (NPS)

strain: C57BL/6 and 129/Sv mixed age: E7.75-8 embryos (0-2 somites) genotype/variation: Wnt3a wild type

Sample_geo_accession	GSM742294
Sample_status	Public on Jun 30 2011
Sample_submission_date	Jun 15 2011
Sample_last_update_date	Jun 30 2011
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	Total RNA was isolated with TRIzol reagent (Invitrogen) from dissected node and primitive streak regions of E7.75-E8 wildtype and Wnt3a mutant embryos as previously described (Dunty et al., 2008, Development Jan;135(1): 85-94).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Protocols for synthesis of cDNA and cRNA were performed using the Affymetrix Two-Cycle Target Labeling Kit (P/N 900494; Affymetrix, Santa Clara, CA) according to manufacturer’s recommendations (701025 Rev.6). Briefly, 30-50ng of total RNA from individual embryos was used as template for first cycle cDNA synthesis. For second cycle cDNA synthesis, equivalent amounts of cRNA from three stage-matched embryos per genotype were pooled (600ng total) to generate labeled-target per array. Following in-vitro transcription, biotin-labeled cRNA was hybridized to GeneChip® Mouse Genome 430 2.0 Arrays (Affymetrix).
Sample_hyb_protocol	Array hybridizations were performed per manufacturer's protocols (701027 Rev.5) in triplicate per genotype. Subsequent washing, staining, and array scanning were carried out according to manufacturer’s protocols (701028 Rev.5). Affymetrix GeneChips MOE430 2.0 39K microarrays were used for this study.
Sample_scan_protocol	Array scanning were carried out according to Affymetrix protocols (701028 Rev.5).
Sample_data_processing	Statistical analysis was performed on probe-intensity level data (CEL files) using BRB ArrayTools v.3.2. Initial filtering and preprocessing was achieved using the robust multi-array analysis (RMA) algorithm. Class comparison analysis was conducted using a random-variance F-test. Genes were considered statistically significant if their parametric p-value was less than 0.05. Moreover, a Multivariate Permutation Test was performed to control for false discoveries such that with 90% confidence the gene list so obtained had a false discovery rate of less than 10%. Hierarchical clustering was carried out for statistically-significant genes using normalized log base 2 of the signal values using BRB ArrayTools.
Sample_platform_id	GPL1261
Sample_contact_name	Terry. P,,Yamaguchi
Sample_contact_email	yamagute@mail.nih.gov
Sample_contact_phone	301-846-1732
Sample_contact_fax	301-846-7117
Sample_contact_laboratory	Cell Signaling in Vertebrate Development Section
Sample_contact_department	Cancer and Developmental Biology
Sample_contact_institute	National Cancer Institute-Frederick
Sample_contact_address	1050 Boyles St, Bldg 539,Rm218
Sample_contact_city	Frederick
Sample_contact_state	MD
Sample_contact_zip/postal_code	21702
Sample_contact_country	USA
Sample_contact_web_link	http://ccr.cancer.gov/staff/staff.asp?profileid=5411
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM742nnn/GSM742294/suppl/GSM742294.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM742nnn/GSM742294/suppl/GSM742294.CHP.gz
Sample_series_id	GSE29995
Sample_data_row_count	45101

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