Result

Search results for the GEO ID: GSE15152

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM378553

GPL339

WT_9.5dpc_PSM_rep1

presomitic mesoderm 9.5 dpc

strain: c57bl/6 age: 9.5 days post coitum embryo tissue: presomitic mesoderm genotype: wild-type

Target labeling, hybridization and data analysis carried out at the Children's Hospital of Philadelphia, PA. Microarray data analysis carried out at the School of Life Sciences, Arizona State University, Tempe, AZ.

Sample_geo_accession	GSM378553
Sample_status	Public on Mar 11 2009
Sample_submission_date	Mar 08 2009
Sample_last_update_date	Mar 10 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_biomaterial_provider_ch1	Duncan Sparrow and Sally Dunwoodie, Victor Chang Cardiac Research Institute, Sydney, Australia
Sample_treatment_protocol_ch1	Embryos were collected at day 9.5 of gestation, and dissected from decidua in cold M2 medium (Nagy et al., 2003) containing 10% fetal calf serum. All remnants of the allantois were carefully removed from intact embryos, which were then cut at the boundary of the PSM and most recently-formed somite. The released tissue (“PSM level” containing tissue from all three germ layers) was placed in cold RNA lysis solution and frozen at -80°C for later RNA extraction.
Sample_growth_protocol_ch1	N/A
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from 9.5 dpc embryos using a SuperScript RT II Kit (Invitrogen) and subsequently used to synthesize double stranded cDNA.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA targets were prepared with a Bioarray HighYield RNA Transcript Labeling Kit (ENZO).
Sample_hyb_protocol	Targets were hybridized to the Affymetrix MOE430A array according to manufacturer’s protocol.
Sample_scan_protocol = Arrays were subsequently scanned using the following parameters: t = 0.015, a1 = 0.05, a2 = 0.065, median intensity value	150.
Sample_data_processing	CEL files were normalized by the Robust Multichip Average method in order to compare the levels of expression between different samples and minimize technical variation accompanying use of the Genespring GX 7.3.2 module (Agilent). CHP files were generated using MAS5.0.
Sample_platform_id	GPL339
Sample_contact_name	Kenro,,Kusumi
Sample_contact_email	kenro@asu.edu
Sample_contact_phone	480-727-8993
Sample_contact_fax	480-965-6899
Sample_contact_department	School of Life Sciences
Sample_contact_institute	Arizona State University
Sample_contact_address	PO Box 874501
Sample_contact_city	Tempe
Sample_contact_state	AZ
Sample_contact_zip/postal_code	85287
Sample_contact_country	USA
Sample_contact_web_link	sols.asu.edu/faculty/kkusumi.php
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378553/suppl/GSM378553.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378553/suppl/GSM378553.CHP.gz
Sample_series_id	GSE15152
Sample_series_id	GSE15178
Sample_data_row_count	22690

GSM378554

GPL339

WT_9.5dpc_PSM_rep2

presomitic mesoderm 9.5 dpc

strain: c57bl/6 age: 9.5 days post coitum embryo tissue: presomitic mesoderm genotype: wild-type

