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Search results for the GEO ID: GSE18587

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GSM462279

GPL1261

ileum_germ_free_non_inoculated_(pool)

ileum from germ-free NMRI-KI mice, not inoculated, pooled samples

strain: NMRI-KI gender: female age: 45-60 days developmental stage: adult tissue: ileum bacterial inoculation: none

A54_01_ILEUM_NEG CTRL

Sample_geo_accession	GSM462279
Sample_status	Public on Sep 21 2011
Sample_submission_date	Oct 15 2009
Sample_last_update_date	Sep 21 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The germ-free female NMRI-KI mice (45 – 65 days of age) were mono-associated using established protocols. In brief, 10 ml of cultures in late log phase of A. muciniphila MucT (ATTC BAA-835) and L. plantarum WCFS1 (NCIMB 8826) were centrifuged (4500 rpm, 10 min). Pellets were resuspended in 1 ml of sterile anaerobic Phosphate Buffer Saline (PBS) and dispensed into sterile ampoules which were heat-sealed. The external surface of each ampoule was sterilized with chromsulfuric acid before transfer into respective isolators. Inside the isolators, the ampoules were broken, and 0.2 ml (10^9 cfu/ml) of the strictly anaerobic A. muciniphila (n=6) was inoculated intragastrically; L. plantarum (n=6) was inoculated orally. Germ-free control mice (n=6) were housed in separate isolators. After 7 days of colonization, mice were killed by cervical dislocation and terminal ileum, cecum and ascending colon specimens were sampled.
Sample_growth_protocol_ch1	Germ-free female NMRI-KI mice were inbred for >60 generations at the Laboratory of Medical Microbial Ecology at Karolinska Institute and they were housed in lightweight stainless-steel isolators. All mice had free access to a steam-sterilized standard mouse chow (R36; Lactamin, Vadstena, Sweden) and to sterilized water. Artificial light was available between 6 a.m. and 6 p.m.; the temperature was 24 ± 2.2°C, and the humidity was 55% ± 10%. The germ-free status was checked weekly by inoculating fecal samples in different media incubated both aerobically and anaerobically at 20 and 37°C for up to 4 weeks.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	After sampling, tissues were immediately preserved in 5 volumes of RNAlater (Ambion, Austin, Texas, USA) and stored at 4 ºC until use. Total RNA was prepared using TRIzol reagent and whereafter Purified total RNA was isolated using Qiagen RNEasy columns. For each part of the intestine, total RNA was pooled per intervention group (n=6).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 ug of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
Sample_hyb_protocol	Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
Sample_scan_protocol	Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
Sample_data_processing	Expression estimates were calculated using the multi-chip modified gamma Model for Oligonucleotide Signal (multi-mgMOS) [PMID: 16020470], using the PUMA package in Bioconductor.
Sample_platform_id	GPL1261
Sample_contact_name	Guido,,Hooiveld
Sample_contact_email	guido.hooiveld@wur.nl
Sample_contact_laboratory	Nutrition, Metabolism & Genomics Group
Sample_contact_department	Div. Human Nutrition
Sample_contact_institute	Wageningen University
Sample_contact_address	Bomenweg 2
Sample_contact_city	Wageningen
Sample_contact_zip/postal_code	NL-6703HD
Sample_contact_country	Netherlands
Sample_contact_web_link	http://nutrigene.4t.com
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM462nnn/GSM462279/suppl/GSM462279.CEL.gz
Sample_series_id	GSE18587
Sample_data_row_count	45101

GSM462280

GPL1261

ileum_germ_free_inoculated_A.muciniphila_(pool)

ileum from germ-free NMRI-KI mice, mono-associated with A. muciniphila, pooled samples

strain: NMRI-KI gender: female age: 45-60 days developmental stage: adult tissue: ileum bacterial inoculation: Akkermansia muciniphila MucT

