Result

Search results for the GEO ID: GSE14485

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GPL ID

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Title

Source name

Description

Characteristics

GSM361871

GPL339

MammaryTissue-24h-Saline-BiologicalRep1

Mouse left mammary gland tissue at 24hr post saline injection

Strain: Balb/cJ, Gender: female, Parturition: first, Age: 5th to 8th day after pups delivery, Tissue: left-side mammary gland, Treatment: Saline injected, Time post-injection: 24hr

gene expression data in mammary tissue sampled at 24 hr post saline injection

Sample_geo_accession	GSM361871
Sample_status	Public on Jun 30 2011
Sample_submission_date	Jan 21 2009
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The tissue samples were stored in RNA Later (Ambion, Austin, TX).
Sample_growth_protocol_ch1	The saline and E. coli challenged mammary glands were excised aseptically after at 24 and 48 hr post-injection.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	total RNA was isolated using Lipid Tissue Midi Kit following the manufacturer's instructions (Qiagen, Valencia, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The target (biotin labeled cRNA) was prepared and fragmented in accordance with instructions in the GeneChip® Mouse Expression Set 430A expression analysis technical manual (Affymetrix, Santa Clara, CA).
Sample_hyb_protocol	The fragmented cRNA target was hybridized to the probe array (GeneChip® Mouse Expression Set 430A) in the Microarray Core Facility at Pennsylvania State University (University Park, PA). One tissue sample or population of mRNAs was hybridized to one GeneChip® array using the Affymetrix System (Affymetrix, Santa Clara, CA) and a Microfluidcs Agilent System (Agilent Technologies, Santa Clara, CA).
Sample_scan_protocol	according to Affymetrix protocol
Sample_data_processing	For the pre-processing of the raw gene expression data, we wrote an R script using functions from the R package version 2.7.0 (Gentleman et al., 2004). We performed a data background correction using the robust multichip average (RMA) procedure suggested by Irizarry et al. (2005). Briefly, this procedure included a log2 transformation of the perfect match signal expression, quantile data normalization and a median Polish summary method. After running these functions in the raw expression data, we obtained an expression “score” for each of the 22,690 gene entries.
Sample_platform_id	GPL339
Sample_contact_name	Roger,Luis,Vallejo
Sample_contact_email	roger.vallejo@ars.usda.gov
Sample_contact_phone	304-724-8340
Sample_contact_department	NCCCWA
Sample_contact_institute	USDA-ARS
Sample_contact_address	11861 Leetown Rd.
Sample_contact_city	Kearneysville
Sample_contact_state	WV
Sample_contact_zip/postal_code	25430
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361871/suppl/GSM361871.CEL.gz
Sample_series_id	GSE14485
Sample_data_row_count	22690

GSM361872

GPL339

MammaryTissue-24h-Ecoli-BiologicalRep1

Mouse right mammary gland tissue at 24hr post Ecoli injection

Strain: Balb/cJ, Gender: female, Parturition: first, Age: 5th to 8th day after pups delivery, Tissue: right-side mammary gland, Treatment: Ecoli injected, Time post-injection: 24hr

