Result

Search results for the GEO ID: GSE11400

(Click on the check boxes provided under "Select for analysis", to initiate grouping)

(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down)

GSM ID

GPL ID

Select for analysis

Title

Source name

Description

Characteristics

GSM287781

GPL1261

R26Pax3/Pax3 E14.5 palatal shelves 1

Mouse palatal shelf tissue at E14.5

Strain: C57BL/6 X SV129, Age: Embryonic Day 14.5, Tissue: Palatal Shelves

Gene expression data during developmental stage of palatal shelves at E14.5

Sample_geo_accession	GSM287781
Sample_status	Public on Jun 01 2008
Sample_submission_date	May 09 2008
Sample_last_update_date	May 09 2008
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 protocol.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the The Affymetrix GeneChip Scanner 3000.
Sample_data_processing	Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.
Sample_platform_id	GPL1261
Sample_contact_name	Jonathan ,A.,Epstein
Sample_contact_email	epsteinj@mail.med.upenn.edu
Sample_contact_laboratory	Jonathan Epstein
Sample_contact_department	Cell and Developmental Biology
Sample_contact_institute	University of Pennsylvania
Sample_contact_address	421 Curie Blvd
Sample_contact_city	Philadelphia
Sample_contact_state	PA
Sample_contact_zip/postal_code	19104
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287781/suppl/GSM287781.CEL.gz
Sample_series_id	GSE11400
Sample_data_row_count	45101

GSM287782

GPL1261

R26Pax3/Pax3 E14.5 palatal shelves 3

Mouse palatal shelf tissue at E14.5

Strain: C57BL/6 X SV129, Age: Embryonic Day 14.5, Tissue: Palatal Shelves

Gene expression data during developmental stage of palatal shelves at E14.5

Sample_geo_accession	GSM287782
Sample_status	Public on Jun 01 2008
Sample_submission_date	May 09 2008
Sample_last_update_date	May 09 2008
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 protocol.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the The Affymetrix GeneChip Scanner 3000.
Sample_data_processing	Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.
Sample_platform_id	GPL1261
Sample_contact_name	Jonathan ,A.,Epstein
Sample_contact_email	epsteinj@mail.med.upenn.edu
Sample_contact_laboratory	Jonathan Epstein
Sample_contact_department	Cell and Developmental Biology
Sample_contact_institute	University of Pennsylvania
Sample_contact_address	421 Curie Blvd
Sample_contact_city	Philadelphia
Sample_contact_state	PA
Sample_contact_zip/postal_code	19104
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287782/suppl/GSM287782.CEL.gz
Sample_series_id	GSE11400
Sample_data_row_count	45101

GSM287783

GPL1261

Pax3 WT E14.5 palatal shelves 6

Mouse wt palatal shelf tissue at E14.5

Strain: C57BL/6 X SV129, Age: Embryonic Day 14.5, Tissue: Palatal Shelves

Gene expression data during developmental stage of palatal shelves at E14.5

Sample_geo_accession	GSM287783
Sample_status	Public on Jun 01 2008
Sample_submission_date	May 09 2008
Sample_last_update_date	May 09 2008
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 protocol.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the The Affymetrix GeneChip Scanner 3000.
Sample_data_processing	Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.
Sample_platform_id	GPL1261
Sample_contact_name	Jonathan ,A.,Epstein
Sample_contact_email	epsteinj@mail.med.upenn.edu
Sample_contact_laboratory	Jonathan Epstein
Sample_contact_department	Cell and Developmental Biology
Sample_contact_institute	University of Pennsylvania
Sample_contact_address	421 Curie Blvd
Sample_contact_city	Philadelphia
Sample_contact_state	PA
Sample_contact_zip/postal_code	19104
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287783/suppl/GSM287783.CEL.gz
Sample_series_id	GSE11400
Sample_data_row_count	45101

GSM287784

GPL1261

Pax3 WT E14.5 palatal shelves 8

Mouse wt palatal shelf tissue at E14.5

Strain: C57BL/6 X SV129, Age: Embryonic Day 14.5, Tissue: Palatal Shelves

Gene expression data during developmental stage of palatal shelves at E14.5

Sample_geo_accession	GSM287784
Sample_status	Public on Jun 01 2008
Sample_submission_date	May 09 2008
Sample_last_update_date	May 09 2008
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 protocol.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the The Affymetrix GeneChip Scanner 3000.
Sample_data_processing	Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.
Sample_platform_id	GPL1261
Sample_contact_name	Jonathan ,A.,Epstein
Sample_contact_email	epsteinj@mail.med.upenn.edu
Sample_contact_laboratory	Jonathan Epstein
Sample_contact_department	Cell and Developmental Biology
Sample_contact_institute	University of Pennsylvania
Sample_contact_address	421 Curie Blvd
Sample_contact_city	Philadelphia
Sample_contact_state	PA
Sample_contact_zip/postal_code	19104
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287784/suppl/GSM287784.CEL.gz
Sample_series_id	GSE11400
Sample_data_row_count	45101

