Result

Search results for the GEO ID: GSE11114

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Title

Source name

Description

Characteristics

GSM280478

GPL339

Adult female murine masseter muscle #1

adult superficial masseter

control tissue from C57Bl/6 mouse

Profiling measurements were completed at the Penn Microarray Core Facility utilizing Affymetrix Mouse 430 2A chips. All protocols were conducted as described in the Affymetrix GeneChip Expression Analysis Technical Manual.

Sample_geo_accession	GSM280478
Sample_status	Public on May 09 2008
Sample_submission_date	Apr 09 2008
Sample_last_update_date	Apr 10 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	Total RNA was isolated from the frozen muscle samples (Trizol, Invitrogen, Carlsbad, CA), and further purified using RNeasy columns (Qiagen, Valencia, CA). RNA integrity was confirmed by gel electrophoresis
Sample_label_ch1	streptavidin-phycoerythrin
Sample_label_protocol_ch1	Total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated UTP. The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to microarray. The microarray was 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. A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.
Sample_hyb_protocol	see above protocol
Sample_scan_protocol	A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.
Sample_data_processing = The Affymetrix Microarray Suite 5.0 algorithm in GeneChip® Operating Software (GCOS) 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. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau	0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated using the One-step Tukey's Biweight Estimate. This Signal value, a relative measure of the expression level, was computed for each assayed gene. 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	GPL339
Sample_contact_name	Elisabeth,R,Barton
Sample_contact_email	erbarton@biochem.dental.upenn.edu
Sample_contact_department	Anatomy and Cell Biology
Sample_contact_institute	University of Pennsylvania Dental School
Sample_contact_address	240 S. 40th Street
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/GSM280nnn/GSM280478/suppl/GSM280478.CEL.gz
Sample_series_id	GSE11114
Sample_data_row_count	22690

GSM280479

GPL339

Adult female murine masseter muscle #2

adult superficial masseter

control tissue from C57Bl/6 mouse

Sample_geo_accession	GSM280479
Sample_status	Public on May 09 2008
Sample_submission_date	Apr 09 2008
Sample_last_update_date	Apr 10 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	Total RNA was isolated from the frozen muscle samples (Trizol, Invitrogen, Carlsbad, CA), and further purified using RNeasy columns (Qiagen, Valencia, CA). RNA integrity was confirmed by gel electrophoresis
Sample_label_ch1	streptavidin-phycoerythrin
Sample_label_protocol_ch1	Total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated UTP. The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to microarray. The microarray was 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. A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.
Sample_hyb_protocol	see above protocol
Sample_scan_protocol	A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.
Sample_data_processing = The Affymetrix Microarray Suite 5.0 algorithm in GeneChip® Operating Software (GCOS) 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. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau	0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated using the One-step Tukey's Biweight Estimate. This Signal value, a relative measure of the expression level, was computed for each assayed gene. 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	GPL339
Sample_contact_name	Elisabeth,R,Barton
Sample_contact_email	erbarton@biochem.dental.upenn.edu
Sample_contact_department	Anatomy and Cell Biology
Sample_contact_institute	University of Pennsylvania Dental School
Sample_contact_address	240 S. 40th Street
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/GSM280nnn/GSM280479/suppl/GSM280479.CEL.gz
Sample_series_id	GSE11114
Sample_data_row_count	22690

GSM280480

GPL339

Adult female murine masseter muscle #3

adult superficial masseter

control tissue from C57Bl/6 mouse

Sample_geo_accession	GSM280480
Sample_status	Public on May 09 2008
Sample_submission_date	Apr 09 2008
Sample_last_update_date	Apr 10 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	Total RNA was isolated from the frozen muscle samples (Trizol, Invitrogen, Carlsbad, CA), and further purified using RNeasy columns (Qiagen, Valencia, CA). RNA integrity was confirmed by gel electrophoresis
Sample_label_ch1	streptavidin-phycoerythrin
Sample_label_protocol_ch1	Total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated UTP. The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to microarray. The microarray was 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. A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.
Sample_hyb_protocol	see above protocol
Sample_scan_protocol	A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.
Sample_data_processing = The Affymetrix Microarray Suite 5.0 algorithm in GeneChip® Operating Software (GCOS) 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. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau	0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated using the One-step Tukey's Biweight Estimate. This Signal value, a relative measure of the expression level, was computed for each assayed gene. 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	GPL339
Sample_contact_name	Elisabeth,R,Barton
Sample_contact_email	erbarton@biochem.dental.upenn.edu
Sample_contact_department	Anatomy and Cell Biology
Sample_contact_institute	University of Pennsylvania Dental School
Sample_contact_address	240 S. 40th Street
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/GSM280nnn/GSM280480/suppl/GSM280480.CEL.gz
Sample_series_id	GSE11114
Sample_data_row_count	22690