Sample_geo_accession	GSM378554
Sample_status	Public on Mar 11 2009
Sample_submission_date	Mar 08 2009
Sample_last_update_date	Mar 10 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_biomaterial_provider_ch1	Duncan Sparrow and Sally Dunwoodie, Victor Chang Cardiac Research Institute, Sydney, Australia
Sample_treatment_protocol_ch1	Embryos were collected at day 9.5 of gestation, and dissected from decidua in cold M2 medium (Nagy et al., 2003) containing 10% fetal calf serum. All remnants of the allantois were carefully removed from intact embryos, which were then cut at the boundary of the PSM and most recently-formed somite. The released tissue (“PSM level” containing tissue from all three germ layers) was placed in cold RNA lysis solution and frozen at -80°C for later RNA extraction.
Sample_growth_protocol_ch1	N/A
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from 9.5 dpc embryos using a SuperScript RT II Kit (Invitrogen) and subsequently used to synthesize double stranded cDNA.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA targets were prepared with a Bioarray HighYield RNA Transcript Labeling Kit (ENZO).
Sample_hyb_protocol	Targets were hybridized to the Affymetrix MOE430A array according to manufacturer’s protocol.
Sample_scan_protocol = Arrays were subsequently scanned using the following parameters: t = 0.015, a1 = 0.05, a2 = 0.065, median intensity value	150.
Sample_data_processing	CEL files were normalized by the Robust Multichip Average method in order to compare the levels of expression between different samples and minimize technical variation accompanying use of the Genespring GX 7.3.2 module (Agilent). CHP files were generated using MAS5.0.
Sample_platform_id	GPL339
Sample_contact_name	Kenro,,Kusumi
Sample_contact_email	kenro@asu.edu
Sample_contact_phone	480-727-8993
Sample_contact_fax	480-965-6899
Sample_contact_department	School of Life Sciences
Sample_contact_institute	Arizona State University
Sample_contact_address	PO Box 874501
Sample_contact_city	Tempe
Sample_contact_state	AZ
Sample_contact_zip/postal_code	85287
Sample_contact_country	USA
Sample_contact_web_link	sols.asu.edu/faculty/kkusumi.php
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378554/suppl/GSM378554.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378554/suppl/GSM378554.CHP.gz
Sample_series_id	GSE15152
Sample_series_id	GSE15178
Sample_data_row_count	22690

GSM378555

GPL339

WT_9.5dpc_PSM_rep3

presomitic mesoderm 9.5 dpc

strain: c57bl/6 age: 9.5 days post coitum embryo tissue: presomitic mesoderm genotype: wild-type

Sample_geo_accession	GSM378555
Sample_status	Public on Mar 11 2009
Sample_submission_date	Mar 08 2009
Sample_last_update_date	Mar 10 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_biomaterial_provider_ch1	Duncan Sparrow and Sally Dunwoodie, Victor Chang Cardiac Research Institute, Sydney, Australia
Sample_treatment_protocol_ch1	Embryos were collected at day 9.5 of gestation, and dissected from decidua in cold M2 medium (Nagy et al., 2003) containing 10% fetal calf serum. All remnants of the allantois were carefully removed from intact embryos, which were then cut at the boundary of the PSM and most recently-formed somite. The released tissue (“PSM level” containing tissue from all three germ layers) was placed in cold RNA lysis solution and frozen at -80°C for later RNA extraction.
Sample_growth_protocol_ch1	N/A
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from 9.5 dpc embryos using a SuperScript RT II Kit (Invitrogen) and subsequently used to synthesize double stranded cDNA.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA targets were prepared with a Bioarray HighYield RNA Transcript Labeling Kit (ENZO).
Sample_hyb_protocol	Targets were hybridized to the Affymetrix MOE430A array according to manufacturer’s protocol.
Sample_scan_protocol = Arrays were subsequently scanned using the following parameters: t = 0.015, a1 = 0.05, a2 = 0.065, median intensity value	150.
Sample_data_processing	CEL files were normalized by the Robust Multichip Average method in order to compare the levels of expression between different samples and minimize technical variation accompanying use of the Genespring GX 7.3.2 module (Agilent). CHP files were generated using MAS5.0.
Sample_platform_id	GPL339
Sample_contact_name	Kenro,,Kusumi
Sample_contact_email	kenro@asu.edu
Sample_contact_phone	480-727-8993
Sample_contact_fax	480-965-6899
Sample_contact_department	School of Life Sciences
Sample_contact_institute	Arizona State University
Sample_contact_address	PO Box 874501
Sample_contact_city	Tempe
Sample_contact_state	AZ
Sample_contact_zip/postal_code	85287
Sample_contact_country	USA
Sample_contact_web_link	sols.asu.edu/faculty/kkusumi.php
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378555/suppl/GSM378555.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378555/suppl/GSM378555.CHP.gz
Sample_series_id	GSE15152
Sample_series_id	GSE15178
Sample_data_row_count	22690