A54_02_ILEUM_MUC INOC

Sample_geo_accession	GSM462280
Sample_status	Public on Sep 21 2011
Sample_submission_date	Oct 15 2009
Sample_last_update_date	Sep 21 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The germ-free female NMRI-KI mice (45 – 65 days of age) were mono-associated using established protocols. In brief, 10 ml of cultures in late log phase of A. muciniphila MucT (ATTC BAA-835) and L. plantarum WCFS1 (NCIMB 8826) were centrifuged (4500 rpm, 10 min). Pellets were resuspended in 1 ml of sterile anaerobic Phosphate Buffer Saline (PBS) and dispensed into sterile ampoules which were heat-sealed. The external surface of each ampoule was sterilized with chromsulfuric acid before transfer into respective isolators. Inside the isolators, the ampoules were broken, and 0.2 ml (10^9 cfu/ml) of the strictly anaerobic A. muciniphila (n=6) was inoculated intragastrically; L. plantarum (n=6) was inoculated orally. Germ-free control mice (n=6) were housed in separate isolators. After 7 days of colonization, mice were killed by cervical dislocation and terminal ileum, cecum and ascending colon specimens were sampled.
Sample_growth_protocol_ch1	Germ-free female NMRI-KI mice were inbred for >60 generations at the Laboratory of Medical Microbial Ecology at Karolinska Institute and they were housed in lightweight stainless-steel isolators. All mice had free access to a steam-sterilized standard mouse chow (R36; Lactamin, Vadstena, Sweden) and to sterilized water. Artificial light was available between 6 a.m. and 6 p.m.; the temperature was 24 ± 2.2°C, and the humidity was 55% ± 10%. The germ-free status was checked weekly by inoculating fecal samples in different media incubated both aerobically and anaerobically at 20 and 37°C for up to 4 weeks.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	After sampling, tissues were immediately preserved in 5 volumes of RNAlater (Ambion, Austin, Texas, USA) and stored at 4 ºC until use. Total RNA was prepared using TRIzol reagent and whereafter Purified total RNA was isolated using Qiagen RNEasy columns. For each part of the intestine, total RNA was pooled per intervention group (n=6).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 ug of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
Sample_hyb_protocol	Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
Sample_scan_protocol	Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
Sample_data_processing	Expression estimates were calculated using the multi-chip modified gamma Model for Oligonucleotide Signal (multi-mgMOS) [PMID: 16020470], using the PUMA package in Bioconductor.
Sample_platform_id	GPL1261
Sample_contact_name	Guido,,Hooiveld
Sample_contact_email	guido.hooiveld@wur.nl
Sample_contact_laboratory	Nutrition, Metabolism & Genomics Group
Sample_contact_department	Div. Human Nutrition
Sample_contact_institute	Wageningen University
Sample_contact_address	Bomenweg 2
Sample_contact_city	Wageningen
Sample_contact_zip/postal_code	NL-6703HD
Sample_contact_country	Netherlands
Sample_contact_web_link	http://nutrigene.4t.com
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM462nnn/GSM462280/suppl/GSM462280.CEL.gz
Sample_series_id	GSE18587
Sample_data_row_count	45101

GSM462281

GPL1261

ileum_germ_free_inoculated_L.plantarum_(pool)

ileum from germ-free NMRI-KI mice, mono-associated with L. plantarum, pooled samples

strain: NMRI-KI gender: female age: 45-60 days developmental stage: adult tissue: ileum bacterial inoculation: Lactobacillus plantarum WCFS1

