Result

Search results for the GEO ID: GSE46426

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM1130053

GPL1261

R26R^AC/AC (Control), biological replicate #1

Mouse control_PSM

strain background: C57BL6/6J genotype/variation: R26R^AC/AC (Control) developmental stage: E8.75 tissue: presomitic mesoderm (PSM)

Gene expression data from control PSM.

Sample_geo_accession	GSM1130053
Sample_status	Public on Apr 27 2013
Sample_submission_date	Apr 26 2013
Sample_last_update_date	Apr 27 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The anterior 2/3 PSM was dissected from the posterior 1/3 PSM and somites. Anterior PSM was briefly rinsed in 1X PBS (Gibco).
Sample_growth_protocol_ch1	Control and mutant embryos were harvested on Embronic day (E) 8.75 in L-15 media under a dissection light and fluorescent microscope setup.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The anterior PSM was pipetted into lysis solution and underwent total RNA purification using the PicoPure RNA Isolation Kit (Life Technologies).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA was prepared using the 3' IVT Express Kit (Affymetrix) for 1 ug total RNA according to the standard protocol for cRNA synthesis (GeneChip 3’ IVT Express Kit).
Sample_hyb_protocol	Following fragmentation, 5.5 ug of cRNA was hybridized to Affymetrix Mouse 430 2.0 GeneChips for 16 hours at 45 °C. GeneChips were washed and stained using a fluidics station.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.
Sample_data_processing	Data was acquired and normalized using Affymetrix Expression Console software under Affymetrix default analysis settings and global scaling as normalization method to generate Microarray Suite version 5.0 (MAS 5.0) files. Data is represented by presence/absence call for each gene using appropriate algorithms and expression data that had an “absent” call was filtered out of data sets using Excel software (Microsoft).
Sample_platform_id	GPL1261
Sample_contact_name	Timothy,Peter,Lopez
Sample_contact_email	tpetelopez@gmail.com
Sample_contact_laboratory	Chen-Ming Fan
Sample_contact_department	Biology
Sample_contact_institute	Johns Hopkins University/Carnegie Institution
Sample_contact_address	3520 San Martin Drive
Sample_contact_city	Baltimore
Sample_contact_state	Maryland
Sample_contact_zip/postal_code	21218
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1130nnn/GSM1130053/suppl/GSM1130053_Control__1.CEL.gz
Sample_series_id	GSE46426
Sample_data_row_count	19606

GSM1130054

GPL1261

R26R^AC/AC (Control), biological replicate #2

Mouse control_PSM

strain background: C57BL6/6J genotype/variation: R26R^AC/AC (Control) developmental stage: E8.75 tissue: presomitic mesoderm (PSM)

Gene expression data from control PSM.

Sample_geo_accession	GSM1130054
Sample_status	Public on Apr 27 2013
Sample_submission_date	Apr 26 2013
Sample_last_update_date	Apr 27 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The anterior 2/3 PSM was dissected from the posterior 1/3 PSM and somites. Anterior PSM was briefly rinsed in 1X PBS (Gibco).
Sample_growth_protocol_ch1	Control and mutant embryos were harvested on Embronic day (E) 8.75 in L-15 media under a dissection light and fluorescent microscope setup.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The anterior PSM was pipetted into lysis solution and underwent total RNA purification using the PicoPure RNA Isolation Kit (Life Technologies).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA was prepared using the 3' IVT Express Kit (Affymetrix) for 1 ug total RNA according to the standard protocol for cRNA synthesis (GeneChip 3’ IVT Express Kit).
Sample_hyb_protocol	Following fragmentation, 5.5 ug of cRNA was hybridized to Affymetrix Mouse 430 2.0 GeneChips for 16 hours at 45 °C. GeneChips were washed and stained using a fluidics station.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.
Sample_data_processing	Data was acquired and normalized using Affymetrix Expression Console software under Affymetrix default analysis settings and global scaling as normalization method to generate Microarray Suite version 5.0 (MAS 5.0) files. Data is represented by presence/absence call for each gene using appropriate algorithms and expression data that had an “absent” call was filtered out of data sets using Excel software (Microsoft).
Sample_platform_id	GPL1261
Sample_contact_name	Timothy,Peter,Lopez
Sample_contact_email	tpetelopez@gmail.com
Sample_contact_laboratory	Chen-Ming Fan
Sample_contact_department	Biology
Sample_contact_institute	Johns Hopkins University/Carnegie Institution
Sample_contact_address	3520 San Martin Drive
Sample_contact_city	Baltimore
Sample_contact_state	Maryland
Sample_contact_zip/postal_code	21218
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1130nnn/GSM1130054/suppl/GSM1130054_Control__2.CEL.gz
Sample_series_id	GSE46426
Sample_data_row_count	19606

GSM1130055

GPL1261

R26R^AC/AC (Control), biological replicate #3

Mouse control_PSM

strain background: C57BL6/6J genotype/variation: R26R^AC/AC (Control) developmental stage: E8.75 tissue: presomitic mesoderm (PSM)

Gene expression data from control PSM.

