Result

Search results for the GEO ID: GSE12748

(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

GSM319519

GPL1261

dol_1_liver_wildtype1

liver_wildtype

Strain: C57BL/6J Gender: male Age: day of life 1 Tissue: liver

Further details are available at www.affymetrix.com.

Sample_geo_accession	GSM319519
Sample_status	Public on Sep 10 2009
Sample_submission_date	Sep 10 2008
Sample_last_update_date	Sep 12 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Age-matched wiltype littermates of glycerol kinase knockout mice
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from one wildtype liver was isolated individually using TRIzol Reagent (Invitrogen Life Technologies) and purified using RNeasy MiniElute Cleanup Kit (Qiagen Inc., Chatsworth, CA, USA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized from the poly(A) mRNA present in the isolated total RNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Life Technologies) and poly(T)-nucleotide primers. Biotin-tagged cRNA was generated using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY, USA) and fragmented to an average strand length of 100 bases (range 35–200 bases) following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).
Sample_hyb_protocol	Ten micrograms of cRNA was hybridized at 45 degrees C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 640) to an Affymetrix Mouse Genome 430 2.0 GeneChip as per the manufacturer’s instructions (Affymetrix, Inc.). The GeneChip arrays were washed and then stained with streptavidin–phycoerythrin on an Affymetrix Fluidics Station 450.
Sample_scan_protocol	Scanning was done on a GeneChipScanner 3000. Results were quantified and analyzed with GeneChip Operating Software (GCOS) 1.2 software (Affymetrix, Inc.) using default values (scaling, target signal intensity 500; normalization, all probe sets; parameters, all set at default values).
Sample_data_processing	Results were quantified and analyzed with GeneChip Operating Software (GCOS) 1.2 software (Affymetrix, Inc.) using default values (scaling, target signal intensity 500; normalization, all probe sets; parameters, all set at default values). We used Affymetrix GeneChip Mouse Expression set 430 2.0 Array which uses mouse maintenance genes for normalization. Details are available on the Affymetrix website (www.affymetrix.com/support/technical/mask_files.affx).
Sample_platform_id	GPL1261
Sample_contact_name	Nicole,Kim,MacLennan
Sample_contact_email	nmaclennan@mednet.ucla.edu
Sample_contact_phone	310-206-3050
Sample_contact_laboratory	McCabe
Sample_contact_department	Pediatrics
Sample_contact_institute	University of California, Los Angeles
Sample_contact_address	10833 LeConte Ave
Sample_contact_city	Los Angeles
Sample_contact_state	CA
Sample_contact_zip/postal_code	90095
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM319nnn/GSM319519/suppl/GSM319519.CEL.gz
Sample_series_id	GSE12748
Sample_data_row_count	45101

GSM319609

GPL1261

dol_1_liver_wildtype2

liver_wildtype

Strain: C57BL/6J Gender: male Age: day of life 1 Tissue: liver

Further details are available at www.affymetrix.com.

Sample_geo_accession	GSM319609
Sample_status	Public on Sep 10 2009
Sample_submission_date	Sep 10 2008
Sample_last_update_date	Sep 12 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Age-matched wiltype littermates of glycerol kinase knockout mice
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from one wildtype liver was isolated individually using TRIzol Reagent (Invitrogen Life Technologies) and purified using RNeasy MiniElute Cleanup Kit (Qiagen Inc., Chatsworth, CA, USA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized from the poly(A) mRNA present in the isolated total RNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Life Technologies) and poly(T)-nucleotide primers. Biotin-tagged cRNA was generated using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY, USA) and fragmented to an average strand length of 100 bases (range 35–200 bases) following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).
Sample_hyb_protocol	Ten micrograms of cRNA was hybridized at 45 degrees C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 640) to an Affymetrix Mouse Genome 430 2.0 GeneChip as per the manufacturer’s instructions (Affymetrix, Inc.). The GeneChip arrays were washed and then stained with streptavidin–phycoerythrin on an Affymetrix Fluidics Station 450.
Sample_scan_protocol	Scanning was done on a GeneChipScanner 3000. Results were quantified and analyzed with GeneChip Operating Software (GCOS) 1.2 software (Affymetrix, Inc.) using default values (scaling, target signal intensity 500; normalization, all probe sets; parameters, all set at default values).
Sample_data_processing	Results were quantified and analyzed with GeneChip Operating Software (GCOS) 1.2 software (Affymetrix, Inc.) using default values (scaling, target signal intensity 500; normalization, all probe sets; parameters, all set at default values). We used Affymetrix GeneChip Mouse Expression set 430 2.0 Array which uses mouse maintenance genes for normalization. Details are available on the Affymetrix website (www.affymetrix.com/support/technical/mask_files.affx).
Sample_platform_id	GPL1261
Sample_contact_name	Nicole,Kim,MacLennan
Sample_contact_email	nmaclennan@mednet.ucla.edu
Sample_contact_phone	310-206-3050
Sample_contact_laboratory	McCabe
Sample_contact_department	Pediatrics
Sample_contact_institute	University of California, Los Angeles
Sample_contact_address	10833 LeConte Ave
Sample_contact_city	Los Angeles
Sample_contact_state	CA
Sample_contact_zip/postal_code	90095
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM319nnn/GSM319609/suppl/GSM319609.CEL.gz
Sample_series_id	GSE12748
Sample_data_row_count	45101