A54_03_ILEUM_LPLANT INOC

Sample_geo_accession	GSM462281
Sample_status	Public on Sep 21 2011
Sample_submission_date	Oct 15 2009
Sample_last_update_date	Sep 21 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The germ-free female NMRI-KI mice (45 – 65 days of age) were mono-associated using established protocols. In brief, 10 ml of cultures in late log phase of A. muciniphila MucT (ATTC BAA-835) and L. plantarum WCFS1 (NCIMB 8826) were centrifuged (4500 rpm, 10 min). Pellets were resuspended in 1 ml of sterile anaerobic Phosphate Buffer Saline (PBS) and dispensed into sterile ampoules which were heat-sealed. The external surface of each ampoule was sterilized with chromsulfuric acid before transfer into respective isolators. Inside the isolators, the ampoules were broken, and 0.2 ml (10^9 cfu/ml) of the strictly anaerobic A. muciniphila (n=6) was inoculated intragastrically; L. plantarum (n=6) was inoculated orally. Germ-free control mice (n=6) were housed in separate isolators. After 7 days of colonization, mice were killed by cervical dislocation and terminal ileum, cecum and ascending colon specimens were sampled.
Sample_growth_protocol_ch1	Germ-free female NMRI-KI mice were inbred for >60 generations at the Laboratory of Medical Microbial Ecology at Karolinska Institute and they were housed in lightweight stainless-steel isolators. All mice had free access to a steam-sterilized standard mouse chow (R36; Lactamin, Vadstena, Sweden) and to sterilized water. Artificial light was available between 6 a.m. and 6 p.m.; the temperature was 24 ± 2.2°C, and the humidity was 55% ± 10%. The germ-free status was checked weekly by inoculating fecal samples in different media incubated both aerobically and anaerobically at 20 and 37°C for up to 4 weeks.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	After sampling, tissues were immediately preserved in 5 volumes of RNAlater (Ambion, Austin, Texas, USA) and stored at 4 ºC until use. Total RNA was prepared using TRIzol reagent and whereafter Purified total RNA was isolated using Qiagen RNEasy columns. For each part of the intestine, total RNA was pooled per intervention group (n=6).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 ug of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
Sample_hyb_protocol	Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
Sample_scan_protocol	Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
Sample_data_processing	Expression estimates were calculated using the multi-chip modified gamma Model for Oligonucleotide Signal (multi-mgMOS) [PMID: 16020470], using the PUMA package in Bioconductor.
Sample_platform_id	GPL1261
Sample_contact_name	Guido,,Hooiveld
Sample_contact_email	guido.hooiveld@wur.nl
Sample_contact_laboratory	Nutrition, Metabolism & Genomics Group
Sample_contact_department	Div. Human Nutrition
Sample_contact_institute	Wageningen University
Sample_contact_address	Bomenweg 2
Sample_contact_city	Wageningen
Sample_contact_zip/postal_code	NL-6703HD
Sample_contact_country	Netherlands
Sample_contact_web_link	http://nutrigene.4t.com
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM462nnn/GSM462281/suppl/GSM462281.CEL.gz
Sample_series_id	GSE18587
Sample_data_row_count	45101

GSM462282

GPL1261

caecum_germ_free_non_inoculated_(pool)

caecum from germ-free NMRI-KI mice, not inoculated, pooled samples

strain: NMRI-KI gender: female age: 45-60 days developmental stage: adult tissue: caecum bacterial inoculation: none

