Result

Search results for the GEO ID: GSE31465

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Title

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Description

Characteristics

GSM781933

GPL1261

CD34+ tumor epithelial cells from wild-type mouse

CD34+ wild type

genotype: wild-type

hyb10567.CEL

Sample_geo_accession	GSM781933
Sample_status	Public on Sep 07 2011
Sample_submission_date	Aug 18 2011
Sample_last_update_date	Sep 07 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	wild type or K14CreER:Rosa-VEGF-164 mice were treated with DMBA at postnatal day 23, 25 and 27 with DMBA (9,10-dimethyl-1,2-benzanthracene) and then treated twice, weekly for several weeks with TPA (12-O-tetradecanoyl phorbol-13-acetate). 7 weeks old mice were treated again twice with DMBA.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Microprep kit, RNeasy, Stratagene
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
Sample_hyb_protocol	A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix MOE 430 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
Sample_scan_protocol	To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
Sample_data_processing	Data processing was done in the R programming environment, in conjunction with the packages developed within the Bioconductor project (http://www.bioconductor.org; Gentleman et al., 2004). Cel-files were processed according to the MAS5.0 algorithm as implemented in the 'simpleaffy' package.
Sample_platform_id	GPL1261
Sample_contact_name	Benjamin,,Beck
Sample_contact_email	g_driessens@hotmail.com
Sample_contact_department	IRIBHM
Sample_contact_institute	ULB
Sample_contact_address	Route de Lennik 808
Sample_contact_city	Brussels
Sample_contact_zip/postal_code	1070
Sample_contact_country	Belgium
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM781nnn/GSM781933/suppl/GSM781933.CEL.gz
Sample_series_id	GSE31465
Sample_data_row_count	45101

GSM781934

GPL1261

CD34+ tumor epithelial cells from VEGF gain of function mouse

CD34+ VEGF

genotype: K14CreER:Rosa-VEGF-164

hyb10568.CEL

Sample_geo_accession	GSM781934
Sample_status	Public on Sep 07 2011
Sample_submission_date	Aug 18 2011
Sample_last_update_date	Sep 07 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	wild type or K14CreER:Rosa-VEGF-164 mice were treated with DMBA at postnatal day 23, 25 and 27 with DMBA (9,10-dimethyl-1,2-benzanthracene) and then treated twice, weekly for several weeks with TPA (12-O-tetradecanoyl phorbol-13-acetate). 7 weeks old mice were treated again twice with DMBA.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Microprep kit, RNeasy, Stratagene
Sample_label_ch1	biotin
Sample_label_protocol_ch1	RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).
Sample_hyb_protocol	A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix MOE 430 2.0 arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.
Sample_scan_protocol	To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).
Sample_data_processing	Data processing was done in the R programming environment, in conjunction with the packages developed within the Bioconductor project (http://www.bioconductor.org; Gentleman et al., 2004). Cel-files were processed according to the MAS5.0 algorithm as implemented in the 'simpleaffy' package.
Sample_platform_id	GPL1261
Sample_contact_name	Benjamin,,Beck
Sample_contact_email	g_driessens@hotmail.com
Sample_contact_department	IRIBHM
Sample_contact_institute	ULB
Sample_contact_address	Route de Lennik 808
Sample_contact_city	Brussels
Sample_contact_zip/postal_code	1070
Sample_contact_country	Belgium
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM781nnn/GSM781934/suppl/GSM781934.CEL.gz
Sample_series_id	GSE31465
Sample_data_row_count	45101

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