Sample_geo_accession	GSM1130055
Sample_status	Public on Apr 27 2013
Sample_submission_date	Apr 26 2013
Sample_last_update_date	Apr 27 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The anterior 2/3 PSM was dissected from the posterior 1/3 PSM and somites. Anterior PSM was briefly rinsed in 1X PBS (Gibco).
Sample_growth_protocol_ch1	Control and mutant embryos were harvested on Embronic day (E) 8.75 in L-15 media under a dissection light and fluorescent microscope setup.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The anterior PSM was pipetted into lysis solution and underwent total RNA purification using the PicoPure RNA Isolation Kit (Life Technologies).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA was prepared using the 3' IVT Express Kit (Affymetrix) for 1 ug total RNA according to the standard protocol for cRNA synthesis (GeneChip 3’ IVT Express Kit).
Sample_hyb_protocol	Following fragmentation, 5.5 ug of cRNA was hybridized to Affymetrix Mouse 430 2.0 GeneChips for 16 hours at 45 °C. GeneChips were washed and stained using a fluidics station.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.
Sample_data_processing	Data was acquired and normalized using Affymetrix Expression Console software under Affymetrix default analysis settings and global scaling as normalization method to generate Microarray Suite version 5.0 (MAS 5.0) files. Data is represented by presence/absence call for each gene using appropriate algorithms and expression data that had an “absent” call was filtered out of data sets using Excel software (Microsoft).
Sample_platform_id	GPL1261
Sample_contact_name	Timothy,Peter,Lopez
Sample_contact_email	tpetelopez@gmail.com
Sample_contact_laboratory	Chen-Ming Fan
Sample_contact_department	Biology
Sample_contact_institute	Johns Hopkins University/Carnegie Institution
Sample_contact_address	3520 San Martin Drive
Sample_contact_city	Baltimore
Sample_contact_state	Maryland
Sample_contact_zip/postal_code	21218
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1130nnn/GSM1130055/suppl/GSM1130055_Control__3.CEL.gz
Sample_series_id	GSE46426
Sample_data_row_count	19606

GSM1130056

GPL1261

R26R^AC/AC;T-Cre (Mutant), biological replicate #1

Mousemutant_PSM

strain background: C57BL6/6J genotype/variation: R26R^AC/AC;T-Cre (Mutant) developmental stage: E8.75 tissue: presomitic mesoderm (PSM)

Gene expression data from mutant PSM.

Sample_geo_accession	GSM1130056
Sample_status	Public on Apr 27 2013
Sample_submission_date	Apr 26 2013
Sample_last_update_date	Apr 27 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The anterior 2/3 PSM was dissected from the posterior 1/3 PSM and somites. Anterior PSM was briefly rinsed in 1X PBS (Gibco).
Sample_growth_protocol_ch1	Control and mutant embryos were harvested on Embronic day (E) 8.75 in L-15 media under a dissection light and fluorescent microscope setup.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The anterior PSM was pipetted into lysis solution and underwent total RNA purification using the PicoPure RNA Isolation Kit (Life Technologies).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA was prepared using the 3' IVT Express Kit (Affymetrix) for 1 ug total RNA according to the standard protocol for cRNA synthesis (GeneChip 3’ IVT Express Kit).
Sample_hyb_protocol	Following fragmentation, 5.5 ug of cRNA was hybridized to Affymetrix Mouse 430 2.0 GeneChips for 16 hours at 45 °C. GeneChips were washed and stained using a fluidics station.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.
Sample_data_processing	Data was acquired and normalized using Affymetrix Expression Console software under Affymetrix default analysis settings and global scaling as normalization method to generate Microarray Suite version 5.0 (MAS 5.0) files. Data is represented by presence/absence call for each gene using appropriate algorithms and expression data that had an “absent” call was filtered out of data sets using Excel software (Microsoft).
Sample_platform_id	GPL1261
Sample_contact_name	Timothy,Peter,Lopez
Sample_contact_email	tpetelopez@gmail.com
Sample_contact_laboratory	Chen-Ming Fan
Sample_contact_department	Biology
Sample_contact_institute	Johns Hopkins University/Carnegie Institution
Sample_contact_address	3520 San Martin Drive
Sample_contact_city	Baltimore
Sample_contact_state	Maryland
Sample_contact_zip/postal_code	21218
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1130nnn/GSM1130056/suppl/GSM1130056_Mutant__1.CEL.gz
Sample_series_id	GSE46426
Sample_data_row_count	19606

GSM1130057

GPL1261

R26R^AC/AC;T-Cre (Mutant), biological replicate #2

Mousemutant_PSM

strain background: C57BL6/6J genotype/variation: R26R^AC/AC;T-Cre (Mutant) developmental stage: E8.75 tissue: presomitic mesoderm (PSM)

Gene expression data from mutant PSM.

