Result

Search results for the GEO ID: GSE28059

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Description

Characteristics

GSM694034

GPL570

Huh7 DEGS1 siRNA, biological rep1

Huh7 72 hours after DEGS1 siRNA treatment

cell line: Huh7 hepatocarcinoma cell line

gene expression from Huh7 cells 72 hours after transfection with siRNA

Sample_geo_accession	GSM694034
Sample_status	Public on Jun 30 2011
Sample_submission_date	Mar 21 2011
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Huh7 cells were seeded at 60,000 cells/well in a 12-well plate or 6 millions cells/500 cm2 plate overnight. Next day, Silencer® Select siRNA (Applied Biosystem, Carlsbad, California) against SPTLC1, 2, 3 or DEGS1 gene and siLentFect™ lipid reagent (BIO-RAD, Hercules, California) was prepared in OptiMEM (Invitrogen) according to the manufacturer protocol. Silencer® Select scramble #1 was used as a control. Then, the siRNA-lipid complex was added to each well to yield the final concentration of 20 nM siRNA and incubated for 24 h at 37C, 5% CO2. Media was replaced with the fresh growing media and cells were incubated for another 24 h, before the conditioned media (DMEM + 1% FBS + BSA) was added to the cells at 72 h after siRNA transfection and incubated for another 24 h prior to harvest.
Sample_growth_protocol_ch1	Human hepatocarcinoma cells, Huh7, were maintained at approximately 70-80% confluence in the growing media consisting of high glucose DMEM (Invitrogen, Carlsbad, California), 10% fetal bovine serum (BSA, Sigma-Aldrich, St. Louis, Missouri), 2 mM L-glutamine (Invitrogen), 10mM hepes (Invitrogen) and 1% penicillin-streptomycin (Invitrogen) at 37C, 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from frozen cell pellet using standard Qiagen Rneasy kit by the vendor Gene Logic Incorporated.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized using 1-2 ug of high quality total RNA. Supercript II™ (Invitrogen) was used to reverse-transcribe the mRNA in the presence of a T7 containing oligo dT24 primer followed by second strand synthesis as recommended by Affymetrix. cDNA was purified using Agencourt RNAClean magnetic beads and used as a template for in vitro transcription using the GeneChip® One-Cycle Labeling Kit from Affymetrix. cRNA was purified using Agencourt magnetic beads and the quantity and purity of the cRNA was determined by absorbance at 260 nm and 260/280 absorbance ratio respectively. The quality of the cRNA was evaluated by assessing the size distribution of the cRNA using a 1.25% MOPS gel. This was performed by the vendor Gene Logic Incorporated.
Sample_hyb_protocol	The labeled cRNA was fragmented as recommended by Affymetrix and 10 µg was added to a hybridization cocktail prior to loading onto individual HG-U133_Plus_2 GeneChip®. The microarrays were hybridized at 45°C for 16- 24 hours and washed and stained on an Affymetrix FS450 fluidics station according to manufacturer recommendations. This was performed by the vendor Gene Logic Incorporated.
Sample_scan_protocol	The microarrays were scanned on a GeneChip® Scanner 3000. This was performed by the vendor Gene Logic Incorporated.
Sample_data_processing	All of the array files were normalized using the Robust Multi-Array Average (RMA) method and log2 transformed using the following Bioconductor and R programs: affy (1.18.2), affyio (1.8.1), annaffy (1.12.1), annotate (1.18.0), AnnotationDbi (1.2.2), base (2.7.2), Biobase (2.0.1), chron (2.3-32), contrast (0.11), datasets (2.7.2), DBI (0.2-4), Design (2.3-0), gcrma (2.12.1), genefilter (1.20.1), GO.db (2.2.0), graphics (2.7.2), grDevices (2.7.2), Hmisc (3.7-0), KEGG.db (2.2.0), lattice (0.17-13), limma (2.14.7), MASS (7.2-44), matchprobes (1.12.1), methods (2.7.2), multtest (2.0.0), nlme (3.1-89), odfWeave (0.7.11), preprocessCore (1.2.1), RSQLite (0.7-3), simpleaffy (2.16.1), splines (2.7.2), stats (2.7.2), survival (2.34-1), tools (2.7.2), utils (2.7.2), XML (2.6-0) and xtable (1.5-5).
Sample_platform_id	GPL570
Sample_contact_name	Wanida,,Ruangsiriluk
Sample_contact_email	wanida.ruangsiriluk@pfizer.com
Sample_contact_department	CVMED
Sample_contact_institute	Pfizer Inc.
Sample_contact_address	Eastern Point Road
Sample_contact_city	Groton
Sample_contact_state	CT
Sample_contact_zip/postal_code	06340
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM694nnn/GSM694034/suppl/GSM694034.CEL.gz
Sample_series_id	GSE28059
Sample_data_row_count	54675