A54_04_CAECUM_NEG CTRL

Sample_geo_accession	GSM462282
Sample_status	Public on Sep 21 2011
Sample_submission_date	Oct 15 2009
Sample_last_update_date	Sep 21 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The germ-free female NMRI-KI mice (45 – 65 days of age) were mono-associated using established protocols. In brief, 10 ml of cultures in late log phase of A. muciniphila MucT (ATTC BAA-835) and L. plantarum WCFS1 (NCIMB 8826) were centrifuged (4500 rpm, 10 min). Pellets were resuspended in 1 ml of sterile anaerobic Phosphate Buffer Saline (PBS) and dispensed into sterile ampoules which were heat-sealed. The external surface of each ampoule was sterilized with chromsulfuric acid before transfer into respective isolators. Inside the isolators, the ampoules were broken, and 0.2 ml (10^9 cfu/ml) of the strictly anaerobic A. muciniphila (n=6) was inoculated intragastrically; L. plantarum (n=6) was inoculated orally. Germ-free control mice (n=6) were housed in separate isolators. After 7 days of colonization, mice were killed by cervical dislocation and terminal ileum, cecum and ascending colon specimens were sampled.
Sample_growth_protocol_ch1	Germ-free female NMRI-KI mice were inbred for >60 generations at the Laboratory of Medical Microbial Ecology at Karolinska Institute and they were housed in lightweight stainless-steel isolators. All mice had free access to a steam-sterilized standard mouse chow (R36; Lactamin, Vadstena, Sweden) and to sterilized water. Artificial light was available between 6 a.m. and 6 p.m.; the temperature was 24 ± 2.2°C, and the humidity was 55% ± 10%. The germ-free status was checked weekly by inoculating fecal samples in different media incubated both aerobically and anaerobically at 20 and 37°C for up to 4 weeks.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	After sampling, tissues were immediately preserved in 5 volumes of RNAlater (Ambion, Austin, Texas, USA) and stored at 4 ºC until use. Total RNA was prepared using TRIzol reagent and whereafter Purified total RNA was isolated using Qiagen RNEasy columns. For each part of the intestine, total RNA was pooled per intervention group (n=6).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 ug of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
Sample_hyb_protocol	Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
Sample_scan_protocol	Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
Sample_data_processing	Expression estimates were calculated using the multi-chip modified gamma Model for Oligonucleotide Signal (multi-mgMOS) [PMID: 16020470], using the PUMA package in Bioconductor.
Sample_platform_id	GPL1261
Sample_contact_name	Guido,,Hooiveld
Sample_contact_email	guido.hooiveld@wur.nl
Sample_contact_laboratory	Nutrition, Metabolism & Genomics Group
Sample_contact_department	Div. Human Nutrition
Sample_contact_institute	Wageningen University
Sample_contact_address	Bomenweg 2
Sample_contact_city	Wageningen
Sample_contact_zip/postal_code	NL-6703HD
Sample_contact_country	Netherlands
Sample_contact_web_link	http://nutrigene.4t.com
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM462nnn/GSM462282/suppl/GSM462282.CEL.gz
Sample_series_id	GSE18587
Sample_data_row_count	45101

GSM462283

GPL1261

caecum_germ_free_inoculated_A.muciniphila_(pool)

caecum from germ-free NMRI-KI mice, mono-associated with A. muciniphila, pooled samples

strain: NMRI-KI gender: female age: 45-60 days developmental stage: adult tissue: caecum bacterial inoculation: Akkermansia muciniphila MucT