GSM287785

GPL1261

R26Pax3/Pax3 E14.5 palatal shelves 4

Mouse palatal shelf tissue at E14.5

Strain: C57BL/6 X SV129, Age: Embryonic Day 14.5, Tissue: Palatal Shelves

Gene expression data during developmental stage of palatal shelves at E14.5

Sample_geo_accession	GSM287785
Sample_status	Public on Jun 01 2008
Sample_submission_date	May 09 2008
Sample_last_update_date	May 09 2008
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 protocol.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the The Affymetrix GeneChip Scanner 3000.
Sample_data_processing	Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.
Sample_platform_id	GPL1261
Sample_contact_name	Jonathan ,A.,Epstein
Sample_contact_email	epsteinj@mail.med.upenn.edu
Sample_contact_laboratory	Jonathan Epstein
Sample_contact_department	Cell and Developmental Biology
Sample_contact_institute	University of Pennsylvania
Sample_contact_address	421 Curie Blvd
Sample_contact_city	Philadelphia
Sample_contact_state	PA
Sample_contact_zip/postal_code	19104
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287785/suppl/GSM287785.CEL.gz
Sample_series_id	GSE11400
Sample_data_row_count	45101

GSM287786

GPL1261

R26Pax3/Pax3 E14.5 palatal shelves 7

Mouse palatal shelf tissue at E14.5

Strain: C57BL/6 X SV129, Age: Embryonic Day 14.5, Tissue: Palatal Shelves

Gene expression data during developmental stage of palatal shelves at E14.5

Sample_geo_accession	GSM287786
Sample_status	Public on Jun 01 2008
Sample_submission_date	May 09 2008
Sample_last_update_date	May 09 2008
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 protocol.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the The Affymetrix GeneChip Scanner 3000.
Sample_data_processing	Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.
Sample_platform_id	GPL1261
Sample_contact_name	Jonathan ,A.,Epstein
Sample_contact_email	epsteinj@mail.med.upenn.edu
Sample_contact_laboratory	Jonathan Epstein
Sample_contact_department	Cell and Developmental Biology
Sample_contact_institute	University of Pennsylvania
Sample_contact_address	421 Curie Blvd
Sample_contact_city	Philadelphia
Sample_contact_state	PA
Sample_contact_zip/postal_code	19104
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287786/suppl/GSM287786.CEL.gz
Sample_series_id	GSE11400
Sample_data_row_count	45101

GSM287787

GPL1261

Pax3 WT E14.5 palatal shelves 2

Mouse wt palatal shelf tissue at E14.5

Strain: C57BL/6 X SV129, Age: Embryonic Day 14.5, Tissue: Palatal Shelves

Gene expression data during developmental stage of palatal shelves at E14.5

Sample_geo_accession	GSM287787
Sample_status	Public on Jun 01 2008
Sample_submission_date	May 09 2008
Sample_last_update_date	May 09 2008
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 protocol.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the The Affymetrix GeneChip Scanner 3000.
Sample_data_processing	Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.
Sample_platform_id	GPL1261
Sample_contact_name	Jonathan ,A.,Epstein
Sample_contact_email	epsteinj@mail.med.upenn.edu
Sample_contact_laboratory	Jonathan Epstein
Sample_contact_department	Cell and Developmental Biology
Sample_contact_institute	University of Pennsylvania
Sample_contact_address	421 Curie Blvd
Sample_contact_city	Philadelphia
Sample_contact_state	PA
Sample_contact_zip/postal_code	19104
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287787/suppl/GSM287787.CEL.gz
Sample_series_id	GSE11400
Sample_data_row_count	45101

GSM287788

GPL1261

Pax3 WT E14.5 palatal shelves 11

Mouse wt palatal shelf tissue at E14.5

Strain: C57BL/6 X SV129, Age: Embryonic Day 14.5, Tissue: Palatal Shelves

Gene expression data during developmental stage of palatal shelves at E14.5

Sample_geo_accession	GSM287788
Sample_status	Public on Jun 01 2008
Sample_submission_date	May 09 2008
Sample_last_update_date	May 09 2008
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 protocol.
Sample_label_ch1	Biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the The Affymetrix GeneChip Scanner 3000.
Sample_data_processing	Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Global scaling was applied to allow comparison of gene Signals across multiple microarrays: after exclusion of the highest and lowest 2%, the average total chip Signal was calculated and used to determine what scaling factor was required to adjust the chip average to an arbitrary target of 150. All Signal values from one microarray were then multiplied by the appropriate scaling factor.
Sample_platform_id	GPL1261
Sample_contact_name	Jonathan ,A.,Epstein
Sample_contact_email	epsteinj@mail.med.upenn.edu
Sample_contact_laboratory	Jonathan Epstein
Sample_contact_department	Cell and Developmental Biology
Sample_contact_institute	University of Pennsylvania
Sample_contact_address	421 Curie Blvd
Sample_contact_city	Philadelphia
Sample_contact_state	PA
Sample_contact_zip/postal_code	19104
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM287nnn/GSM287788/suppl/GSM287788.CEL.gz
Sample_series_id	GSE11400
Sample_data_row_count	45101

Make groups for comparisons

(2 groups will be compared at a time)

Select GSMs and click on "Add groups"

Enter the group name here:

Select expression type

Transcripts profile based on;

A. Differential status (Up/Down regulation)

B. Absolute calls (Transcribed/Not-detected)

Filter results by number of probes