Result

Search results for the GEO ID: GSE10658

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM269602

GPL1261

TG_pool

small intestine from IL-9 transgenic mice

small intestine, IL-9 transgenic mice

small intestine of a pool of three Wt mice and a pool of 3 IL-9tg mice in a balb/c backround

Sample_geo_accession	GSM269602
Sample_status	Public on Mar 01 2008
Sample_submission_date	Feb 27 2008
Sample_last_update_date	Mar 03 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	none
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	trizol (invitrogen)
Sample_extract_protocol_ch1	Quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
Sample_label_ch1	biotin
Sample_label_protocol_ch1	10ug of total RNA from 1 pool of 3 wild type [WT] mice and 1 pool of 3 Il-9 Transgenic mice were amplified and cRNA was labeled with biotin-UTP, CTP using T7 RNA polymerase
Sample_hyb_protocol	Full Protocol Description: Create a hybridization cocktail for a single probe array that contains 0.067 mg/mL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 99°C for 5 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 mL of 1X Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 mL of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization Oven rotating at 60 rpm.
Sample_hyb_protocol	Fluidics: Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol EukGE-WS2v5_450. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.
Sample_scan_protocol	Images were scanned using a GeneChip scanner 3000 [Affymetrix]
Sample_data_processing	Affymetrix murine MOE 430 2.0 gene chips were used.GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.1.
Sample_data_processing	Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
Sample_data_processing	GeneSpring GX (Agilent technologies Inc. Palo Alto, California) was used in normalization, Clustering and filtering. Individual clusters were then analyzed for functional relatedness of genes within the cluster using David 2.0 (http://david.abcc.ncifcrf.gov/summary.jsp).
Sample_platform_id	GPL1261
Sample_contact_name	Simon,,Hogan
Sample_contact_email	Simon.Hogan@cchmc.org
Sample_contact_phone	513-636-6620
Sample_contact_fax	513-636-3310
Sample_contact_laboratory	Hogan's lab
Sample_contact_department	Allergy and Immunology
Sample_contact_institute	Cincinnati Children's Hospital
Sample_contact_address	3333 burnet avenue
Sample_contact_city	Cincinnati
Sample_contact_state	OH
Sample_contact_zip/postal_code	45229
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM269nnn/GSM269602/suppl/GSM269602.CEL.gz
Sample_series_id	GSE10658
Sample_data_row_count	45101

GSM269603

GPL1261

WT_pool

small intestine from WT mice

small intestine, WT mice

small intestine of a pool of three Wt mice and a pool of 3 IL-9tg mice in a balb/c backround

Sample_geo_accession	GSM269603
Sample_status	Public on Mar 01 2008
Sample_submission_date	Feb 27 2008
Sample_last_update_date	Mar 03 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	none
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	trizol (invitrogen)
Sample_extract_protocol_ch1	Quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].
Sample_label_ch1	biotin
Sample_label_protocol_ch1	10ug of total RNA from 1 pool of 3 wild type [WT] mice and 1 pool of 3 Il-9 Transgenic mice were amplified and cRNA was labeled with biotin-UTP, CTP using T7 RNA polymerase
Sample_hyb_protocol	Full Protocol Description: Create a hybridization cocktail for a single probe array that contains 0.067 mg/mL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 99°C for 5 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 mL of 1X Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 mL of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization Oven rotating at 60 rpm.
Sample_hyb_protocol	Fluidics: Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol EukGE-WS2v5_450. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.
Sample_scan_protocol	Images were scanned using a GeneChip scanner 3000 [Affymetrix]
Sample_data_processing	Affymetrix murine MOE 430 2.0 gene chips were used.GeneChip CEL files were subjected to RMA normalization using the GeneSpring GX 7.1.
Sample_data_processing	Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine the hybridization of target RNA to the array occurred properly.
Sample_data_processing	GeneSpring GX (Agilent technologies Inc. Palo Alto, California) was used in normalization, Clustering and filtering. Individual clusters were then analyzed for functional relatedness of genes within the cluster using David 2.0 (http://david.abcc.ncifcrf.gov/summary.jsp).
Sample_platform_id	GPL1261
Sample_contact_name	Simon,,Hogan
Sample_contact_email	Simon.Hogan@cchmc.org
Sample_contact_phone	513-636-6620
Sample_contact_fax	513-636-3310
Sample_contact_laboratory	Hogan's lab
Sample_contact_department	Allergy and Immunology
Sample_contact_institute	Cincinnati Children's Hospital
Sample_contact_address	3333 burnet avenue
Sample_contact_city	Cincinnati
Sample_contact_state	OH
Sample_contact_zip/postal_code	45229
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM269nnn/GSM269603/suppl/GSM269603.CEL.gz
Sample_series_id	GSE10658
Sample_data_row_count	45101

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