GSM694035

GPL570

Huh7 DEGS1 siRNA, biological rep2

Huh7 72 hours after DEGS1 siRNA treatment

cell line: Huh7 hepatocarcinoma cell line

gene expression from Huh7 cells 72 hours after transfection with siRNA

Sample_geo_accession	GSM694035
Sample_status	Public on Jun 30 2011
Sample_submission_date	Mar 21 2011
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Huh7 cells were seeded at 60,000 cells/well in a 12-well plate or 6 millions cells/500 cm2 plate overnight. Next day, Silencer® Select siRNA (Applied Biosystem, Carlsbad, California) against SPTLC1, 2, 3 or DEGS1 gene and siLentFect™ lipid reagent (BIO-RAD, Hercules, California) was prepared in OptiMEM (Invitrogen) according to the manufacturer protocol. Silencer® Select scramble #1 was used as a control. Then, the siRNA-lipid complex was added to each well to yield the final concentration of 20 nM siRNA and incubated for 24 h at 37C, 5% CO2. Media was replaced with the fresh growing media and cells were incubated for another 24 h, before the conditioned media (DMEM + 1% FBS + BSA) was added to the cells at 72 h after siRNA transfection and incubated for another 24 h prior to harvest.
Sample_growth_protocol_ch1	Human hepatocarcinoma cells, Huh7, were maintained at approximately 70-80% confluence in the growing media consisting of high glucose DMEM (Invitrogen, Carlsbad, California), 10% fetal bovine serum (BSA, Sigma-Aldrich, St. Louis, Missouri), 2 mM L-glutamine (Invitrogen), 10mM hepes (Invitrogen) and 1% penicillin-streptomycin (Invitrogen) at 37C, 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from frozen cell pellet using standard Qiagen Rneasy kit by the vendor Gene Logic Incorporated.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized using 1-2 ug of high quality total RNA. Supercript II™ (Invitrogen) was used to reverse-transcribe the mRNA in the presence of a T7 containing oligo dT24 primer followed by second strand synthesis as recommended by Affymetrix. cDNA was purified using Agencourt RNAClean magnetic beads and used as a template for in vitro transcription using the GeneChip® One-Cycle Labeling Kit from Affymetrix. cRNA was purified using Agencourt magnetic beads and the quantity and purity of the cRNA was determined by absorbance at 260 nm and 260/280 absorbance ratio respectively. The quality of the cRNA was evaluated by assessing the size distribution of the cRNA using a 1.25% MOPS gel. This was performed by the vendor Gene Logic Incorporated.
Sample_hyb_protocol	The labeled cRNA was fragmented as recommended by Affymetrix and 10 µg was added to a hybridization cocktail prior to loading onto individual HG-U133_Plus_2 GeneChip®. The microarrays were hybridized at 45°C for 16- 24 hours and washed and stained on an Affymetrix FS450 fluidics station according to manufacturer recommendations. This was performed by the vendor Gene Logic Incorporated.
Sample_scan_protocol	The microarrays were scanned on a GeneChip® Scanner 3000. This was performed by the vendor Gene Logic Incorporated.
Sample_data_processing	All of the array files were normalized using the Robust Multi-Array Average (RMA) method and log2 transformed using the following Bioconductor and R programs: affy (1.18.2), affyio (1.8.1), annaffy (1.12.1), annotate (1.18.0), AnnotationDbi (1.2.2), base (2.7.2), Biobase (2.0.1), chron (2.3-32), contrast (0.11), datasets (2.7.2), DBI (0.2-4), Design (2.3-0), gcrma (2.12.1), genefilter (1.20.1), GO.db (2.2.0), graphics (2.7.2), grDevices (2.7.2), Hmisc (3.7-0), KEGG.db (2.2.0), lattice (0.17-13), limma (2.14.7), MASS (7.2-44), matchprobes (1.12.1), methods (2.7.2), multtest (2.0.0), nlme (3.1-89), odfWeave (0.7.11), preprocessCore (1.2.1), RSQLite (0.7-3), simpleaffy (2.16.1), splines (2.7.2), stats (2.7.2), survival (2.34-1), tools (2.7.2), utils (2.7.2), XML (2.6-0) and xtable (1.5-5).
Sample_platform_id	GPL570
Sample_contact_name	Wanida,,Ruangsiriluk
Sample_contact_email	wanida.ruangsiriluk@pfizer.com
Sample_contact_department	CVMED
Sample_contact_institute	Pfizer Inc.
Sample_contact_address	Eastern Point Road
Sample_contact_city	Groton
Sample_contact_state	CT
Sample_contact_zip/postal_code	06340
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM694nnn/GSM694035/suppl/GSM694035.CEL.gz
Sample_series_id	GSE28059
Sample_data_row_count	54675