GSM378556

GPL339

Dll3tm1Rbe_9.5dpc_PSM_rep1

presomitic mesoderm 9.5 dpc

strain: c57bl/6-dll3-tm1rbe/tm1rbe age: 9.5 days post coitum embryo tissue: presomitic mesoderm genotype: Dll3-tm1Rbe/tm1Rbe or Dll3neo/neo

Sample_geo_accession	GSM378556
Sample_status	Public on Mar 11 2009
Sample_submission_date	Mar 08 2009
Sample_last_update_date	Mar 10 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_biomaterial_provider_ch1	Duncan Sparrow and Sally Dunwoodie, Victor Chang Cardiac Research Institute, Sydney, Australia
Sample_treatment_protocol_ch1	Embryos were collected at day 9.5 of gestation, and dissected from decidua in cold M2 medium (Nagy et al., 2003) containing 10% fetal calf serum. All remnants of the allantois were carefully removed from intact embryos, which were then cut at the boundary of the PSM and the area corresponding to the most recently-formed somite. The released tissue (“PSM level” containing tissue from all three germ layers) was placed in cold RNA lysis solution and frozen at -80°C for later RNA extraction.
Sample_growth_protocol_ch1	N/A
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from 9.5 dpc embryos using a SuperScript RT II Kit (Invitrogen) and subsequently used to synthesize double stranded cDNA.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA targets were prepared with a Bioarray HighYield RNA Transcript Labeling Kit (ENZO).
Sample_hyb_protocol	Targets were hybridized to the Affymetrix MOE430A array according to manufacturer’s protocol.
Sample_scan_protocol = Arrays were subsequently scanned using the following parameters: t = 0.015, a1 = 0.05, a2 = 0.065, median intensity value	150.
Sample_data_processing	CEL files were normalized by the Robust Multichip Average method in order to compare the levels of expression between different samples and minimize technical variation accompanying use of the Genespring GX 7.3.2 module (Agilent). CHP files were generated using MAS5.0.
Sample_platform_id	GPL339
Sample_contact_name	Kenro,,Kusumi
Sample_contact_email	kenro@asu.edu
Sample_contact_phone	480-727-8993
Sample_contact_fax	480-965-6899
Sample_contact_department	School of Life Sciences
Sample_contact_institute	Arizona State University
Sample_contact_address	PO Box 874501
Sample_contact_city	Tempe
Sample_contact_state	AZ
Sample_contact_zip/postal_code	85287
Sample_contact_country	USA
Sample_contact_web_link	sols.asu.edu/faculty/kkusumi.php
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378556/suppl/GSM378556.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378556/suppl/GSM378556.CHP.gz
Sample_series_id	GSE15152
Sample_series_id	GSE15178
Sample_data_row_count	22690

GSM378557

GPL339

Dll3tm1Rbe_9.5dpc_PSM_rep2

presomitic mesoderm 9.5 dpc

strain: c57bl/6-dll3tm1rbe/tm1rbe age: 9.5 days post coitum embryo tissue: presomitic mesoderm genotype: Dll3-tm1Rbe/tm1Rbe or Dll3neo/neo

