Result

Search results for the GEO ID: GSE23421

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Title

Source name

Description

Characteristics

GSM574340

GPL1261

colonic tissue from floxed mouse, biological rep1

colon from floxed mouse, wild-type phenotype

strain: C57BL/6 tissue: colon genotype: PPAR g fl/fl; Lysozyme M cre- phenotype: wild-type treatment: dextran sodium sulfate (DSS)

wild4 Gene expression data from colon of control littermate mice.

Sample_geo_accession	GSM574340
Sample_status	Public on Nov 12 2011
Sample_submission_date	Aug 04 2010
Sample_last_update_date	Nov 12 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Colitis was induced with 2.5% dextran sodium sulfate (DSS), 36,000–44,000 mol wt (ICN Biomedicals, Aurora, OH) in the drinking water. After the DSS challenge mice were weighed on a daily basis and examined for clinical signs of disease associated with colitis (i.e., perianal soiling, rectal bleeding, diarrhea, and piloerection). For the DSS challenge, the disease activity indices and rectal bleeding scores were calculated using a modification of a previously published compounded clinical score. Briefly, disease activity index consisted of a scoring for diarrhea and lethargy, whereas rectal bleeding consisted of a visual observation of blood in feces and the perianal area. Mice in the DSS study were euthanized on day 7 of the DSS challenge by CO2 asphyxiation and blood was withdrawn from the heart. Colons and spleens were scored based on size and macroscopic inflammatory lesions.
Sample_growth_protocol_ch1	Six- to eight-week-old PPAR gamma flfl Cre+ mice, with a Cre recombinase targeted to the LysM promoter, and control Cre- littermates (n=20) were housed at the animal facilities at Virginia Polytechnic Institute and State University in a room maintained at 75 F, with a 12:12 h light-dark cycle starting from 6:00 AM. All experimental procedures were approved by the Institutional Animal Care and Use Committee of Virginia Polytechnic Institute and State University and met or exceeded requirements of the Public Health Service/National Institutes of Health and the Animal Welfare Act.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Whole colonic tissue was collected from mice and preserved in RNAlater® (Applied Biosystems/Ambion Foster City, CA). After homogenization, total RNA was extracted and purified using the RNAeasy system according to manufacturer's instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	According to Affymetrix standard method.
Sample_hyb_protocol	According to Affymetrix standard method.
Sample_scan_protocol	According to Affymetrix standard method.
Sample_data_processing	gcRMA normalized by using Bioconductor package 'gcrma' in R 2.8.
Sample_platform_id	GPL1261
Sample_contact_name	Maria,,Salvato
Sample_contact_email	MSalvato@ihv.umaryland.edu
Sample_contact_phone	410-706-1368
Sample_contact_fax	410-706-5198
Sample_contact_laboratory	Rm 510
Sample_contact_department	Institute of Human Virology
Sample_contact_institute	University of Maryland School of Medicine
Sample_contact_address	725 W Lombard Street
Sample_contact_city	Baltimore
Sample_contact_state	MD
Sample_contact_zip/postal_code	21201
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574340/suppl/GSM574340.CEL.gz
Sample_series_id	GSE23421
Sample_data_row_count	45101

GSM574341

GPL1261

colonic tissue from floxed mouse, biological rep2

colon from floxed mouse, wild-type phenotype

strain: C57BL/6 tissue: colon genotype: PPAR g fl/fl; Lysozyme M cre- phenotype: wild-type treatment: dextran sodium sulfate (DSS)

wild7 Gene expression data from colon of control littermate mice.

