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Search results for the GEO ID: GSE28895

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Description

Characteristics

GSM716058

GPL1261

germ-free mice in experiment_1

Mouse stomach, germ free mouse in experiment_1, pooled RNA

mouse strain: BALB/c colonised bacteria: germ free

Gene expression data from stomach of germ free mouse, equal amount of RNA from three mice were pooled, and each experiment was performed independently.

Sample_geo_accession	GSM716058
Sample_status	Public on Apr 28 2011
Sample_submission_date	Apr 27 2011
Sample_last_update_date	Apr 28 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	To colonize the mice with lactobacilli, 109 colony-forming unit (CFU) of live lactobacilli suspended in 0.5 ml of PBS were orally inoculated once into 8-week-old germfree mice using a stomach tube. For infection with H. pylori, 8-week-old mice were orally inoculated using a stomach tube on three consecutive days with 109 CFU of H. pylori that were freshly prepared and re-suspended in 0.5 ml PBS. Ten days after the last inoculation, the stomach was excised for microarray analysis.
Sample_growth_protocol_ch1	For inoculation bacteria into germ free mice, Lactobacillus gasseri OLL2716 (LG21) strain was grown in DifcoTM MRS broth for 37℃ for 1 day, and the Helicobacter pylori WT strain, had CagA, CagE and CagG, was incubated in DifcoTM Brucella broth containing 5% FBS at 37℃ for 3 days. Male BALB/c germ free mice were maintained in Trexler type flexible film plastic isolators with sterile food and water.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was prepared individually from the stomachs using a QIAGEN RNeasy Mini Kit according to the manufacturer's instructions. The quality and quantity of RNA in the samples were examined by measuring the optical density at 260 nm and 280 nm and by observing the gel electrophoresis pattern by Agilent 2100 Bioanalyzer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug pooled total RNA from three mice in each group(GeneChip Expression Analysis Technical Manual, 2005-2009, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global normarization as normalization method.
Sample_platform_id	GPL1261
Sample_contact_name	Yukio,,Asami
Sample_contact_email	yukio.asami@meiji.com
Sample_contact_laboratory	Genomics
Sample_contact_department	Functional Evaluation
Sample_contact_institute	Meiji Corporation, Food Science Institute
Sample_contact_address	540 Naruda
Sample_contact_city	Odawara
Sample_contact_state	Kanagawa
Sample_contact_zip/postal_code	250-0862
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM716nnn/GSM716058/suppl/GSM716058.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM716nnn/GSM716058/suppl/GSM716058.CHP.gz
Sample_series_id	GSE28895
Sample_data_row_count	45101

GSM716059

GPL1261

lactobacilli associated gnotobiotic mice in experiment_1

Mouse stomach, lactobacilli associated gnotobiotic mouse in experiment_1, pooled RNA

mouse strain: BALB/c colonised bacteria: Lactobacillus gasseri OLL2716 strain

Gene expression data from stomach of lactobacilli associated gnotobiotic mouse, equal amount of RNA from three mice were pooled, and each experiment was performed independently.