GSM319903

GPL1261

dol_1_liver_wildtype3

liver_wildtype

Strain: C57BL/6J Gender: male Age: day of life 1 Tissue: liver

Further details are available at www.affymetrix.com.

Sample_geo_accession	GSM319903
Sample_status	Public on Sep 10 2009
Sample_submission_date	Sep 11 2008
Sample_last_update_date	Sep 12 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Age-matched wiltype littermates of glycerol kinase knockout mice
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from one wildtype liver was isolated individually using TRIzol Reagent (Invitrogen Life Technologies) and purified using RNeasy MiniElute Cleanup Kit (Qiagen Inc., Chatsworth, CA, USA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized from the poly(A) mRNA present in the isolated total RNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Life Technologies) and poly(T)-nucleotide primers. Biotin-tagged cRNA was generated using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY, USA) and fragmented to an average strand length of 100 bases (range 35–200 bases) following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).
Sample_hyb_protocol	Ten micrograms of cRNA was hybridized at 45 degrees C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 640) to an Affymetrix Mouse Genome 430 2.0 GeneChip as per the manufacturer’s instructions (Affymetrix, Inc.). The GeneChip arrays were washed and then stained with streptavidin–phycoerythrin on an Affymetrix Fluidics Station 450.
Sample_scan_protocol	Scanning was done on a GeneChipScanner 3000. Results were quantified and analyzed with GeneChip Operating Software (GCOS) 1.2 software (Affymetrix, Inc.) using default values (scaling, target signal intensity 500; normalization, all probe sets; parameters, all set at default values).
Sample_data_processing	Results were quantified and analyzed with GeneChip Operating Software (GCOS) 1.2 software (Affymetrix, Inc.) using default values (scaling, target signal intensity 500; normalization, all probe sets; parameters, all set at default values). We used Affymetrix GeneChip Mouse Expression set 430 2.0 Array which uses mouse maintenance genes for normalization. Details are available on the Affymetrix website (www.affymetrix.com/support/technical/mask_files.affx).
Sample_platform_id	GPL1261
Sample_contact_name	Nicole,Kim,MacLennan
Sample_contact_email	nmaclennan@mednet.ucla.edu
Sample_contact_phone	310-206-3050
Sample_contact_laboratory	McCabe
Sample_contact_department	Pediatrics
Sample_contact_institute	University of California, Los Angeles
Sample_contact_address	10833 LeConte Ave
Sample_contact_city	Los Angeles
Sample_contact_state	CA
Sample_contact_zip/postal_code	90095
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM319nnn/GSM319903/suppl/GSM319903.CEL.gz
Sample_series_id	GSE12748
Sample_data_row_count	45101

GSM319923

GPL1261

dol_1_liver_KnockOut1

liver_KnockOut

Strain: C57BL/6J Gender: male Age: day of life 1 Tissue: liver

Further details are available at www.affymetrix.com.