Sample_geo_accession	GSM1130057
Sample_status	Public on Apr 27 2013
Sample_submission_date	Apr 26 2013
Sample_last_update_date	Apr 27 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The anterior 2/3 PSM was dissected from the posterior 1/3 PSM and somites. Anterior PSM was briefly rinsed in 1X PBS (Gibco).
Sample_growth_protocol_ch1	Control and mutant embryos were harvested on Embronic day (E) 8.75 in L-15 media under a dissection light and fluorescent microscope setup.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The anterior PSM was pipetted into lysis solution and underwent total RNA purification using the PicoPure RNA Isolation Kit (Life Technologies).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA was prepared using the 3' IVT Express Kit (Affymetrix) for 1 ug total RNA according to the standard protocol for cRNA synthesis (GeneChip 3’ IVT Express Kit).
Sample_hyb_protocol	Following fragmentation, 5.5 ug of cRNA was hybridized to Affymetrix Mouse 430 2.0 GeneChips for 16 hours at 45 °C. GeneChips were washed and stained using a fluidics station.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.
Sample_data_processing	Data was acquired and normalized using Affymetrix Expression Console software under Affymetrix default analysis settings and global scaling as normalization method to generate Microarray Suite version 5.0 (MAS 5.0) files. Data is represented by presence/absence call for each gene using appropriate algorithms and expression data that had an “absent” call was filtered out of data sets using Excel software (Microsoft).
Sample_platform_id	GPL1261
Sample_contact_name	Timothy,Peter,Lopez
Sample_contact_email	tpetelopez@gmail.com
Sample_contact_laboratory	Chen-Ming Fan
Sample_contact_department	Biology
Sample_contact_institute	Johns Hopkins University/Carnegie Institution
Sample_contact_address	3520 San Martin Drive
Sample_contact_city	Baltimore
Sample_contact_state	Maryland
Sample_contact_zip/postal_code	21218
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1130nnn/GSM1130057/suppl/GSM1130057_Mutant__2.CEL.gz
Sample_series_id	GSE46426
Sample_data_row_count	19606

GSM1130058

GPL1261

R26R^AC/AC;T-Cre (Mutant), biological replicate #3

Mousemutant_PSM

strain background: C57BL6/6J genotype/variation: R26R^AC/AC;T-Cre (Mutant) developmental stage: E8.75 tissue: presomitic mesoderm (PSM)

Gene expression data from mutant PSM.

Sample_geo_accession	GSM1130058
Sample_status	Public on Apr 27 2013
Sample_submission_date	Apr 26 2013
Sample_last_update_date	Apr 27 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The anterior 2/3 PSM was dissected from the posterior 1/3 PSM and somites. Anterior PSM was briefly rinsed in 1X PBS (Gibco).
Sample_growth_protocol_ch1	Control and mutant embryos were harvested on Embronic day (E) 8.75 in L-15 media under a dissection light and fluorescent microscope setup.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	The anterior PSM was pipetted into lysis solution and underwent total RNA purification using the PicoPure RNA Isolation Kit (Life Technologies).
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA was prepared using the 3' IVT Express Kit (Affymetrix) for 1 ug total RNA according to the standard protocol for cRNA synthesis (GeneChip 3’ IVT Express Kit).
Sample_hyb_protocol	Following fragmentation, 5.5 ug of cRNA was hybridized to Affymetrix Mouse 430 2.0 GeneChips for 16 hours at 45 °C. GeneChips were washed and stained using a fluidics station.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000. The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.
Sample_data_processing	Data was acquired and normalized using Affymetrix Expression Console software under Affymetrix default analysis settings and global scaling as normalization method to generate Microarray Suite version 5.0 (MAS 5.0) files. Data is represented by presence/absence call for each gene using appropriate algorithms and expression data that had an “absent” call was filtered out of data sets using Excel software (Microsoft).
Sample_platform_id	GPL1261
Sample_contact_name	Timothy,Peter,Lopez
Sample_contact_email	tpetelopez@gmail.com
Sample_contact_laboratory	Chen-Ming Fan
Sample_contact_department	Biology
Sample_contact_institute	Johns Hopkins University/Carnegie Institution
Sample_contact_address	3520 San Martin Drive
Sample_contact_city	Baltimore
Sample_contact_state	Maryland
Sample_contact_zip/postal_code	21218
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1130nnn/GSM1130058/suppl/GSM1130058_Mutant__3.CEL.gz
Sample_series_id	GSE46426
Sample_data_row_count	19606

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