Sample_geo_accession	GSM716059
Sample_status	Public on Apr 28 2011
Sample_submission_date	Apr 27 2011
Sample_last_update_date	Apr 28 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	To colonize the mice with lactobacilli, 109 colony-forming unit (CFU) of live lactobacilli suspended in 0.5 ml of PBS were orally inoculated once into 8-week-old germfree mice using a stomach tube. For infection with H. pylori, 8-week-old mice were orally inoculated using a stomach tube on three consecutive days with 109 CFU of H. pylori that were freshly prepared and re-suspended in 0.5 ml PBS. Ten days after the last inoculation, the stomach was excised for microarray analysis.
Sample_growth_protocol_ch1	For inoculation bacteria into germ free mice, Lactobacillus gasseri OLL2716 (LG21) strain was grown in DifcoTM MRS broth for 37℃ for 1 day, and the Helicobacter pylori WT strain, had CagA, CagE and CagG, was incubated in DifcoTM Brucella broth containing 5% FBS at 37℃ for 3 days. Male BALB/c germ free mice were maintained in Trexler type flexible film plastic isolators with sterile food and water.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was prepared individually from the stomachs using a QIAGEN RNeasy Mini Kit according to the manufacturer's instructions. The quality and quantity of RNA in the samples were examined by measuring the optical density at 260 nm and 280 nm and by observing the gel electrophoresis pattern by Agilent 2100 Bioanalyzer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug pooled total RNA from three mice in each group(GeneChip Expression Analysis Technical Manual, 2005-2009, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global normarization as normalization method.
Sample_platform_id	GPL1261
Sample_contact_name	Yukio,,Asami
Sample_contact_email	yukio.asami@meiji.com
Sample_contact_laboratory	Genomics
Sample_contact_department	Functional Evaluation
Sample_contact_institute	Meiji Corporation, Food Science Institute
Sample_contact_address	540 Naruda
Sample_contact_city	Odawara
Sample_contact_state	Kanagawa
Sample_contact_zip/postal_code	250-0862
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM716nnn/GSM716059/suppl/GSM716059.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM716nnn/GSM716059/suppl/GSM716059.CHP.gz
Sample_series_id	GSE28895
Sample_data_row_count	45101

GSM716060

GPL1261

germ-free mice in experiment_2

Mouse stomach, germ free mouse in experiment_2, pooled RNA

mouse strain: BALB/c colonised bacteria: germ free

Gene expression data from stomach of germ free mouse, equal amount of RNA from three mice were pooled, and each experiment was performed independently.

Sample_geo_accession	GSM716060
Sample_status	Public on Apr 28 2011
Sample_submission_date	Apr 27 2011
Sample_last_update_date	Apr 28 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	To colonize the mice with lactobacilli, 109 colony-forming unit (CFU) of live lactobacilli suspended in 0.5 ml of PBS were orally inoculated once into 8-week-old germfree mice using a stomach tube. For infection with H. pylori, 8-week-old mice were orally inoculated using a stomach tube on three consecutive days with 109 CFU of H. pylori that were freshly prepared and re-suspended in 0.5 ml PBS. Ten days after the last inoculation, the stomach was excised for microarray analysis.
Sample_growth_protocol_ch1	For inoculation bacteria into germ free mice, Lactobacillus gasseri OLL2716 (LG21) strain was grown in DifcoTM MRS broth for 37℃ for 1 day, and the Helicobacter pylori WT strain, had CagA, CagE and CagG, was incubated in DifcoTM Brucella broth containing 5% FBS at 37℃ for 3 days. Male BALB/c germ free mice were maintained in Trexler type flexible film plastic isolators with sterile food and water.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was prepared individually from the stomachs using a QIAGEN RNeasy Mini Kit according to the manufacturer's instructions. The quality and quantity of RNA in the samples were examined by measuring the optical density at 260 nm and 280 nm and by observing the gel electrophoresis pattern by Agilent 2100 Bioanalyzer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug pooled total RNA from three mice in each group(GeneChip Expression Analysis Technical Manual, 2005-2009, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global normarization as normalization method.
Sample_platform_id	GPL1261
Sample_contact_name	Yukio,,Asami
Sample_contact_email	yukio.asami@meiji.com
Sample_contact_laboratory	Genomics
Sample_contact_department	Functional Evaluation
Sample_contact_institute	Meiji Corporation, Food Science Institute
Sample_contact_address	540 Naruda
Sample_contact_city	Odawara
Sample_contact_state	Kanagawa
Sample_contact_zip/postal_code	250-0862
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM716nnn/GSM716060/suppl/GSM716060.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM716nnn/GSM716060/suppl/GSM716060.CHP.gz
Sample_series_id	GSE28895
Sample_data_row_count	45101

GSM716061

GPL1261

lactobacilli associated gnotobiotic mice in experiment_2

Mouse stomach, lactobacilli associated gnotobiotic mouse in experiment_2, pooled RNA

mouse strain: BALB/c colonised bacteria: Lactobacillus gasseri OLL2716 strain

Gene expression data from stomach of lactobacilli associated gnotobiotic mouse, equal amount of RNA from three mice were pooled, and each experiment was performed independently.