Sample_geo_accession	GSM319923
Sample_status	Public on Sep 10 2009
Sample_submission_date	Sep 11 2008
Sample_last_update_date	Sep 12 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	glycerol kinase knockout mice
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from one KnockOut liver was isolated individually using TRIzol Reagent (Invitrogen Life Technologies) and purified using RNeasy MiniElute Cleanup Kit (Qiagen Inc., Chatsworth, CA, USA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized from the poly(A) mRNA present in the isolated total RNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Life Technologies) and poly(T)-nucleotide primers. Biotin-tagged cRNA was generated using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY, USA) and fragmented to an average strand length of 100 bases (range 35–200 bases) following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).
Sample_hyb_protocol	Ten micrograms of cRNA was hybridized at 45 degrees C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 640) to an Affymetrix Mouse Genome 430 2.0 GeneChip as per the manufacturer’s instructions (Affymetrix, Inc.). The GeneChip arrays were washed and then stained with streptavidin–phycoerythrin on an Affymetrix Fluidics Station 450.
Sample_scan_protocol	Scanning was done on a GeneChipScanner 3000. Results were quantified and analyzed with GeneChip Operating Software (GCOS) 1.2 software (Affymetrix, Inc.) using default values (scaling, target signal intensity 500; normalization, all probe sets; parameters, all set at default values).
Sample_data_processing	Results were quantified and analyzed with GeneChip Operating Software (GCOS) 1.2 software (Affymetrix, Inc.) using default values (scaling, target signal intensity 500; normalization, all probe sets; parameters, all set at default values). We used Affymetrix GeneChip Mouse Expression set 430 2.0 Array which uses mouse maintenance genes for normalization. Details are available on the Affymetrix website (www.affymetrix.com/support/technical/mask_files.affx).
Sample_platform_id	GPL1261
Sample_contact_name	Nicole,Kim,MacLennan
Sample_contact_email	nmaclennan@mednet.ucla.edu
Sample_contact_phone	310-206-3050
Sample_contact_laboratory	McCabe
Sample_contact_department	Pediatrics
Sample_contact_institute	University of California, Los Angeles
Sample_contact_address	10833 LeConte Ave
Sample_contact_city	Los Angeles
Sample_contact_state	CA
Sample_contact_zip/postal_code	90095
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM319nnn/GSM319923/suppl/GSM319923.CEL.gz
Sample_series_id	GSE12748
Sample_data_row_count	45101

GSM319924

GPL1261

dol_1_liver_KnockOut2

liver_KnockOut

Strain: C57BL/6J Gender: male Age: day of life 1 Tissue: liver

Further details are available at www.affymetrix.com.

Sample_geo_accession	GSM319924
Sample_status	Public on Sep 10 2009
Sample_submission_date	Sep 11 2008
Sample_last_update_date	Sep 12 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	glycerol kinase knockout mice
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from one KnockOut liver was isolated individually using TRIzol Reagent (Invitrogen Life Technologies) and purified using RNeasy MiniElute Cleanup Kit (Qiagen Inc., Chatsworth, CA, USA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized from the poly(A) mRNA present in the isolated total RNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Life Technologies) and poly(T)-nucleotide primers. Biotin-tagged cRNA was generated using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY, USA) and fragmented to an average strand length of 100 bases (range 35–200 bases) following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).
Sample_hyb_protocol	Ten micrograms of cRNA was hybridized at 45 degrees C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 640) to an Affymetrix Mouse Genome 430 2.0 GeneChip as per the manufacturer’s instructions (Affymetrix, Inc.). The GeneChip arrays were washed and then stained with streptavidin–phycoerythrin on an Affymetrix Fluidics Station 450.
Sample_scan_protocol	Scanning was done on a GeneChipScanner 3000. Results were quantified and analyzed with GeneChip Operating Software (GCOS) 1.2 software (Affymetrix, Inc.) using default values (scaling, target signal intensity 500; normalization, all probe sets; parameters, all set at default values).
Sample_data_processing	Results were quantified and analyzed with GeneChip Operating Software (GCOS) 1.2 software (Affymetrix, Inc.) using default values (scaling, target signal intensity 500; normalization, all probe sets; parameters, all set at default values). We used Affymetrix GeneChip Mouse Expression set 430 2.0 Array which uses mouse maintenance genes for normalization. Details are available on the Affymetrix website (www.affymetrix.com/support/technical/mask_files.affx).
Sample_platform_id	GPL1261
Sample_contact_name	Nicole,Kim,MacLennan
Sample_contact_email	nmaclennan@mednet.ucla.edu
Sample_contact_phone	310-206-3050
Sample_contact_laboratory	McCabe
Sample_contact_department	Pediatrics
Sample_contact_institute	University of California, Los Angeles
Sample_contact_address	10833 LeConte Ave
Sample_contact_city	Los Angeles
Sample_contact_state	CA
Sample_contact_zip/postal_code	90095
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM319nnn/GSM319924/suppl/GSM319924.CEL.gz
Sample_series_id	GSE12748
Sample_data_row_count	45101

GSM319925

GPL1261

dol_1_liver_KnockOut3

liver_KnockOut

Strain: C57BL/6J Gender: male Age: day of life 1 Tissue: liver

Further details are available at www.affymetrix.com.