GSM280481

GPL339

Adult female murine tibialis anterior muscle #1

adult tibialis anterior

control tissue from C57Bl/6 mouse

Sample_geo_accession	GSM280481
Sample_status	Public on May 09 2008
Sample_submission_date	Apr 09 2008
Sample_last_update_date	Apr 10 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	Total RNA was isolated from the frozen muscle samples (Trizol, Invitrogen, Carlsbad, CA), and further purified using RNeasy columns (Qiagen, Valencia, CA). RNA integrity was confirmed by gel electrophoresis
Sample_label_ch1	streptavidin-phycoerythrin
Sample_label_protocol_ch1	Total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated UTP. The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to microarray. The microarray was 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. A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.
Sample_hyb_protocol	see above protocol
Sample_scan_protocol	A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.
Sample_data_processing = The Affymetrix Microarray Suite 5.0 algorithm in GeneChip® Operating Software (GCOS) 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. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau	0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated using the One-step Tukey's Biweight Estimate. This Signal value, a relative measure of the expression level, was computed for each assayed gene. 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	GPL339
Sample_contact_name	Elisabeth,R,Barton
Sample_contact_email	erbarton@biochem.dental.upenn.edu
Sample_contact_department	Anatomy and Cell Biology
Sample_contact_institute	University of Pennsylvania Dental School
Sample_contact_address	240 S. 40th Street
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/GSM280nnn/GSM280481/suppl/GSM280481.CEL.gz
Sample_series_id	GSE11114
Sample_data_row_count	22690

GSM280483

GPL339

Adult female murine tibialis anterior muscle #2

adult tibialis anterior

control tissue from C57Bl/6 mouse

Sample_geo_accession	GSM280483
Sample_status	Public on May 09 2008
Sample_submission_date	Apr 09 2008
Sample_last_update_date	Apr 10 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	Total RNA was isolated from the frozen muscle samples (Trizol, Invitrogen, Carlsbad, CA), and further purified using RNeasy columns (Qiagen, Valencia, CA). RNA integrity was confirmed by gel electrophoresis
Sample_label_ch1	streptavidin-phycoerythrin
Sample_label_protocol_ch1	Total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated UTP. The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to microarray. The microarray was 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. A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.
Sample_hyb_protocol	see above protocol
Sample_scan_protocol	A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.
Sample_data_processing = The Affymetrix Microarray Suite 5.0 algorithm in GeneChip® Operating Software (GCOS) 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. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau	0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated using the One-step Tukey's Biweight Estimate. This Signal value, a relative measure of the expression level, was computed for each assayed gene. 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	GPL339
Sample_contact_name	Elisabeth,R,Barton
Sample_contact_email	erbarton@biochem.dental.upenn.edu
Sample_contact_department	Anatomy and Cell Biology
Sample_contact_institute	University of Pennsylvania Dental School
Sample_contact_address	240 S. 40th Street
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/GSM280nnn/GSM280483/suppl/GSM280483.CEL.gz
Sample_series_id	GSE11114
Sample_data_row_count	22690

GSM280484

GPL339

Adult female murine tibialis anterior muscle #3

adult tibialis anterior

control tissue from C57Bl/6 mouse

Sample_geo_accession	GSM280484
Sample_status	Public on May 09 2008
Sample_submission_date	Apr 09 2008
Sample_last_update_date	Apr 10 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	Total RNA was isolated from the frozen muscle samples (Trizol, Invitrogen, Carlsbad, CA), and further purified using RNeasy columns (Qiagen, Valencia, CA). RNA integrity was confirmed by gel electrophoresis
Sample_label_ch1	streptavidin-phycoerythrin
Sample_label_protocol_ch1	Total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated UTP. The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to microarray. The microarray was 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. A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.
Sample_hyb_protocol	see above protocol
Sample_scan_protocol	A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.
Sample_data_processing = The Affymetrix Microarray Suite 5.0 algorithm in GeneChip® Operating Software (GCOS) 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. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features. The number of probe pairs meeting the default discrimination threshold (tau	0.015) was used to assign a call of absent, present or marginal for each assayed gene, and a p-value was calculated to reflect confidence in the detection call. A weighted mean of probe fluorescence (corrected for nonspecific signal by subtracting the mismatch probe value) was calculated using the One-step Tukey's Biweight Estimate. This Signal value, a relative measure of the expression level, was computed for each assayed gene. 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	GPL339
Sample_contact_name	Elisabeth,R,Barton
Sample_contact_email	erbarton@biochem.dental.upenn.edu
Sample_contact_department	Anatomy and Cell Biology
Sample_contact_institute	University of Pennsylvania Dental School
Sample_contact_address	240 S. 40th Street
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/GSM280nnn/GSM280484/suppl/GSM280484.CEL.gz
Sample_series_id	GSE11114
Sample_data_row_count	22690

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