Result

Search results for the GEO ID: GSE16623

(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

GSM417399

GPL1261

WT biological replicate 1

WT kidneys

gender: male age: 2-3 months tissue: kidney genotype: WT

IG080507VGE023-2_01

Sample_geo_accession	GSM417399
Sample_status	Public on Apr 11 2010
Sample_submission_date	Jun 15 2009
Sample_last_update_date	Apr 11 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Left and right kidneys were removed, snap frozen in liquid nitrogen and stored at -80C. Before RNA isolation, both kidneys were ground together in liquid nitrogen using a frozen mortar and pestle.
Sample_growth_protocol_ch1	Mice were housed in standard conditions (12h light-dark, ad libitum standard diet and water).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNeasy midi RNA extraction kit was used according to manufacturer protocol.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Target RNA was reverse transcribed into cDNA, and in-vitro transcription was performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA was stained with streptavidin phycoerythrin. Performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.
Sample_hyb_protocol	Standard protocols were performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.
Sample_scan_protocol	Arrays were scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the array. Performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.
Sample_data_processing	The data were analyzed with Genespring GX (Agilent) using RMA normalization method and statistical analysis was done using unpaired Students' t-test and asymptotic p-value computation.
Sample_platform_id	GPL1261
Sample_contact_name	Vincent,,Giguere
Sample_contact_email	vincent.giguere@mcgill.ca
Sample_contact_phone	514-398-5899
Sample_contact_fax	514-398-6769
Sample_contact_laboratory	Vincent Giguere
Sample_contact_department	Biochemistry
Sample_contact_institute	McGill University
Sample_contact_address	1160 Pine avenue West
Sample_contact_city	Montreal
Sample_contact_state	Quebec
Sample_contact_zip/postal_code	H3A 1A3
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417399/suppl/GSM417399.CEL.gz
Sample_series_id	GSE16623
Sample_data_row_count	45101

GSM417400

GPL1261

WT biological replicate 2

WT kidneys

gender: male age: 2-3 months tissue: kidney genotype: WT

IG080507VGE024-2_01

Sample_geo_accession	GSM417400
Sample_status	Public on Apr 11 2010
Sample_submission_date	Jun 15 2009
Sample_last_update_date	Apr 11 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Left and right kidneys were removed, snap frozen in liquid nitrogen and stored at -80C. Before RNA isolation, both kidneys were ground together in liquid nitrogen using a frozen mortar and pestle.
Sample_growth_protocol_ch1	Mice were housed in standard conditions (12h light-dark, ad libitum standard diet and water).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNeasy midi RNA extraction kit was used according to manufacturer protocol.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Target RNA was reverse transcribed into cDNA, and in-vitro transcription was performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA was stained with streptavidin phycoerythrin. Performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.
Sample_hyb_protocol	Standard protocols were performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.
Sample_scan_protocol	Arrays were scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the array. Performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.
Sample_data_processing	The data were analyzed with Genespring GX (Agilent) using RMA normalization method and statistical analysis was done using unpaired Students' t-test and asymptotic p-value computation.
Sample_platform_id	GPL1261
Sample_contact_name	Vincent,,Giguere
Sample_contact_email	vincent.giguere@mcgill.ca
Sample_contact_phone	514-398-5899
Sample_contact_fax	514-398-6769
Sample_contact_laboratory	Vincent Giguere
Sample_contact_department	Biochemistry
Sample_contact_institute	McGill University
Sample_contact_address	1160 Pine avenue West
Sample_contact_city	Montreal
Sample_contact_state	Quebec
Sample_contact_zip/postal_code	H3A 1A3
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417400/suppl/GSM417400.CEL.gz
Sample_series_id	GSE16623
Sample_data_row_count	45101

GSM417401

GPL1261

WT biological replicate 3

WT kidneys

gender: male age: 2-3 months tissue: kidney genotype: WT

IG080507VGE025-2_01

Sample_geo_accession	GSM417401
Sample_status	Public on Apr 11 2010
Sample_submission_date	Jun 15 2009
Sample_last_update_date	Apr 11 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Left and right kidneys were removed, snap frozen in liquid nitrogen and stored at -80C. Before RNA isolation, both kidneys were ground together in liquid nitrogen using a frozen mortar and pestle.
Sample_growth_protocol_ch1	Mice were housed in standard conditions (12h light-dark, ad libitum standard diet and water).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNeasy midi RNA extraction kit was used according to manufacturer protocol.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Target RNA was reverse transcribed into cDNA, and in-vitro transcription was performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA was stained with streptavidin phycoerythrin. Performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.
Sample_hyb_protocol	Standard protocols were performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.
Sample_scan_protocol	Arrays were scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the array. Performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.
Sample_data_processing	The data were analyzed with Genespring GX (Agilent) using RMA normalization method and statistical analysis was done using unpaired Students' t-test and asymptotic p-value computation.
Sample_platform_id	GPL1261
Sample_contact_name	Vincent,,Giguere
Sample_contact_email	vincent.giguere@mcgill.ca
Sample_contact_phone	514-398-5899
Sample_contact_fax	514-398-6769
Sample_contact_laboratory	Vincent Giguere
Sample_contact_department	Biochemistry
Sample_contact_institute	McGill University
Sample_contact_address	1160 Pine avenue West
Sample_contact_city	Montreal
Sample_contact_state	Quebec
Sample_contact_zip/postal_code	H3A 1A3
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417401/suppl/GSM417401.CEL.gz
Sample_series_id	GSE16623
Sample_data_row_count	45101