Sample_geo_accession	GSM716061
Sample_status	Public on Apr 28 2011
Sample_submission_date	Apr 27 2011
Sample_last_update_date	Apr 28 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	To colonize the mice with lactobacilli, 109 colony-forming unit (CFU) of live lactobacilli suspended in 0.5 ml of PBS were orally inoculated once into 8-week-old germfree mice using a stomach tube. For infection with H. pylori, 8-week-old mice were orally inoculated using a stomach tube on three consecutive days with 109 CFU of H. pylori that were freshly prepared and re-suspended in 0.5 ml PBS. Ten days after the last inoculation, the stomach was excised for microarray analysis.
Sample_growth_protocol_ch1	For inoculation bacteria into germ free mice, Lactobacillus gasseri OLL2716 (LG21) strain was grown in DifcoTM MRS broth for 37℃ for 1 day, and the Helicobacter pylori WT strain, had CagA, CagE and CagG, was incubated in DifcoTM Brucella broth containing 5% FBS at 37℃ for 3 days. Male BALB/c germ free mice were maintained in Trexler type flexible film plastic isolators with sterile food and water.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was prepared individually from the stomachs using a QIAGEN RNeasy Mini Kit according to the manufacturer's instructions. The quality and quantity of RNA in the samples were examined by measuring the optical density at 260 nm and 280 nm and by observing the gel electrophoresis pattern by Agilent 2100 Bioanalyzer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug pooled total RNA from three mice in each group(GeneChip Expression Analysis Technical Manual, 2005-2009, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global normarization as normalization method.
Sample_platform_id	GPL1261
Sample_contact_name	Yukio,,Asami
Sample_contact_email	yukio.asami@meiji.com
Sample_contact_laboratory	Genomics
Sample_contact_department	Functional Evaluation
Sample_contact_institute	Meiji Corporation, Food Science Institute
Sample_contact_address	540 Naruda
Sample_contact_city	Odawara
Sample_contact_state	Kanagawa
Sample_contact_zip/postal_code	250-0862
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM716nnn/GSM716061/suppl/GSM716061.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM716nnn/GSM716061/suppl/GSM716061.CHP.gz
Sample_series_id	GSE28895
Sample_data_row_count	45101

GSM716062

GPL1261

germ-free mice in experiment_3

Mouse stomach, germ free mouse in experiment_3, pooled RNA

mouse strain: BALB/c colonised bacteria: germ free

Gene expression data from stomach of germ free mouse, equal amount of RNA from three mice were pooled, and each experiment was performed independently.