gene expression data in mammary tissue sampled at 24 hr post Ecoli injection

Sample_geo_accession	GSM361872
Sample_status	Public on Jun 30 2011
Sample_submission_date	Jan 21 2009
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The tissue samples were stored in RNA Later (Ambion, Austin, TX).
Sample_growth_protocol_ch1	The saline and E. coli challenged mammary glands were excised aseptically after at 24 and 48 hr post-injection.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	total RNA was isolated using Lipid Tissue Midi Kit following the manufacturer's instructions (Qiagen, Valencia, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The target (biotin labeled cRNA) was prepared and fragmented in accordance with instructions in the GeneChip® Mouse Expression Set 430A expression analysis technical manual (Affymetrix, Santa Clara, CA).
Sample_hyb_protocol	The fragmented cRNA target was hybridized to the probe array (GeneChip® Mouse Expression Set 430A) in the Microarray Core Facility at Pennsylvania State University (University Park, PA). One tissue sample or population of mRNAs was hybridized to one GeneChip® array using the Affymetrix System (Affymetrix, Santa Clara, CA) and a Microfluidcs Agilent System (Agilent Technologies, Santa Clara, CA).
Sample_scan_protocol	according to Affymetrix protocol
Sample_data_processing	For the pre-processing of the raw gene expression data, we wrote an R script using functions from the R package version 2.7.0 (Gentleman et al., 2004). We performed a data background correction using the robust multichip average (RMA) procedure suggested by Irizarry et al. (2005). Briefly, this procedure included a log2 transformation of the perfect match signal expression, quantile data normalization and a median Polish summary method. After running these functions in the raw expression data, we obtained an expression “score” for each of the 22,690 gene entries.
Sample_platform_id	GPL339
Sample_contact_name	Roger,Luis,Vallejo
Sample_contact_email	roger.vallejo@ars.usda.gov
Sample_contact_phone	304-724-8340
Sample_contact_department	NCCCWA
Sample_contact_institute	USDA-ARS
Sample_contact_address	11861 Leetown Rd.
Sample_contact_city	Kearneysville
Sample_contact_state	WV
Sample_contact_zip/postal_code	25430
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361872/suppl/GSM361872.CEL.gz
Sample_series_id	GSE14485
Sample_data_row_count	22690

GSM361873

GPL339

MammaryTissue-24h-Saline-BiologicalRep2

Mouse left mammary gland tissue at 24hr post saline injection

Strain: Balb/cJ, Gender: female, Parturition: first, Age: 5th to 8th day after pups delivery, Tissue: left-side mammary gland, Treatment: Saline injected, Time post-injection: 24hr

gene expression data in mammary tissue sampled at 24 hr post saline injection

Sample_geo_accession	GSM361873
Sample_status	Public on Jun 30 2011
Sample_submission_date	Jan 21 2009
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The tissue samples were stored in RNA Later (Ambion, Austin, TX).
Sample_growth_protocol_ch1	The saline and E. coli challenged mammary glands were excised aseptically after at 24 and 48 hr post-injection.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	total RNA was isolated using Lipid Tissue Midi Kit following the manufacturer's instructions (Qiagen, Valencia, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The target (biotin labeled cRNA) was prepared and fragmented in accordance with instructions in the GeneChip® Mouse Expression Set 430A expression analysis technical manual (Affymetrix, Santa Clara, CA).
Sample_hyb_protocol	The fragmented cRNA target was hybridized to the probe array (GeneChip® Mouse Expression Set 430A) in the Microarray Core Facility at Pennsylvania State University (University Park, PA). One tissue sample or population of mRNAs was hybridized to one GeneChip® array using the Affymetrix System (Affymetrix, Santa Clara, CA) and a Microfluidcs Agilent System (Agilent Technologies, Santa Clara, CA).
Sample_scan_protocol	according to Affymetrix protocol
Sample_data_processing	For the pre-processing of the raw gene expression data, we wrote an R script using functions from the R package version 2.7.0 (Gentleman et al., 2004). We performed a data background correction using the robust multichip average (RMA) procedure suggested by Irizarry et al. (2005). Briefly, this procedure included a log2 transformation of the perfect match signal expression, quantile data normalization and a median Polish summary method. After running these functions in the raw expression data, we obtained an expression “score” for each of the 22,690 gene entries.
Sample_platform_id	GPL339
Sample_contact_name	Roger,Luis,Vallejo
Sample_contact_email	roger.vallejo@ars.usda.gov
Sample_contact_phone	304-724-8340
Sample_contact_department	NCCCWA
Sample_contact_institute	USDA-ARS
Sample_contact_address	11861 Leetown Rd.
Sample_contact_city	Kearneysville
Sample_contact_state	WV
Sample_contact_zip/postal_code	25430
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361873/suppl/GSM361873.CEL.gz
Sample_series_id	GSE14485
Sample_data_row_count	22690