Sample_geo_accession	GSM574341
Sample_status	Public on Nov 12 2011
Sample_submission_date	Aug 04 2010
Sample_last_update_date	Nov 12 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Colitis was induced with 2.5% dextran sodium sulfate (DSS), 36,000–44,000 mol wt (ICN Biomedicals, Aurora, OH) in the drinking water. After the DSS challenge mice were weighed on a daily basis and examined for clinical signs of disease associated with colitis (i.e., perianal soiling, rectal bleeding, diarrhea, and piloerection). For the DSS challenge, the disease activity indices and rectal bleeding scores were calculated using a modification of a previously published compounded clinical score. Briefly, disease activity index consisted of a scoring for diarrhea and lethargy, whereas rectal bleeding consisted of a visual observation of blood in feces and the perianal area. Mice in the DSS study were euthanized on day 7 of the DSS challenge by CO2 asphyxiation and blood was withdrawn from the heart. Colons and spleens were scored based on size and macroscopic inflammatory lesions.
Sample_growth_protocol_ch1	Six- to eight-week-old PPAR gamma flfl Cre+ mice, with a Cre recombinase targeted to the LysM promoter, and control Cre- littermates (n=20) were housed at the animal facilities at Virginia Polytechnic Institute and State University in a room maintained at 75 F, with a 12:12 h light-dark cycle starting from 6:00 AM. All experimental procedures were approved by the Institutional Animal Care and Use Committee of Virginia Polytechnic Institute and State University and met or exceeded requirements of the Public Health Service/National Institutes of Health and the Animal Welfare Act.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Whole colonic tissue was collected from mice and preserved in RNAlater® (Applied Biosystems/Ambion Foster City, CA). After homogenization, total RNA was extracted and purified using the RNAeasy system according to manufacturer's instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	According to Affymetrix standard method.
Sample_hyb_protocol	According to Affymetrix standard method.
Sample_scan_protocol	According to Affymetrix standard method.
Sample_data_processing	gcRMA normalized by using Bioconductor package 'gcrma' in R 2.8.
Sample_platform_id	GPL1261
Sample_contact_name	Maria,,Salvato
Sample_contact_email	MSalvato@ihv.umaryland.edu
Sample_contact_phone	410-706-1368
Sample_contact_fax	410-706-5198
Sample_contact_laboratory	Rm 510
Sample_contact_department	Institute of Human Virology
Sample_contact_institute	University of Maryland School of Medicine
Sample_contact_address	725 W Lombard Street
Sample_contact_city	Baltimore
Sample_contact_state	MD
Sample_contact_zip/postal_code	21201
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574341/suppl/GSM574341.CEL.gz
Sample_series_id	GSE23421
Sample_data_row_count	45101

GSM574342

GPL1261

colonic tissue from floxed mouse, biological rep3

colon from floxed mouse, wild-type phenotype

strain: C57BL/6 tissue: colon genotype: PPAR g fl/fl; Lysozyme M cre- phenotype: wild-type treatment: dextran sodium sulfate (DSS)

wild8 Gene expression data from colon of control littermate mice.

Sample_geo_accession	GSM574342
Sample_status	Public on Nov 12 2011
Sample_submission_date	Aug 04 2010
Sample_last_update_date	Nov 12 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Colitis was induced with 2.5% dextran sodium sulfate (DSS), 36,000–44,000 mol wt (ICN Biomedicals, Aurora, OH) in the drinking water. After the DSS challenge mice were weighed on a daily basis and examined for clinical signs of disease associated with colitis (i.e., perianal soiling, rectal bleeding, diarrhea, and piloerection). For the DSS challenge, the disease activity indices and rectal bleeding scores were calculated using a modification of a previously published compounded clinical score. Briefly, disease activity index consisted of a scoring for diarrhea and lethargy, whereas rectal bleeding consisted of a visual observation of blood in feces and the perianal area. Mice in the DSS study were euthanized on day 7 of the DSS challenge by CO2 asphyxiation and blood was withdrawn from the heart. Colons and spleens were scored based on size and macroscopic inflammatory lesions.
Sample_growth_protocol_ch1	Six- to eight-week-old PPAR gamma flfl Cre+ mice, with a Cre recombinase targeted to the LysM promoter, and control Cre- littermates (n=20) were housed at the animal facilities at Virginia Polytechnic Institute and State University in a room maintained at 75 F, with a 12:12 h light-dark cycle starting from 6:00 AM. All experimental procedures were approved by the Institutional Animal Care and Use Committee of Virginia Polytechnic Institute and State University and met or exceeded requirements of the Public Health Service/National Institutes of Health and the Animal Welfare Act.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Whole colonic tissue was collected from mice and preserved in RNAlater® (Applied Biosystems/Ambion Foster City, CA). After homogenization, total RNA was extracted and purified using the RNAeasy system according to manufacturer's instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	According to Affymetrix standard method.
Sample_hyb_protocol	According to Affymetrix standard method.
Sample_scan_protocol	According to Affymetrix standard method.
Sample_data_processing	gcRMA normalized by using Bioconductor package 'gcrma' in R 2.8.
Sample_platform_id	GPL1261
Sample_contact_name	Maria,,Salvato
Sample_contact_email	MSalvato@ihv.umaryland.edu
Sample_contact_phone	410-706-1368
Sample_contact_fax	410-706-5198
Sample_contact_laboratory	Rm 510
Sample_contact_department	Institute of Human Virology
Sample_contact_institute	University of Maryland School of Medicine
Sample_contact_address	725 W Lombard Street
Sample_contact_city	Baltimore
Sample_contact_state	MD
Sample_contact_zip/postal_code	21201
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574342/suppl/GSM574342.CEL.gz
Sample_series_id	GSE23421
Sample_data_row_count	45101

GSM574343

GPL1261

colonic tissue from macrophage-specific PPARgamma-deficient mouse, biological rep1

colon from macrophage-specific PPARg-deficient mouse

strain: C57BL/6 tissue: colon genotype: PPAR g fl/fl; Lysozyme M cre+ phenotype: PPAR gamma deficient treatment: dextran sodium sulfate (DSS)

mut14 Gene expression data from colon of PPARr-deficient littermate mice.