A54_05_CAECUM_MUC INOC

Sample_geo_accession	GSM462283
Sample_status	Public on Sep 21 2011
Sample_submission_date	Oct 15 2009
Sample_last_update_date	Sep 21 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The germ-free female NMRI-KI mice (45 – 65 days of age) were mono-associated using established protocols. In brief, 10 ml of cultures in late log phase of A. muciniphila MucT (ATTC BAA-835) and L. plantarum WCFS1 (NCIMB 8826) were centrifuged (4500 rpm, 10 min). Pellets were resuspended in 1 ml of sterile anaerobic Phosphate Buffer Saline (PBS) and dispensed into sterile ampoules which were heat-sealed. The external surface of each ampoule was sterilized with chromsulfuric acid before transfer into respective isolators. Inside the isolators, the ampoules were broken, and 0.2 ml (10^9 cfu/ml) of the strictly anaerobic A. muciniphila (n=6) was inoculated intragastrically; L. plantarum (n=6) was inoculated orally. Germ-free control mice (n=6) were housed in separate isolators. After 7 days of colonization, mice were killed by cervical dislocation and terminal ileum, cecum and ascending colon specimens were sampled.
Sample_growth_protocol_ch1	Germ-free female NMRI-KI mice were inbred for >60 generations at the Laboratory of Medical Microbial Ecology at Karolinska Institute and they were housed in lightweight stainless-steel isolators. All mice had free access to a steam-sterilized standard mouse chow (R36; Lactamin, Vadstena, Sweden) and to sterilized water. Artificial light was available between 6 a.m. and 6 p.m.; the temperature was 24 ± 2.2°C, and the humidity was 55% ± 10%. The germ-free status was checked weekly by inoculating fecal samples in different media incubated both aerobically and anaerobically at 20 and 37°C for up to 4 weeks.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	After sampling, tissues were immediately preserved in 5 volumes of RNAlater (Ambion, Austin, Texas, USA) and stored at 4 ºC until use. Total RNA was prepared using TRIzol reagent and whereafter Purified total RNA was isolated using Qiagen RNEasy columns. For each part of the intestine, total RNA was pooled per intervention group (n=6).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 ug of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
Sample_hyb_protocol	Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
Sample_scan_protocol	Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
Sample_data_processing	Expression estimates were calculated using the multi-chip modified gamma Model for Oligonucleotide Signal (multi-mgMOS) [PMID: 16020470], using the PUMA package in Bioconductor.
Sample_platform_id	GPL1261
Sample_contact_name	Guido,,Hooiveld
Sample_contact_email	guido.hooiveld@wur.nl
Sample_contact_laboratory	Nutrition, Metabolism & Genomics Group
Sample_contact_department	Div. Human Nutrition
Sample_contact_institute	Wageningen University
Sample_contact_address	Bomenweg 2
Sample_contact_city	Wageningen
Sample_contact_zip/postal_code	NL-6703HD
Sample_contact_country	Netherlands
Sample_contact_web_link	http://nutrigene.4t.com
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM462nnn/GSM462283/suppl/GSM462283.CEL.gz
Sample_series_id	GSE18587
Sample_data_row_count	45101

GSM462284

GPL1261

caecum_germ_free_inoculated_L.plantarum_(pool)

caecum from germ-free NMRI-KI mice, mono-associated with L. plantarum, pooled samples

strain: NMRI-KI gender: female age: 45-60 days developmental stage: adult tissue: caecum bacterial inoculation: Lactobacillus plantarum WCFS1

A54_06_CAECUM_LPLANT INOC

Sample_geo_accession	GSM462284
Sample_status	Public on Sep 21 2011
Sample_submission_date	Oct 15 2009
Sample_last_update_date	Sep 21 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The germ-free female NMRI-KI mice (45 – 65 days of age) were mono-associated using established protocols. In brief, 10 ml of cultures in late log phase of A. muciniphila MucT (ATTC BAA-835) and L. plantarum WCFS1 (NCIMB 8826) were centrifuged (4500 rpm, 10 min). Pellets were resuspended in 1 ml of sterile anaerobic Phosphate Buffer Saline (PBS) and dispensed into sterile ampoules which were heat-sealed. The external surface of each ampoule was sterilized with chromsulfuric acid before transfer into respective isolators. Inside the isolators, the ampoules were broken, and 0.2 ml (10^9 cfu/ml) of the strictly anaerobic A. muciniphila (n=6) was inoculated intragastrically; L. plantarum (n=6) was inoculated orally. Germ-free control mice (n=6) were housed in separate isolators. After 7 days of colonization, mice were killed by cervical dislocation and terminal ileum, cecum and ascending colon specimens were sampled.
Sample_growth_protocol_ch1	Germ-free female NMRI-KI mice were inbred for >60 generations at the Laboratory of Medical Microbial Ecology at Karolinska Institute and they were housed in lightweight stainless-steel isolators. All mice had free access to a steam-sterilized standard mouse chow (R36; Lactamin, Vadstena, Sweden) and to sterilized water. Artificial light was available between 6 a.m. and 6 p.m.; the temperature was 24 ± 2.2°C, and the humidity was 55% ± 10%. The germ-free status was checked weekly by inoculating fecal samples in different media incubated both aerobically and anaerobically at 20 and 37°C for up to 4 weeks.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	After sampling, tissues were immediately preserved in 5 volumes of RNAlater (Ambion, Austin, Texas, USA) and stored at 4 ºC until use. Total RNA was prepared using TRIzol reagent and whereafter Purified total RNA was isolated using Qiagen RNEasy columns. For each part of the intestine, total RNA was pooled per intervention group (n=6).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 ug of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
Sample_hyb_protocol	Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
Sample_scan_protocol	Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
Sample_data_processing	Expression estimates were calculated using the multi-chip modified gamma Model for Oligonucleotide Signal (multi-mgMOS) [PMID: 16020470], using the PUMA package in Bioconductor.
Sample_platform_id	GPL1261
Sample_contact_name	Guido,,Hooiveld
Sample_contact_email	guido.hooiveld@wur.nl
Sample_contact_laboratory	Nutrition, Metabolism & Genomics Group
Sample_contact_department	Div. Human Nutrition
Sample_contact_institute	Wageningen University
Sample_contact_address	Bomenweg 2
Sample_contact_city	Wageningen
Sample_contact_zip/postal_code	NL-6703HD
Sample_contact_country	Netherlands
Sample_contact_web_link	http://nutrigene.4t.com
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM462nnn/GSM462284/suppl/GSM462284.CEL.gz
Sample_series_id	GSE18587
Sample_data_row_count	45101