GSM361874

GPL339

MammaryTissue-24h-Ecoli-BiologicalRep2

Mouse right mammary gland tissue at 24hr post Ecoli injection

Strain: Balb/cJ, Gender: female, Parturition: first, Age: 5th to 8th day after pups delivery, Tissue: right-side mammary gland, Treatment: Ecoli injected, Time post-injection: 24hr

gene expression data in mammary tissue sampled at 24 hr post Ecoli injection

Sample_geo_accession	GSM361874
Sample_status	Public on Jun 30 2011
Sample_submission_date	Jan 21 2009
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The tissue samples were stored in RNA Later (Ambion, Austin, TX).
Sample_growth_protocol_ch1	The saline and E. coli challenged mammary glands were excised aseptically after at 24 and 48 hr post-injection.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	total RNA was isolated using Lipid Tissue Midi Kit following the manufacturer's instructions (Qiagen, Valencia, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The target (biotin labeled cRNA) was prepared and fragmented in accordance with instructions in the GeneChip® Mouse Expression Set 430A expression analysis technical manual (Affymetrix, Santa Clara, CA).
Sample_hyb_protocol	The fragmented cRNA target was hybridized to the probe array (GeneChip® Mouse Expression Set 430A) in the Microarray Core Facility at Pennsylvania State University (University Park, PA). One tissue sample or population of mRNAs was hybridized to one GeneChip® array using the Affymetrix System (Affymetrix, Santa Clara, CA) and a Microfluidcs Agilent System (Agilent Technologies, Santa Clara, CA).
Sample_scan_protocol	according to Affymetrix protocol
Sample_data_processing	For the pre-processing of the raw gene expression data, we wrote an R script using functions from the R package version 2.7.0 (Gentleman et al., 2004). We performed a data background correction using the robust multichip average (RMA) procedure suggested by Irizarry et al. (2005). Briefly, this procedure included a log2 transformation of the perfect match signal expression, quantile data normalization and a median Polish summary method. After running these functions in the raw expression data, we obtained an expression “score” for each of the 22,690 gene entries.
Sample_platform_id	GPL339
Sample_contact_name	Roger,Luis,Vallejo
Sample_contact_email	roger.vallejo@ars.usda.gov
Sample_contact_phone	304-724-8340
Sample_contact_department	NCCCWA
Sample_contact_institute	USDA-ARS
Sample_contact_address	11861 Leetown Rd.
Sample_contact_city	Kearneysville
Sample_contact_state	WV
Sample_contact_zip/postal_code	25430
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361874/suppl/GSM361874.CEL.gz
Sample_series_id	GSE14485
Sample_data_row_count	22690

GSM361875

GPL339

MammaryTissue-48h-Saline-BiologicalRep1

Mouse left mammary gland tissue at 48hr post saline injection

Strain: Balb/cJ, Gender: female, Parturition: first, Age: 5th to 8th day after pups delivery, Tissue: left-side mammary gland, Treatment: Saline injected, Time post-injection: 48hr

gene expression data in mammary tissue sampled at 48 hr post saline injection

Sample_geo_accession	GSM361875
Sample_status	Public on Jun 30 2011
Sample_submission_date	Jan 21 2009
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The tissue samples were stored in RNA Later (Ambion, Austin, TX).
Sample_growth_protocol_ch1	The saline and E. coli challenged mammary glands were excised aseptically after at 24 and 48 hr post-injection.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	total RNA was isolated using Lipid Tissue Midi Kit following the manufacturer's instructions (Qiagen, Valencia, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The target (biotin labeled cRNA) was prepared and fragmented in accordance with instructions in the GeneChip® Mouse Expression Set 430A expression analysis technical manual (Affymetrix, Santa Clara, CA).
Sample_hyb_protocol	The fragmented cRNA target was hybridized to the probe array (GeneChip® Mouse Expression Set 430A) in the Microarray Core Facility at Pennsylvania State University (University Park, PA). One tissue sample or population of mRNAs was hybridized to one GeneChip® array using the Affymetrix System (Affymetrix, Santa Clara, CA) and a Microfluidcs Agilent System (Agilent Technologies, Santa Clara, CA).
Sample_scan_protocol	according to Affymetrix protocol
Sample_data_processing	For the pre-processing of the raw gene expression data, we wrote an R script using functions from the R package version 2.7.0 (Gentleman et al., 2004). We performed a data background correction using the robust multichip average (RMA) procedure suggested by Irizarry et al. (2005). Briefly, this procedure included a log2 transformation of the perfect match signal expression, quantile data normalization and a median Polish summary method. After running these functions in the raw expression data, we obtained an expression “score” for each of the 22,690 gene entries.
Sample_platform_id	GPL339
Sample_contact_name	Roger,Luis,Vallejo
Sample_contact_email	roger.vallejo@ars.usda.gov
Sample_contact_phone	304-724-8340
Sample_contact_department	NCCCWA
Sample_contact_institute	USDA-ARS
Sample_contact_address	11861 Leetown Rd.
Sample_contact_city	Kearneysville
Sample_contact_state	WV
Sample_contact_zip/postal_code	25430
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361875/suppl/GSM361875.CEL.gz
Sample_series_id	GSE14485
Sample_data_row_count	22690