Sample_geo_accession	GSM574343
Sample_status	Public on Nov 12 2011
Sample_submission_date	Aug 04 2010
Sample_last_update_date	Nov 12 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Colitis was induced with 2.5% dextran sodium sulfate (DSS), 36,000–44,000 mol wt (ICN Biomedicals, Aurora, OH) in the drinking water. After the DSS challenge mice were weighed on a daily basis and examined for clinical signs of disease associated with colitis (i.e., perianal soiling, rectal bleeding, diarrhea, and piloerection). For the DSS challenge, the disease activity indices and rectal bleeding scores were calculated using a modification of a previously published compounded clinical score. Briefly, disease activity index consisted of a scoring for diarrhea and lethargy, whereas rectal bleeding consisted of a visual observation of blood in feces and the perianal area. Mice in the DSS study were euthanized on day 7 of the DSS challenge by CO2 asphyxiation and blood was withdrawn from the heart. Colons and spleens were scored based on size and macroscopic inflammatory lesions.
Sample_growth_protocol_ch1	Six- to eight-week-old PPAR gamma flfl Cre+ mice, with a Cre recombinase targeted to the LysM promoter, and control Cre- littermates (n=20) were housed at the animal facilities at Virginia Polytechnic Institute and State University in a room maintained at 75 F, with a 12:12 h light-dark cycle starting from 6:00 AM. All experimental procedures were approved by the Institutional Animal Care and Use Committee of Virginia Polytechnic Institute and State University and met or exceeded requirements of the Public Health Service/National Institutes of Health and the Animal Welfare Act.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Whole colonic tissue was collected from mice and preserved in RNAlater® (Applied Biosystems/Ambion Foster City, CA). After homogenization, total RNA was extracted and purified using the RNAeasy system according to manufacturer's instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	According to Affymetrix standard method.
Sample_hyb_protocol	According to Affymetrix standard method.
Sample_scan_protocol	According to Affymetrix standard method.
Sample_data_processing	gcRMA normalized by using Bioconductor package 'gcrma' in R 2.8.
Sample_platform_id	GPL1261
Sample_contact_name	Maria,,Salvato
Sample_contact_email	MSalvato@ihv.umaryland.edu
Sample_contact_phone	410-706-1368
Sample_contact_fax	410-706-5198
Sample_contact_laboratory	Rm 510
Sample_contact_department	Institute of Human Virology
Sample_contact_institute	University of Maryland School of Medicine
Sample_contact_address	725 W Lombard Street
Sample_contact_city	Baltimore
Sample_contact_state	MD
Sample_contact_zip/postal_code	21201
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574343/suppl/GSM574343.CEL.gz
Sample_series_id	GSE23421
Sample_data_row_count	45101

GSM574344

GPL1261

colonic tissue from macrophage-specific PPARgamma-deficient mouse, biological rep2

colon from macrophage-specific PPARg-deficient mouse

strain: C57BL/6 tissue: colon genotype: PPAR g fl/fl; Lysozyme M cre+ phenotype: PPAR gamma deficient treatment: dextran sodium sulfate (DSS)

mut22 Gene expression data from colon of PPARr-deficient littermate mice.