GSM694036

GPL570

Huh7 DEGS1 siRNA, biological rep3

Huh7 72 hours after DEGS1 siRNA treatment

cell line: Huh7 hepatocarcinoma cell line

gene expression from Huh7 cells 72 hours after transfection with siRNA

Sample_geo_accession	GSM694036
Sample_status	Public on Jun 30 2011
Sample_submission_date	Mar 21 2011
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Huh7 cells were seeded at 60,000 cells/well in a 12-well plate or 6 millions cells/500 cm2 plate overnight. Next day, Silencer® Select siRNA (Applied Biosystem, Carlsbad, California) against SPTLC1, 2, 3 or DEGS1 gene and siLentFect™ lipid reagent (BIO-RAD, Hercules, California) was prepared in OptiMEM (Invitrogen) according to the manufacturer protocol. Silencer® Select scramble #1 was used as a control. Then, the siRNA-lipid complex was added to each well to yield the final concentration of 20 nM siRNA and incubated for 24 h at 37C, 5% CO2. Media was replaced with the fresh growing media and cells were incubated for another 24 h, before the conditioned media (DMEM + 1% FBS + BSA) was added to the cells at 72 h after siRNA transfection and incubated for another 24 h prior to harvest.
Sample_growth_protocol_ch1	Human hepatocarcinoma cells, Huh7, were maintained at approximately 70-80% confluence in the growing media consisting of high glucose DMEM (Invitrogen, Carlsbad, California), 10% fetal bovine serum (BSA, Sigma-Aldrich, St. Louis, Missouri), 2 mM L-glutamine (Invitrogen), 10mM hepes (Invitrogen) and 1% penicillin-streptomycin (Invitrogen) at 37C, 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from frozen cell pellet using standard Qiagen Rneasy kit by the vendor Gene Logic Incorporated.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized using 1-2 ug of high quality total RNA. Supercript II™ (Invitrogen) was used to reverse-transcribe the mRNA in the presence of a T7 containing oligo dT24 primer followed by second strand synthesis as recommended by Affymetrix. cDNA was purified using Agencourt RNAClean magnetic beads and used as a template for in vitro transcription using the GeneChip® One-Cycle Labeling Kit from Affymetrix. cRNA was purified using Agencourt magnetic beads and the quantity and purity of the cRNA was determined by absorbance at 260 nm and 260/280 absorbance ratio respectively. The quality of the cRNA was evaluated by assessing the size distribution of the cRNA using a 1.25% MOPS gel. This was performed by the vendor Gene Logic Incorporated.
Sample_hyb_protocol	The labeled cRNA was fragmented as recommended by Affymetrix and 10 µg was added to a hybridization cocktail prior to loading onto individual HG-U133_Plus_2 GeneChip®. The microarrays were hybridized at 45°C for 16- 24 hours and washed and stained on an Affymetrix FS450 fluidics station according to manufacturer recommendations. This was performed by the vendor Gene Logic Incorporated.
Sample_scan_protocol	The microarrays were scanned on a GeneChip® Scanner 3000. This was performed by the vendor Gene Logic Incorporated.
Sample_data_processing	All of the array files were normalized using the Robust Multi-Array Average (RMA) method and log2 transformed using the following Bioconductor and R programs: affy (1.18.2), affyio (1.8.1), annaffy (1.12.1), annotate (1.18.0), AnnotationDbi (1.2.2), base (2.7.2), Biobase (2.0.1), chron (2.3-32), contrast (0.11), datasets (2.7.2), DBI (0.2-4), Design (2.3-0), gcrma (2.12.1), genefilter (1.20.1), GO.db (2.2.0), graphics (2.7.2), grDevices (2.7.2), Hmisc (3.7-0), KEGG.db (2.2.0), lattice (0.17-13), limma (2.14.7), MASS (7.2-44), matchprobes (1.12.1), methods (2.7.2), multtest (2.0.0), nlme (3.1-89), odfWeave (0.7.11), preprocessCore (1.2.1), RSQLite (0.7-3), simpleaffy (2.16.1), splines (2.7.2), stats (2.7.2), survival (2.34-1), tools (2.7.2), utils (2.7.2), XML (2.6-0) and xtable (1.5-5).
Sample_platform_id	GPL570
Sample_contact_name	Wanida,,Ruangsiriluk
Sample_contact_email	wanida.ruangsiriluk@pfizer.com
Sample_contact_department	CVMED
Sample_contact_institute	Pfizer Inc.
Sample_contact_address	Eastern Point Road
Sample_contact_city	Groton
Sample_contact_state	CT
Sample_contact_zip/postal_code	06340
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM694nnn/GSM694036/suppl/GSM694036.CEL.gz
Sample_series_id	GSE28059
Sample_data_row_count	54675

