Result

Search results for the GEO ID: GSE33106

(Click on the check boxes provided under "Select for analysis", to initiate grouping)

(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down)

GSM ID

GPL ID

Select for analysis

Title

Source name

Description

Characteristics

GSM819919

GPL1261

liver from wildtype mouse embryo at 17dpc, biological rep1

liver in wildtype mouse embryo

tissue: liver strain: C57BL/6 (B6) genotype/variation: wildtype gestational stage: day 17 of pregnancy

Gene expression data from liver in wildtype mouse at 17dpc Mouse_WT-1 080207_WT.CEL

Sample_geo_accession	GSM819919
Sample_status	Public on Jan 09 2013
Sample_submission_date	Oct 20 2011
Sample_last_update_date	Jan 09 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	On gestation day 17, female mice were sacrificed and liver with biliary system collected. Liver tissues were dissected from liver with biliary system.
Sample_growth_protocol_ch1	Virgin female mice 6–8 wk of age for C57BL6 strain were cohabited with adult Sox17+/- males (>3 mo of age) of the same strain. Mating was assessed by daily vaginal plug check. The presence of the vaginal plug was considered as day 0.5 of pregnancy.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was quantified by spectrophotometry (nano drop 2000 ThermoScientific) and quality was verified using spectrophotometry (nano drop 2000 Thermo Scientific).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	RNA samples were hybridized to Affymetrix Mouse 430 2.0 DNA microarray chips using the GeneChip® Hybridization Oven 640 (Affymetrix,Clara, CA). Washing and staining of the hybridized chips were conducted using the GeneChip® Fluidics Station 450 (Affymetrix). Santa
Sample_scan_protocol	Chips were scanned using the Affymetrix GeneChip® Scanner 3000 (Affymetrix) with autoloader.
Sample_data_processing	Expression data sets were analyzed using the R statistics software (http://www.r-project.org/) with BioConductor software (http://www.bioconductor.org/) packages. The MAS5 method from the BioConductor software was used for background correction and normalization of the DNA microarray data.
Sample_platform_id	GPL1261
Sample_contact_name	Mami,,Uemura
Sample_contact_email	3144527465@mail.ecc.u-tokyo.ac.jp
Sample_contact_phone	03-5841-5384
Sample_contact_fax	03-5841-8181
Sample_contact_department	Veterinary Anatomy
Sample_contact_institute	The University of Tokyo
Sample_contact_address	Yayoi 1-1-1, Bunkyo-ku
Sample_contact_city	Tokyo
Sample_contact_zip/postal_code	113-8657
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM819nnn/GSM819919/suppl/GSM819919.CEL.gz
Sample_series_id	GSE33106
Sample_data_row_count	45101

GSM819920

GPL1261

liver from wildtype mouse embryo at 17dpc, biological rep2

liver in wildtype mouse embryo

tissue: liver strain: C57BL/6 (B6) genotype/variation: wildtype gestational stage: day 17 of pregnancy

Gene expression data from liver in wildtype mouse at 17dpc Mouse_WT-2 080418-WT.CEL

Sample_geo_accession	GSM819920
Sample_status	Public on Jan 09 2013
Sample_submission_date	Oct 20 2011
Sample_last_update_date	Jan 09 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	On gestation day 17, female mice were sacrificed and liver with biliary system collected. Liver tissues were dissected from liver with biliary system.
Sample_growth_protocol_ch1	Virgin female mice 6–8 wk of age for C57BL6 strain were cohabited with adult Sox17+/- males (>3 mo of age) of the same strain. Mating was assessed by daily vaginal plug check. The presence of the vaginal plug was considered as day 0.5 of pregnancy.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was quantified by spectrophotometry (nano drop 2000 ThermoScientific) and quality was verified using spectrophotometry (nano drop 2000 Thermo Scientific).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	RNA samples were hybridized to Affymetrix Mouse 430 2.0 DNA microarray chips using the GeneChip® Hybridization Oven 640 (Affymetrix,Clara, CA). Washing and staining of the hybridized chips were conducted using the GeneChip® Fluidics Station 450 (Affymetrix). Santa
Sample_scan_protocol	Chips were scanned using the Affymetrix GeneChip® Scanner 3000 (Affymetrix) with autoloader.
Sample_data_processing	Expression data sets were analyzed using the R statistics software (http://www.r-project.org/) with BioConductor software (http://www.bioconductor.org/) packages. The MAS5 method from the BioConductor software was used for background correction and normalization of the DNA microarray data.
Sample_platform_id	GPL1261
Sample_contact_name	Mami,,Uemura
Sample_contact_email	3144527465@mail.ecc.u-tokyo.ac.jp
Sample_contact_phone	03-5841-5384
Sample_contact_fax	03-5841-8181
Sample_contact_department	Veterinary Anatomy
Sample_contact_institute	The University of Tokyo
Sample_contact_address	Yayoi 1-1-1, Bunkyo-ku
Sample_contact_city	Tokyo
Sample_contact_zip/postal_code	113-8657
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM819nnn/GSM819920/suppl/GSM819920.CEL.gz
Sample_series_id	GSE33106
Sample_data_row_count	45101