GSM361876

GPL339

MammaryTissue-48h-Ecoli-BiologicalRep1

Mouse right mammary gland tissue at 48hr post Ecoli injection

Strain: Balb/cJ, Gender: female, Parturition: first, Age: 5th to 8th day after pups delivery, Tissue: right-side mammary gland, Treatment: Ecoli injected, Time post-injection: 48hr

gene expression data in mammary tissue sampled at 48 hr post Ecoli injection

Sample_geo_accession	GSM361876
Sample_status	Public on Jun 30 2011
Sample_submission_date	Jan 21 2009
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The tissue samples were stored in RNA Later (Ambion, Austin, TX).
Sample_growth_protocol_ch1	The saline and E. coli challenged mammary glands were excised aseptically after at 24 and 48 hr post-injection.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	total RNA was isolated using Lipid Tissue Midi Kit following the manufacturer's instructions (Qiagen, Valencia, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The target (biotin labeled cRNA) was prepared and fragmented in accordance with instructions in the GeneChip® Mouse Expression Set 430A expression analysis technical manual (Affymetrix, Santa Clara, CA).
Sample_hyb_protocol	The fragmented cRNA target was hybridized to the probe array (GeneChip® Mouse Expression Set 430A) in the Microarray Core Facility at Pennsylvania State University (University Park, PA). One tissue sample or population of mRNAs was hybridized to one GeneChip® array using the Affymetrix System (Affymetrix, Santa Clara, CA) and a Microfluidcs Agilent System (Agilent Technologies, Santa Clara, CA).
Sample_scan_protocol	according to Affymetrix protocol
Sample_data_processing	For the pre-processing of the raw gene expression data, we wrote an R script using functions from the R package version 2.7.0 (Gentleman et al., 2004). We performed a data background correction using the robust multichip average (RMA) procedure suggested by Irizarry et al. (2005). Briefly, this procedure included a log2 transformation of the perfect match signal expression, quantile data normalization and a median Polish summary method. After running these functions in the raw expression data, we obtained an expression “score” for each of the 22,690 gene entries.
Sample_platform_id	GPL339
Sample_contact_name	Roger,Luis,Vallejo
Sample_contact_email	roger.vallejo@ars.usda.gov
Sample_contact_phone	304-724-8340
Sample_contact_department	NCCCWA
Sample_contact_institute	USDA-ARS
Sample_contact_address	11861 Leetown Rd.
Sample_contact_city	Kearneysville
Sample_contact_state	WV
Sample_contact_zip/postal_code	25430
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361876/suppl/GSM361876.CEL.gz
Sample_series_id	GSE14485
Sample_data_row_count	22690

GSM361877

GPL339

MammaryTissue-48h-Saline-BiologicalRep2

Mouse left mammary gland tissue at 48hr post saline injection

Strain: Balb/cJ, Gender: female, Parturition: first, Age: 5th to 8th day after pups delivery, Tissue: left-side mammary gland, Treatment: Saline injected, Time post-injection: 48hr