Sample_geo_accession	GSM716062
Sample_status	Public on Apr 28 2011
Sample_submission_date	Apr 27 2011
Sample_last_update_date	Apr 28 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	To colonize the mice with lactobacilli, 109 colony-forming unit (CFU) of live lactobacilli suspended in 0.5 ml of PBS were orally inoculated once into 8-week-old germfree mice using a stomach tube. For infection with H. pylori, 8-week-old mice were orally inoculated using a stomach tube on three consecutive days with 109 CFU of H. pylori that were freshly prepared and re-suspended in 0.5 ml PBS. Ten days after the last inoculation, the stomach was excised for microarray analysis.
Sample_growth_protocol_ch1	For inoculation bacteria into germ free mice, Lactobacillus gasseri OLL2716 (LG21) strain was grown in DifcoTM MRS broth for 37℃ for 1 day, and the Helicobacter pylori WT strain, had CagA, CagE and CagG, was incubated in DifcoTM Brucella broth containing 5% FBS at 37℃ for 3 days. Male BALB/c germ free mice were maintained in Trexler type flexible film plastic isolators with sterile food and water.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was prepared individually from the stomachs using a QIAGEN RNeasy Mini Kit according to the manufacturer's instructions. The quality and quantity of RNA in the samples were examined by measuring the optical density at 260 nm and 280 nm and by observing the gel electrophoresis pattern by Agilent 2100 Bioanalyzer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug pooled total RNA from three mice in each group(GeneChip Expression Analysis Technical Manual, 2005-2009, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global normarization as normalization method.
Sample_platform_id	GPL1261
Sample_contact_name	Yukio,,Asami
Sample_contact_email	yukio.asami@meiji.com
Sample_contact_laboratory	Genomics
Sample_contact_department	Functional Evaluation
Sample_contact_institute	Meiji Corporation, Food Science Institute
Sample_contact_address	540 Naruda
Sample_contact_city	Odawara
Sample_contact_state	Kanagawa
Sample_contact_zip/postal_code	250-0862
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM716nnn/GSM716062/suppl/GSM716062.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM716nnn/GSM716062/suppl/GSM716062.CHP.gz
Sample_series_id	GSE28895
Sample_data_row_count	45101

GSM716063

GPL1261

H. pylori associated gnotobiotic mice in experiment_3

Mouse stomach, H. pylori associated gnotobiotic mouse in experiment_3, pooled RNA

mouse strain: BALB/c colonised bacteria: Helicobacter pylori

Gene expression data from stomach of Helicobacter pylori associated gnotobiotic mouse, equal amount of RNA from three mice were pooled, and each experiment was performed independently.

Sample_geo_accession	GSM716063
Sample_status	Public on Apr 28 2011
Sample_submission_date	Apr 27 2011
Sample_last_update_date	Apr 28 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	To colonize the mice with lactobacilli, 109 colony-forming unit (CFU) of live lactobacilli suspended in 0.5 ml of PBS were orally inoculated once into 8-week-old germfree mice using a stomach tube. For infection with H. pylori, 8-week-old mice were orally inoculated using a stomach tube on three consecutive days with 109 CFU of H. pylori that were freshly prepared and re-suspended in 0.5 ml PBS. Ten days after the last inoculation, the stomach was excised for microarray analysis.
Sample_growth_protocol_ch1	For inoculation bacteria into germ free mice, Lactobacillus gasseri OLL2716 (LG21) strain was grown in DifcoTM MRS broth for 37℃ for 1 day, and the Helicobacter pylori WT strain, had CagA, CagE and CagG, was incubated in DifcoTM Brucella broth containing 5% FBS at 37℃ for 3 days. Male BALB/c germ free mice were maintained in Trexler type flexible film plastic isolators with sterile food and water.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was prepared individually from the stomachs using a QIAGEN RNeasy Mini Kit according to the manufacturer's instructions. The quality and quantity of RNA in the samples were examined by measuring the optical density at 260 nm and 280 nm and by observing the gel electrophoresis pattern by Agilent 2100 Bioanalyzer.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug pooled total RNA from three mice in each group(GeneChip Expression Analysis Technical Manual, 2005-2009, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global normarization as normalization method.
Sample_platform_id	GPL1261
Sample_contact_name	Yukio,,Asami
Sample_contact_email	yukio.asami@meiji.com
Sample_contact_laboratory	Genomics
Sample_contact_department	Functional Evaluation
Sample_contact_institute	Meiji Corporation, Food Science Institute
Sample_contact_address	540 Naruda
Sample_contact_city	Odawara
Sample_contact_state	Kanagawa
Sample_contact_zip/postal_code	250-0862
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM716nnn/GSM716063/suppl/GSM716063.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM716nnn/GSM716063/suppl/GSM716063.CHP.gz
Sample_series_id	GSE28895
Sample_data_row_count	45101

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