GSM819921

GPL1261

liver from Sox17+/- mouse embryo at 17dpc, biological rep1

liver in sox17+/- mouse embryo

tissue: liver strain: C57BL/6 (B6) genotype/variation: sox17+/- gestational stage: day 17 of pregnancy

Gene expression data from liver in Sox17+/- mouse at 17dpc Mouse_MUT-1 080207_MU.CEL

Sample_geo_accession	GSM819921
Sample_status	Public on Jan 09 2013
Sample_submission_date	Oct 20 2011
Sample_last_update_date	Jan 09 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	On gestation day 17, female mice were sacrificed and liver with biliary system collected. Liver tissues were dissected from liver with biliary system.
Sample_growth_protocol_ch1	Virgin female mice 6–8 wk of age for C57BL6 strain were cohabited with adult Sox17+/- males (>3 mo of age) of the same strain. Mating was assessed by daily vaginal plug check. The presence of the vaginal plug was considered as day 0.5 of pregnancy.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was quantified by spectrophotometry (nano drop 2000 ThermoScientific) and quality was verified using spectrophotometry (nano drop 2000 Thermo Scientific).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	RNA samples were hybridized to Affymetrix Mouse 430 2.0 DNA microarray chips using the GeneChip® Hybridization Oven 640 (Affymetrix,Clara, CA). Washing and staining of the hybridized chips were conducted using the GeneChip® Fluidics Station 450 (Affymetrix). Santa
Sample_scan_protocol	Chips were scanned using the Affymetrix GeneChip® Scanner 3000 (Affymetrix) with autoloader.
Sample_data_processing	Expression data sets were analyzed using the R statistics software (http://www.r-project.org/) with BioConductor software (http://www.bioconductor.org/) packages. The MAS5 method from the BioConductor software was used for background correction and normalization of the DNA microarray data.
Sample_platform_id	GPL1261
Sample_contact_name	Mami,,Uemura
Sample_contact_email	3144527465@mail.ecc.u-tokyo.ac.jp
Sample_contact_phone	03-5841-5384
Sample_contact_fax	03-5841-8181
Sample_contact_department	Veterinary Anatomy
Sample_contact_institute	The University of Tokyo
Sample_contact_address	Yayoi 1-1-1, Bunkyo-ku
Sample_contact_city	Tokyo
Sample_contact_zip/postal_code	113-8657
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM819nnn/GSM819921/suppl/GSM819921.CEL.gz
Sample_series_id	GSE33106
Sample_data_row_count	45101

GSM819922

GPL1261

liver from Sox17+/- mouse embryo at 17dpc, biological rep2

liver in sox17+/- mouse embryo

tissue: liver strain: C57BL/6 (B6) genotype/variation: sox17+/- gestational stage: day 17 of pregnancy

Gene expression data from liver in Sox17+/- mouse at 17dpc Mouse_MUT-2 080418-Mts.CEL

Sample_geo_accession	GSM819922
Sample_status	Public on Jan 09 2013
Sample_submission_date	Oct 20 2011
Sample_last_update_date	Jan 09 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	On gestation day 17, female mice were sacrificed and liver with biliary system collected. Liver tissues were dissected from liver with biliary system.
Sample_growth_protocol_ch1	Virgin female mice 6–8 wk of age for C57BL6 strain were cohabited with adult Sox17+/- males (>3 mo of age) of the same strain. Mating was assessed by daily vaginal plug check. The presence of the vaginal plug was considered as day 0.5 of pregnancy.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was quantified by spectrophotometry (nano drop 2000 ThermoScientific) and quality was verified using spectrophotometry (nano drop 2000 Thermo Scientific).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	RNA samples were hybridized to Affymetrix Mouse 430 2.0 DNA microarray chips using the GeneChip® Hybridization Oven 640 (Affymetrix,Clara, CA). Washing and staining of the hybridized chips were conducted using the GeneChip® Fluidics Station 450 (Affymetrix). Santa
Sample_scan_protocol	Chips were scanned using the Affymetrix GeneChip® Scanner 3000 (Affymetrix) with autoloader.
Sample_data_processing	Expression data sets were analyzed using the R statistics software (http://www.r-project.org/) with BioConductor software (http://www.bioconductor.org/) packages. The MAS5 method from the BioConductor software was used for background correction and normalization of the DNA microarray data.
Sample_platform_id	GPL1261
Sample_contact_name	Mami,,Uemura
Sample_contact_email	3144527465@mail.ecc.u-tokyo.ac.jp
Sample_contact_phone	03-5841-5384
Sample_contact_fax	03-5841-8181
Sample_contact_department	Veterinary Anatomy
Sample_contact_institute	The University of Tokyo
Sample_contact_address	Yayoi 1-1-1, Bunkyo-ku
Sample_contact_city	Tokyo
Sample_contact_zip/postal_code	113-8657
Sample_contact_country	Japan
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM819nnn/GSM819922/suppl/GSM819922.CEL.gz
Sample_series_id	GSE33106
Sample_data_row_count	45101

Make groups for comparisons

(2 groups will be compared at a time)

Select GSMs and click on "Add groups"

Enter the group name here:

Select expression type

Transcripts profile based on;

A. Differential status (Up/Down regulation)

B. Absolute calls (Transcribed/Not-detected)

Filter results by number of probes