GSM462285

GPL1261

colon_germ_free_non_inoculated_(pool)

colon from germ-free NMRI-KI mice, not inoculated, pooled samples

strain: NMRI-KI gender: female age: 45-60 days developmental stage: adult tissue: colon bacterial inoculation: none

A54_07_COLON_NEG CTRL

Sample_geo_accession	GSM462285
Sample_status	Public on Sep 21 2011
Sample_submission_date	Oct 15 2009
Sample_last_update_date	Sep 21 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The germ-free female NMRI-KI mice (45 – 65 days of age) were mono-associated using established protocols. In brief, 10 ml of cultures in late log phase of A. muciniphila MucT (ATTC BAA-835) and L. plantarum WCFS1 (NCIMB 8826) were centrifuged (4500 rpm, 10 min). Pellets were resuspended in 1 ml of sterile anaerobic Phosphate Buffer Saline (PBS) and dispensed into sterile ampoules which were heat-sealed. The external surface of each ampoule was sterilized with chromsulfuric acid before transfer into respective isolators. Inside the isolators, the ampoules were broken, and 0.2 ml (10^9 cfu/ml) of the strictly anaerobic A. muciniphila (n=6) was inoculated intragastrically; L. plantarum (n=6) was inoculated orally. Germ-free control mice (n=6) were housed in separate isolators. After 7 days of colonization, mice were killed by cervical dislocation and terminal ileum, cecum and ascending colon specimens were sampled.
Sample_growth_protocol_ch1	Germ-free female NMRI-KI mice were inbred for >60 generations at the Laboratory of Medical Microbial Ecology at Karolinska Institute and they were housed in lightweight stainless-steel isolators. All mice had free access to a steam-sterilized standard mouse chow (R36; Lactamin, Vadstena, Sweden) and to sterilized water. Artificial light was available between 6 a.m. and 6 p.m.; the temperature was 24 ± 2.2°C, and the humidity was 55% ± 10%. The germ-free status was checked weekly by inoculating fecal samples in different media incubated both aerobically and anaerobically at 20 and 37°C for up to 4 weeks.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	After sampling, tissues were immediately preserved in 5 volumes of RNAlater (Ambion, Austin, Texas, USA) and stored at 4 ºC until use. Total RNA was prepared using TRIzol reagent and whereafter Purified total RNA was isolated using Qiagen RNEasy columns. For each part of the intestine, total RNA was pooled per intervention group (n=6).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 ug of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
Sample_hyb_protocol	Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
Sample_scan_protocol	Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
Sample_data_processing	Expression estimates were calculated using the multi-chip modified gamma Model for Oligonucleotide Signal (multi-mgMOS) [PMID: 16020470], using the PUMA package in Bioconductor.
Sample_platform_id	GPL1261
Sample_contact_name	Guido,,Hooiveld
Sample_contact_email	guido.hooiveld@wur.nl
Sample_contact_laboratory	Nutrition, Metabolism & Genomics Group
Sample_contact_department	Div. Human Nutrition
Sample_contact_institute	Wageningen University
Sample_contact_address	Bomenweg 2
Sample_contact_city	Wageningen
Sample_contact_zip/postal_code	NL-6703HD
Sample_contact_country	Netherlands
Sample_contact_web_link	http://nutrigene.4t.com
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM462nnn/GSM462285/suppl/GSM462285.CEL.gz
Sample_series_id	GSE18587
Sample_data_row_count	45101