GSM694037

GPL570

Huh7 scramble siRNA, biological rep1

Huh7 72 hours after scramble siRNA treatment, control

cell line: Huh7 hepatocarcinoma cell line

gene expression from Huh7 cells 72 hours after transfection with siRNA

Sample_geo_accession	GSM694037
Sample_status	Public on Jun 30 2011
Sample_submission_date	Mar 21 2011
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Huh7 cells were seeded at 60,000 cells/well in a 12-well plate or 6 millions cells/500 cm2 plate overnight. Next day, Silencer® Select siRNA (Applied Biosystem, Carlsbad, California) against SPTLC1, 2, 3 or DEGS1 gene and siLentFect™ lipid reagent (BIO-RAD, Hercules, California) was prepared in OptiMEM (Invitrogen) according to the manufacturer protocol. Silencer® Select scramble #1 was used as a control. Then, the siRNA-lipid complex was added to each well to yield the final concentration of 20 nM siRNA and incubated for 24 h at 37C, 5% CO2. Media was replaced with the fresh growing media and cells were incubated for another 24 h, before the conditioned media (DMEM + 1% FBS + BSA) was added to the cells at 72 h after siRNA transfection and incubated for another 24 h prior to harvest.
Sample_growth_protocol_ch1	Human hepatocarcinoma cells, Huh7, were maintained at approximately 70-80% confluence in the growing media consisting of high glucose DMEM (Invitrogen, Carlsbad, California), 10% fetal bovine serum (BSA, Sigma-Aldrich, St. Louis, Missouri), 2 mM L-glutamine (Invitrogen), 10mM hepes (Invitrogen) and 1% penicillin-streptomycin (Invitrogen) at 37C, 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from frozen cell pellet using standard Qiagen Rneasy kit by the vendor Gene Logic Incorporated.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized using 1-2 ug of high quality total RNA. Supercript II™ (Invitrogen) was used to reverse-transcribe the mRNA in the presence of a T7 containing oligo dT24 primer followed by second strand synthesis as recommended by Affymetrix. cDNA was purified using Agencourt RNAClean magnetic beads and used as a template for in vitro transcription using the GeneChip® One-Cycle Labeling Kit from Affymetrix. cRNA was purified using Agencourt magnetic beads and the quantity and purity of the cRNA was determined by absorbance at 260 nm and 260/280 absorbance ratio respectively. The quality of the cRNA was evaluated by assessing the size distribution of the cRNA using a 1.25% MOPS gel. This was performed by the vendor Gene Logic Incorporated.