GSM417402

GPL1261

ERRa KO biological replicate 1

ERRa KO kidneys

gender: male age: 2-3 months tissue: kidney genotype: ERRa KO

IG080507VGE026-2_01

Sample_geo_accession	GSM417402
Sample_status	Public on Apr 11 2010
Sample_submission_date	Jun 15 2009
Sample_last_update_date	Apr 11 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Left and right kidneys were removed, snap frozen in liquid nitrogen and stored at -80C. Before RNA isolation, both kidneys were ground together in liquid nitrogen using a frozen mortar and pestle.
Sample_growth_protocol_ch1	Mice were housed in standard conditions (12h light-dark, ad libitum standard diet and water).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNeasy midi RNA extraction kit was used according to manufacturer protocol.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Target RNA was reverse transcribed into cDNA, and in-vitro transcription was performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA was stained with streptavidin phycoerythrin. Performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.
Sample_hyb_protocol	Standard protocols were performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.
Sample_scan_protocol	Arrays were scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the array. Performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.
Sample_data_processing	The data were analyzed with Genespring GX (Agilent) using RMA normalization method and statistical analysis was done using unpaired Students' t-test and asymptotic p-value computation.
Sample_platform_id	GPL1261
Sample_contact_name	Vincent,,Giguere
Sample_contact_email	vincent.giguere@mcgill.ca
Sample_contact_phone	514-398-5899
Sample_contact_fax	514-398-6769
Sample_contact_laboratory	Vincent Giguere
Sample_contact_department	Biochemistry
Sample_contact_institute	McGill University
Sample_contact_address	1160 Pine avenue West
Sample_contact_city	Montreal
Sample_contact_state	Quebec
Sample_contact_zip/postal_code	H3A 1A3
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417402/suppl/GSM417402.CEL.gz
Sample_series_id	GSE16623
Sample_data_row_count	45101

GSM417403

GPL1261

ERRa KO biological replicate 2

ERRa KO kidneys

gender: male age: 2-3 months tissue: kidney genotype: ERRa KO

IG080507VGE027-2_01

Sample_geo_accession	GSM417403
Sample_status	Public on Apr 11 2010
Sample_submission_date	Jun 15 2009
Sample_last_update_date	Apr 11 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Left and right kidneys were removed, snap frozen in liquid nitrogen and stored at -80C. Before RNA isolation, both kidneys were ground together in liquid nitrogen using a frozen mortar and pestle.
Sample_growth_protocol_ch1	Mice were housed in standard conditions (12h light-dark, ad libitum standard diet and water).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNeasy midi RNA extraction kit was used according to manufacturer protocol.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Target RNA was reverse transcribed into cDNA, and in-vitro transcription was performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA was stained with streptavidin phycoerythrin. Performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.
Sample_hyb_protocol	Standard protocols were performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.
Sample_scan_protocol	Arrays were scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the array. Performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.
Sample_data_processing	The data were analyzed with Genespring GX (Agilent) using RMA normalization method and statistical analysis was done using unpaired Students' t-test and asymptotic p-value computation.
Sample_platform_id	GPL1261
Sample_contact_name	Vincent,,Giguere
Sample_contact_email	vincent.giguere@mcgill.ca
Sample_contact_phone	514-398-5899
Sample_contact_fax	514-398-6769
Sample_contact_laboratory	Vincent Giguere
Sample_contact_department	Biochemistry
Sample_contact_institute	McGill University
Sample_contact_address	1160 Pine avenue West
Sample_contact_city	Montreal
Sample_contact_state	Quebec
Sample_contact_zip/postal_code	H3A 1A3
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417403/suppl/GSM417403.CEL.gz
Sample_series_id	GSE16623
Sample_data_row_count	45101

GSM417404

GPL1261

ERRa KO biological replicate 3

ERRa KO kidneys

gender: male age: 2-3 months tissue: kidney genotype: ERRa KO

IG080507VGE028-2_01

Sample_geo_accession	GSM417404
Sample_status	Public on Apr 11 2010
Sample_submission_date	Jun 15 2009
Sample_last_update_date	Apr 11 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Left and right kidneys were removed, snap frozen in liquid nitrogen and stored at -80C. Before RNA isolation, both kidneys were ground together in liquid nitrogen using a frozen mortar and pestle.
Sample_growth_protocol_ch1	Mice were housed in standard conditions (12h light-dark, ad libitum standard diet and water).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNeasy midi RNA extraction kit was used according to manufacturer protocol.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Target RNA was reverse transcribed into cDNA, and in-vitro transcription was performed to generate biotin-labeled cRNA for subsequent hybridization. Hybridized target cRNA was stained with streptavidin phycoerythrin. Performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.
Sample_hyb_protocol	Standard protocols were performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.
Sample_scan_protocol	Arrays were scanned using a GeneArray Scanner at an excitation wavelength of 488nm. Light emissions at 570nm are proportional to the bound target at each oligonucleotides position on the array. Performed at The Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre.
Sample_data_processing	The data were analyzed with Genespring GX (Agilent) using RMA normalization method and statistical analysis was done using unpaired Students' t-test and asymptotic p-value computation.
Sample_platform_id	GPL1261
Sample_contact_name	Vincent,,Giguere
Sample_contact_email	vincent.giguere@mcgill.ca
Sample_contact_phone	514-398-5899
Sample_contact_fax	514-398-6769
Sample_contact_laboratory	Vincent Giguere
Sample_contact_department	Biochemistry
Sample_contact_institute	McGill University
Sample_contact_address	1160 Pine avenue West
Sample_contact_city	Montreal
Sample_contact_state	Quebec
Sample_contact_zip/postal_code	H3A 1A3
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM417nnn/GSM417404/suppl/GSM417404.CEL.gz
Sample_series_id	GSE16623
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