Sample_geo_accession	GSM574344
Sample_status	Public on Nov 12 2011
Sample_submission_date	Aug 04 2010
Sample_last_update_date	Nov 12 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Colitis was induced with 2.5% dextran sodium sulfate (DSS), 36,000–44,000 mol wt (ICN Biomedicals, Aurora, OH) in the drinking water. After the DSS challenge mice were weighed on a daily basis and examined for clinical signs of disease associated with colitis (i.e., perianal soiling, rectal bleeding, diarrhea, and piloerection). For the DSS challenge, the disease activity indices and rectal bleeding scores were calculated using a modification of a previously published compounded clinical score. Briefly, disease activity index consisted of a scoring for diarrhea and lethargy, whereas rectal bleeding consisted of a visual observation of blood in feces and the perianal area. Mice in the DSS study were euthanized on day 7 of the DSS challenge by CO2 asphyxiation and blood was withdrawn from the heart. Colons and spleens were scored based on size and macroscopic inflammatory lesions.
Sample_growth_protocol_ch1	Six- to eight-week-old PPAR gamma flfl Cre+ mice, with a Cre recombinase targeted to the LysM promoter, and control Cre- littermates (n=20) were housed at the animal facilities at Virginia Polytechnic Institute and State University in a room maintained at 75 F, with a 12:12 h light-dark cycle starting from 6:00 AM. All experimental procedures were approved by the Institutional Animal Care and Use Committee of Virginia Polytechnic Institute and State University and met or exceeded requirements of the Public Health Service/National Institutes of Health and the Animal Welfare Act.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Whole colonic tissue was collected from mice and preserved in RNAlater® (Applied Biosystems/Ambion Foster City, CA). After homogenization, total RNA was extracted and purified using the RNAeasy system according to manufacturer's instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	According to Affymetrix standard method.
Sample_hyb_protocol	According to Affymetrix standard method.
Sample_scan_protocol	According to Affymetrix standard method.
Sample_data_processing	gcRMA normalized by using Bioconductor package 'gcrma' in R 2.8.
Sample_platform_id	GPL1261
Sample_contact_name	Maria,,Salvato
Sample_contact_email	MSalvato@ihv.umaryland.edu
Sample_contact_phone	410-706-1368
Sample_contact_fax	410-706-5198
Sample_contact_laboratory	Rm 510
Sample_contact_department	Institute of Human Virology
Sample_contact_institute	University of Maryland School of Medicine
Sample_contact_address	725 W Lombard Street
Sample_contact_city	Baltimore
Sample_contact_state	MD
Sample_contact_zip/postal_code	21201
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574344/suppl/GSM574344.CEL.gz
Sample_series_id	GSE23421
Sample_data_row_count	45101

GSM574345

GPL1261

colonic tissue from macrophage-specific PPARgamma-deficient mouse, biological rep3

colon from macrophage-specific PPARg-deficient mouse

strain: C57BL/6 tissue: colon genotype: PPAR g fl/fl; Lysozyme M cre+ phenotype: PPAR gamma deficient treatment: dextran sodium sulfate (DSS)

mut25 Gene expression data from colon of PPARr-deficient littermate mice.

Sample_geo_accession	GSM574345
Sample_status	Public on Nov 12 2011
Sample_submission_date	Aug 04 2010
Sample_last_update_date	Nov 12 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Colitis was induced with 2.5% dextran sodium sulfate (DSS), 36,000–44,000 mol wt (ICN Biomedicals, Aurora, OH) in the drinking water. After the DSS challenge mice were weighed on a daily basis and examined for clinical signs of disease associated with colitis (i.e., perianal soiling, rectal bleeding, diarrhea, and piloerection). For the DSS challenge, the disease activity indices and rectal bleeding scores were calculated using a modification of a previously published compounded clinical score. Briefly, disease activity index consisted of a scoring for diarrhea and lethargy, whereas rectal bleeding consisted of a visual observation of blood in feces and the perianal area. Mice in the DSS study were euthanized on day 7 of the DSS challenge by CO2 asphyxiation and blood was withdrawn from the heart. Colons and spleens were scored based on size and macroscopic inflammatory lesions.
Sample_growth_protocol_ch1	Six- to eight-week-old PPAR gamma flfl Cre+ mice, with a Cre recombinase targeted to the LysM promoter, and control Cre- littermates (n=20) were housed at the animal facilities at Virginia Polytechnic Institute and State University in a room maintained at 75 F, with a 12:12 h light-dark cycle starting from 6:00 AM. All experimental procedures were approved by the Institutional Animal Care and Use Committee of Virginia Polytechnic Institute and State University and met or exceeded requirements of the Public Health Service/National Institutes of Health and the Animal Welfare Act.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Whole colonic tissue was collected from mice and preserved in RNAlater® (Applied Biosystems/Ambion Foster City, CA). After homogenization, total RNA was extracted and purified using the RNAeasy system according to manufacturer's instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	According to Affymetrix standard method.
Sample_hyb_protocol	According to Affymetrix standard method.
Sample_scan_protocol	According to Affymetrix standard method.
Sample_data_processing	gcRMA normalized by using Bioconductor package 'gcrma' in R 2.8.
Sample_platform_id	GPL1261
Sample_contact_name	Maria,,Salvato
Sample_contact_email	MSalvato@ihv.umaryland.edu
Sample_contact_phone	410-706-1368
Sample_contact_fax	410-706-5198
Sample_contact_laboratory	Rm 510
Sample_contact_department	Institute of Human Virology
Sample_contact_institute	University of Maryland School of Medicine
Sample_contact_address	725 W Lombard Street
Sample_contact_city	Baltimore
Sample_contact_state	MD
Sample_contact_zip/postal_code	21201
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM574nnn/GSM574345/suppl/GSM574345.CEL.gz
Sample_series_id	GSE23421
Sample_data_row_count	45101

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