gene expression data in mammary tissue sampled at 48 hr post saline injection

Sample_geo_accession	GSM361877
Sample_status	Public on Jun 30 2011
Sample_submission_date	Jan 21 2009
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The tissue samples were stored in RNA Later (Ambion, Austin, TX).
Sample_growth_protocol_ch1	The saline and E. coli challenged mammary glands were excised aseptically after at 24 and 48 hr post-injection.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	total RNA was isolated using Lipid Tissue Midi Kit following the manufacturer's instructions (Qiagen, Valencia, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The target (biotin labeled cRNA) was prepared and fragmented in accordance with instructions in the GeneChip® Mouse Expression Set 430A expression analysis technical manual (Affymetrix, Santa Clara, CA).
Sample_hyb_protocol	The fragmented cRNA target was hybridized to the probe array (GeneChip® Mouse Expression Set 430A) in the Microarray Core Facility at Pennsylvania State University (University Park, PA). One tissue sample or population of mRNAs was hybridized to one GeneChip® array using the Affymetrix System (Affymetrix, Santa Clara, CA) and a Microfluidcs Agilent System (Agilent Technologies, Santa Clara, CA).
Sample_scan_protocol	according to Affymetrix protocol
Sample_data_processing	For the pre-processing of the raw gene expression data, we wrote an R script using functions from the R package version 2.7.0 (Gentleman et al., 2004). We performed a data background correction using the robust multichip average (RMA) procedure suggested by Irizarry et al. (2005). Briefly, this procedure included a log2 transformation of the perfect match signal expression, quantile data normalization and a median Polish summary method. After running these functions in the raw expression data, we obtained an expression “score” for each of the 22,690 gene entries.
Sample_platform_id	GPL339
Sample_contact_name	Roger,Luis,Vallejo
Sample_contact_email	roger.vallejo@ars.usda.gov
Sample_contact_phone	304-724-8340
Sample_contact_department	NCCCWA
Sample_contact_institute	USDA-ARS
Sample_contact_address	11861 Leetown Rd.
Sample_contact_city	Kearneysville
Sample_contact_state	WV
Sample_contact_zip/postal_code	25430
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361877/suppl/GSM361877.CEL.gz
Sample_series_id	GSE14485
Sample_data_row_count	22690

GSM361878

GPL339

MammaryTissue-48h-Ecoli-BiologicalRep2

Mouse right mammary gland tissue at 48hr post Ecoli injection

Strain: Balb/cJ, Gender: female, Parturition: first, Age: 5th to 8th day after pups delivery, Tissue: right-side mammary gland, Treatment: Ecoli injected, Time post-injection: 48hr

gene expression data in mammary tissue sampled at 48 hr post Ecoli injection

Sample_geo_accession	GSM361878
Sample_status	Public on Jun 30 2011
Sample_submission_date	Jan 21 2009
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The tissue samples were stored in RNA Later (Ambion, Austin, TX).
Sample_growth_protocol_ch1	The saline and E. coli challenged mammary glands were excised aseptically after at 24 and 48 hr post-injection.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	total RNA was isolated using Lipid Tissue Midi Kit following the manufacturer's instructions (Qiagen, Valencia, CA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The target (biotin labeled cRNA) was prepared and fragmented in accordance with instructions in the GeneChip® Mouse Expression Set 430A expression analysis technical manual (Affymetrix, Santa Clara, CA).
Sample_hyb_protocol	The fragmented cRNA target was hybridized to the probe array (GeneChip® Mouse Expression Set 430A) in the Microarray Core Facility at Pennsylvania State University (University Park, PA). One tissue sample or population of mRNAs was hybridized to one GeneChip® array using the Affymetrix System (Affymetrix, Santa Clara, CA) and a Microfluidcs Agilent System (Agilent Technologies, Santa Clara, CA).
Sample_scan_protocol	according to Affymetrix protocol
Sample_data_processing	For the pre-processing of the raw gene expression data, we wrote an R script using functions from the R package version 2.7.0 (Gentleman et al., 2004). We performed a data background correction using the robust multichip average (RMA) procedure suggested by Irizarry et al. (2005). Briefly, this procedure included a log2 transformation of the perfect match signal expression, quantile data normalization and a median Polish summary method. After running these functions in the raw expression data, we obtained an expression “score” for each of the 22,690 gene entries.
Sample_platform_id	GPL339
Sample_contact_name	Roger,Luis,Vallejo
Sample_contact_email	roger.vallejo@ars.usda.gov
Sample_contact_phone	304-724-8340
Sample_contact_department	NCCCWA
Sample_contact_institute	USDA-ARS
Sample_contact_address	11861 Leetown Rd.
Sample_contact_city	Kearneysville
Sample_contact_state	WV
Sample_contact_zip/postal_code	25430
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM361nnn/GSM361878/suppl/GSM361878.CEL.gz
Sample_series_id	GSE14485
Sample_data_row_count	22690

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