GSM462286

GPL1261

colon_germ_free_inoculated_A.muciniphila_(pool)

colon from germ-free NMRI-KI mice, mono-associated with A. muciniphila, pooled samples

strain: NMRI-KI gender: female age: 45-60 days developmental stage: adult tissue: colon bacterial inoculation: Akkermansia muciniphila MucT

A54_08_COLON_MUC INOC

Sample_geo_accession	GSM462286
Sample_status	Public on Sep 21 2011
Sample_submission_date	Oct 15 2009
Sample_last_update_date	Sep 21 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The germ-free female NMRI-KI mice (45 – 65 days of age) were mono-associated using established protocols. In brief, 10 ml of cultures in late log phase of A. muciniphila MucT (ATTC BAA-835) and L. plantarum WCFS1 (NCIMB 8826) were centrifuged (4500 rpm, 10 min). Pellets were resuspended in 1 ml of sterile anaerobic Phosphate Buffer Saline (PBS) and dispensed into sterile ampoules which were heat-sealed. The external surface of each ampoule was sterilized with chromsulfuric acid before transfer into respective isolators. Inside the isolators, the ampoules were broken, and 0.2 ml (10^9 cfu/ml) of the strictly anaerobic A. muciniphila (n=6) was inoculated intragastrically; L. plantarum (n=6) was inoculated orally. Germ-free control mice (n=6) were housed in separate isolators. After 7 days of colonization, mice were killed by cervical dislocation and terminal ileum, cecum and ascending colon specimens were sampled.
Sample_growth_protocol_ch1	Germ-free female NMRI-KI mice were inbred for >60 generations at the Laboratory of Medical Microbial Ecology at Karolinska Institute and they were housed in lightweight stainless-steel isolators. All mice had free access to a steam-sterilized standard mouse chow (R36; Lactamin, Vadstena, Sweden) and to sterilized water. Artificial light was available between 6 a.m. and 6 p.m.; the temperature was 24 ± 2.2°C, and the humidity was 55% ± 10%. The germ-free status was checked weekly by inoculating fecal samples in different media incubated both aerobically and anaerobically at 20 and 37°C for up to 4 weeks.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	After sampling, tissues were immediately preserved in 5 volumes of RNAlater (Ambion, Austin, Texas, USA) and stored at 4 ºC until use. Total RNA was prepared using TRIzol reagent and whereafter Purified total RNA was isolated using Qiagen RNEasy columns. For each part of the intestine, total RNA was pooled per intervention group (n=6).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 ug of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
Sample_hyb_protocol	Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
Sample_scan_protocol	Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
Sample_data_processing	Expression estimates were calculated using the multi-chip modified gamma Model for Oligonucleotide Signal (multi-mgMOS) [PMID: 16020470], using the PUMA package in Bioconductor.
Sample_platform_id	GPL1261
Sample_contact_name	Guido,,Hooiveld
Sample_contact_email	guido.hooiveld@wur.nl
Sample_contact_laboratory	Nutrition, Metabolism & Genomics Group
Sample_contact_department	Div. Human Nutrition
Sample_contact_institute	Wageningen University
Sample_contact_address	Bomenweg 2
Sample_contact_city	Wageningen
Sample_contact_zip/postal_code	NL-6703HD
Sample_contact_country	Netherlands
Sample_contact_web_link	http://nutrigene.4t.com
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM462nnn/GSM462286/suppl/GSM462286.CEL.gz
Sample_series_id	GSE18587
Sample_data_row_count	45101