Sample_geo_accession	GSM319925
Sample_status	Public on Sep 10 2009
Sample_submission_date	Sep 11 2008
Sample_last_update_date	Sep 12 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	glycerol kinase knockout mice
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from one KnockOut liver was isolated individually using TRIzol Reagent (Invitrogen Life Technologies) and purified using RNeasy MiniElute Cleanup Kit (Qiagen Inc., Chatsworth, CA, USA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized from the poly(A) mRNA present in the isolated total RNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Life Technologies) and poly(T)-nucleotide primers. Biotin-tagged cRNA was generated using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY, USA) and fragmented to an average strand length of 100 bases (range 35–200 bases) following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).
Sample_hyb_protocol	Ten micrograms of cRNA was hybridized at 45 degrees C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 640) to an Affymetrix Mouse Genome 430 2.0 GeneChip as per the manufacturer’s instructions (Affymetrix, Inc.). The GeneChip arrays were washed and then stained with streptavidin–phycoerythrin on an Affymetrix Fluidics Station 450.
Sample_scan_protocol	Scanning was done on a GeneChipScanner 3000. Results were quantified and analyzed with GeneChip Operating Software (GCOS) 1.2 software (Affymetrix, Inc.) using default values (scaling, target signal intensity 500; normalization, all probe sets; parameters, all set at default values).
Sample_data_processing	Results were quantified and analyzed with GeneChip Operating Software (GCOS) 1.2 software (Affymetrix, Inc.) using default values (scaling, target signal intensity 500; normalization, all probe sets; parameters, all set at default values). We used Affymetrix GeneChip Mouse Expression set 430 2.0 Array which uses mouse maintenance genes for normalization. Details are available on the Affymetrix website (www.affymetrix.com/support/technical/mask_files.affx).
Sample_platform_id	GPL1261
Sample_contact_name	Nicole,Kim,MacLennan
Sample_contact_email	nmaclennan@mednet.ucla.edu
Sample_contact_phone	310-206-3050
Sample_contact_laboratory	McCabe
Sample_contact_department	Pediatrics
Sample_contact_institute	University of California, Los Angeles
Sample_contact_address	10833 LeConte Ave
Sample_contact_city	Los Angeles
Sample_contact_state	CA
Sample_contact_zip/postal_code	90095
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM319nnn/GSM319925/suppl/GSM319925.CEL.gz
Sample_series_id	GSE12748
Sample_data_row_count	45101

GSM319926

GPL1261

dol_1_liver_KnockOut4

liver_KnockOut

Strain: C57BL/6J Gender: male Age: day of life 1 Tissue: liver

Further details are available at www.affymetrix.com.

Sample_geo_accession	GSM319926
Sample_status	Public on Sep 10 2009
Sample_submission_date	Sep 11 2008
Sample_last_update_date	Sep 12 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	glycerol kinase knockout mice
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from one KnockOut liver was isolated individually using TRIzol Reagent (Invitrogen Life Technologies) and purified using RNeasy MiniElute Cleanup Kit (Qiagen Inc., Chatsworth, CA, USA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized from the poly(A) mRNA present in the isolated total RNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Life Technologies) and poly(T)-nucleotide primers. Biotin-tagged cRNA was generated using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY, USA) and fragmented to an average strand length of 100 bases (range 35–200 bases) following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).
Sample_hyb_protocol	Ten micrograms of cRNA was hybridized at 45 degrees C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 640) to an Affymetrix Mouse Genome 430 2.0 GeneChip as per the manufacturer’s instructions (Affymetrix, Inc.). The GeneChip arrays were washed and then stained with streptavidin–phycoerythrin on an Affymetrix Fluidics Station 450.
Sample_scan_protocol	Scanning was done on a GeneChipScanner 3000. Results were quantified and analyzed with GeneChip Operating Software (GCOS) 1.2 software (Affymetrix, Inc.) using default values (scaling, target signal intensity 500; normalization, all probe sets; parameters, all set at default values).
Sample_data_processing	Results were quantified and analyzed with GeneChip Operating Software (GCOS) 1.2 software (Affymetrix, Inc.) using default values (scaling, target signal intensity 500; normalization, all probe sets; parameters, all set at default values). We used Affymetrix GeneChip Mouse Expression set 430 2.0 Array which uses mouse maintenance genes for normalization. Details are available on the Affymetrix website (www.affymetrix.com/support/technical/mask_files.affx).
Sample_platform_id	GPL1261
Sample_contact_name	Nicole,Kim,MacLennan
Sample_contact_email	nmaclennan@mednet.ucla.edu
Sample_contact_phone	310-206-3050
Sample_contact_laboratory	McCabe
Sample_contact_department	Pediatrics
Sample_contact_institute	University of California, Los Angeles
Sample_contact_address	10833 LeConte Ave
Sample_contact_city	Los Angeles
Sample_contact_state	CA
Sample_contact_zip/postal_code	90095
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM319nnn/GSM319926/suppl/GSM319926.CEL.gz
Sample_series_id	GSE12748
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