Sample_geo_accession	GSM378557
Sample_status	Public on Mar 11 2009
Sample_submission_date	Mar 08 2009
Sample_last_update_date	Mar 10 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_biomaterial_provider_ch1	Duncan Sparrow and Sally Dunwoodie, Victor Chang Cardiac Research Institute, Sydney, Australia
Sample_treatment_protocol_ch1	Embryos were collected at day 9.5 of gestation, and dissected from decidua in cold M2 medium (Nagy et al., 2003) containing 10% fetal calf serum. All remnants of the allantois were carefully removed from intact embryos, which were then cut at the boundary of the PSM and the area corresponding to the most recently-formed somite. The released tissue (“PSM level” containing tissue from all three germ layers) was placed in cold RNA lysis solution and frozen at -80°C for later RNA extraction.
Sample_growth_protocol_ch1	N/A
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from 9.5 dpc embryos using a SuperScript RT II Kit (Invitrogen) and subsequently used to synthesize double stranded cDNA.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA targets were prepared with a Bioarray HighYield RNA Transcript Labeling Kit (ENZO).
Sample_hyb_protocol	Targets were hybridized to the Affymetrix MOE430A array according to manufacturer’s protocol.
Sample_scan_protocol = Arrays were subsequently scanned using the following parameters: t = 0.015, a1 = 0.05, a2 = 0.065, median intensity value	150.
Sample_data_processing	CEL files were normalized by the Robust Multichip Average method in order to compare the levels of expression between different samples and minimize technical variation accompanying use of the Genespring GX 7.3.2 module (Agilent). CHP files were generated using MAS5.0.
Sample_platform_id	GPL339
Sample_contact_name	Kenro,,Kusumi
Sample_contact_email	kenro@asu.edu
Sample_contact_phone	480-727-8993
Sample_contact_fax	480-965-6899
Sample_contact_department	School of Life Sciences
Sample_contact_institute	Arizona State University
Sample_contact_address	PO Box 874501
Sample_contact_city	Tempe
Sample_contact_state	AZ
Sample_contact_zip/postal_code	85287
Sample_contact_country	USA
Sample_contact_web_link	sols.asu.edu/faculty/kkusumi.php
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378557/suppl/GSM378557.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378557/suppl/GSM378557.CHP.gz
Sample_series_id	GSE15152
Sample_series_id	GSE15178
Sample_data_row_count	22690

GSM378558

GPL339

Dll3tm1Rbe_9.5dpc_PSM_rep3

presomitic mesoderm 9.5 dpc

strain: c57bl/6-dll3tm1rbe/tm1rbe age: 9.5 days post coitum embryo tissue: presomitic mesoderm genotype: Dll3-tm1Rbe/tm1Rbe or Dll3neo/neo

Sample_geo_accession	GSM378558
Sample_status	Public on Mar 11 2009
Sample_submission_date	Mar 08 2009
Sample_last_update_date	Mar 10 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_biomaterial_provider_ch1	Duncan Sparrow and Sally Dunwoodie, Victor Chang Cardiac Research Institute, Sydney, Australia
Sample_treatment_protocol_ch1	Embryos were collected at day 9.5 of gestation, and dissected from decidua in cold M2 medium (Nagy et al., 2003) containing 10% fetal calf serum. All remnants of the allantois were carefully removed from intact embryos, which were then cut at the boundary of the PSM and the area corresponding to the most recently-formed somite. The released tissue (“PSM level” containing tissue from all three germ layers) was placed in cold RNA lysis solution and frozen at -80°C for later RNA extraction.
Sample_growth_protocol_ch1	N/A
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted from 9.5 dpc embryos using a SuperScript RT II Kit (Invitrogen) and subsequently used to synthesize double stranded cDNA.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA targets were prepared with a Bioarray HighYield RNA Transcript Labeling Kit (ENZO).
Sample_hyb_protocol	Targets were hybridized to the Affymetrix MOE430A array according to manufacturer’s protocol.
Sample_scan_protocol = Arrays were subsequently scanned using the following parameters: t = 0.015, a1 = 0.05, a2 = 0.065, median intensity value	150.
Sample_data_processing	CEL files were normalized by the Robust Multichip Average method in order to compare the levels of expression between different samples and minimize technical variation accompanying use of the Genespring GX 7.3.2 module (Agilent). CHP files were generated using MAS5.0.
Sample_platform_id	GPL339
Sample_contact_name	Kenro,,Kusumi
Sample_contact_email	kenro@asu.edu
Sample_contact_phone	480-727-8993
Sample_contact_fax	480-965-6899
Sample_contact_department	School of Life Sciences
Sample_contact_institute	Arizona State University
Sample_contact_address	PO Box 874501
Sample_contact_city	Tempe
Sample_contact_state	AZ
Sample_contact_zip/postal_code	85287
Sample_contact_country	USA
Sample_contact_web_link	sols.asu.edu/faculty/kkusumi.php
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378558/suppl/GSM378558.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378558/suppl/GSM378558.CHP.gz
Sample_series_id	GSE15152
Sample_series_id	GSE15178
Sample_data_row_count	22690

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