GSM462287

GPL1261

colon_germ_free_inoculated_L.plantarum_(pool)

colon from germ-free NMRI-KI mice, mono-associated with L. plantarum, pooled samples

strain: NMRI-KI gender: female age: 45-60 days developmental stage: adult tissue: colon bacterial inoculation: Lactobacillus plantarum WCFS1

A54_09_COLON_LPLANT INOC

Sample_geo_accession	GSM462287
Sample_status	Public on Sep 21 2011
Sample_submission_date	Oct 15 2009
Sample_last_update_date	Sep 21 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	The germ-free female NMRI-KI mice (45 – 65 days of age) were mono-associated using established protocols. In brief, 10 ml of cultures in late log phase of A. muciniphila MucT (ATTC BAA-835) and L. plantarum WCFS1 (NCIMB 8826) were centrifuged (4500 rpm, 10 min). Pellets were resuspended in 1 ml of sterile anaerobic Phosphate Buffer Saline (PBS) and dispensed into sterile ampoules which were heat-sealed. The external surface of each ampoule was sterilized with chromsulfuric acid before transfer into respective isolators. Inside the isolators, the ampoules were broken, and 0.2 ml (10^9 cfu/ml) of the strictly anaerobic A. muciniphila (n=6) was inoculated intragastrically; L. plantarum (n=6) was inoculated orally. Germ-free control mice (n=6) were housed in separate isolators. After 7 days of colonization, mice were killed by cervical dislocation and terminal ileum, cecum and ascending colon specimens were sampled.
Sample_growth_protocol_ch1	Germ-free female NMRI-KI mice were inbred for >60 generations at the Laboratory of Medical Microbial Ecology at Karolinska Institute and they were housed in lightweight stainless-steel isolators. All mice had free access to a steam-sterilized standard mouse chow (R36; Lactamin, Vadstena, Sweden) and to sterilized water. Artificial light was available between 6 a.m. and 6 p.m.; the temperature was 24 ± 2.2°C, and the humidity was 55% ± 10%. The germ-free status was checked weekly by inoculating fecal samples in different media incubated both aerobically and anaerobically at 20 and 37°C for up to 4 weeks.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	After sampling, tissues were immediately preserved in 5 volumes of RNAlater (Ambion, Austin, Texas, USA) and stored at 4 ºC until use. Total RNA was prepared using TRIzol reagent and whereafter Purified total RNA was isolated using Qiagen RNEasy columns. For each part of the intestine, total RNA was pooled per intervention group (n=6).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 ug of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
Sample_hyb_protocol	Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
Sample_scan_protocol	Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
Sample_data_processing	Expression estimates were calculated using the multi-chip modified gamma Model for Oligonucleotide Signal (multi-mgMOS) [PMID: 16020470], using the PUMA package in Bioconductor.
Sample_platform_id	GPL1261
Sample_contact_name	Guido,,Hooiveld
Sample_contact_email	guido.hooiveld@wur.nl
Sample_contact_laboratory	Nutrition, Metabolism & Genomics Group
Sample_contact_department	Div. Human Nutrition
Sample_contact_institute	Wageningen University
Sample_contact_address	Bomenweg 2
Sample_contact_city	Wageningen
Sample_contact_zip/postal_code	NL-6703HD
Sample_contact_country	Netherlands
Sample_contact_web_link	http://nutrigene.4t.com
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM462nnn/GSM462287/suppl/GSM462287.CEL.gz
Sample_series_id	GSE18587
Sample_data_row_count	45101

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