Sample_hyb_protocol	The labeled cRNA was fragmented as recommended by Affymetrix and 10 µg was added to a hybridization cocktail prior to loading onto individual HG-U133_Plus_2 GeneChip®. The microarrays were hybridized at 45°C for 16- 24 hours and washed and stained on an Affymetrix FS450 fluidics station according to manufacturer recommendations. This was performed by the vendor Gene Logic Incorporated.
Sample_scan_protocol	The microarrays were scanned on a GeneChip® Scanner 3000. This was performed by the vendor Gene Logic Incorporated.
Sample_data_processing	All of the array files were normalized using the Robust Multi-Array Average (RMA) method and log2 transformed using the following Bioconductor and R programs: affy (1.18.2), affyio (1.8.1), annaffy (1.12.1), annotate (1.18.0), AnnotationDbi (1.2.2), base (2.7.2), Biobase (2.0.1), chron (2.3-32), contrast (0.11), datasets (2.7.2), DBI (0.2-4), Design (2.3-0), gcrma (2.12.1), genefilter (1.20.1), GO.db (2.2.0), graphics (2.7.2), grDevices (2.7.2), Hmisc (3.7-0), KEGG.db (2.2.0), lattice (0.17-13), limma (2.14.7), MASS (7.2-44), matchprobes (1.12.1), methods (2.7.2), multtest (2.0.0), nlme (3.1-89), odfWeave (0.7.11), preprocessCore (1.2.1), RSQLite (0.7-3), simpleaffy (2.16.1), splines (2.7.2), stats (2.7.2), survival (2.34-1), tools (2.7.2), utils (2.7.2), XML (2.6-0) and xtable (1.5-5).
Sample_platform_id	GPL570
Sample_contact_name	Wanida,,Ruangsiriluk
Sample_contact_email	wanida.ruangsiriluk@pfizer.com
Sample_contact_department	CVMED
Sample_contact_institute	Pfizer Inc.
Sample_contact_address	Eastern Point Road
Sample_contact_city	Groton
Sample_contact_state	CT
Sample_contact_zip/postal_code	06340
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM694nnn/GSM694037/suppl/GSM694037.CEL.gz
Sample_series_id	GSE28059
Sample_data_row_count	54675

GSM694038

GPL570

Huh7 scramble siRNA, biological rep2

Huh7 72 hours after scramble siRNA treatment, control

cell line: Huh7 hepatocarcinoma cell line

gene expression from Huh7 cells 72 hours after transfection with siRNA

Sample_geo_accession	GSM694038
Sample_status	Public on Jun 30 2011
Sample_submission_date	Mar 21 2011
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Huh7 cells were seeded at 60,000 cells/well in a 12-well plate or 6 millions cells/500 cm2 plate overnight. Next day, Silencer® Select siRNA (Applied Biosystem, Carlsbad, California) against SPTLC1, 2, 3 or DEGS1 gene and siLentFect™ lipid reagent (BIO-RAD, Hercules, California) was prepared in OptiMEM (Invitrogen) according to the manufacturer protocol. Silencer® Select scramble #1 was used as a control. Then, the siRNA-lipid complex was added to each well to yield the final concentration of 20 nM siRNA and incubated for 24 h at 37C, 5% CO2. Media was replaced with the fresh growing media and cells were incubated for another 24 h, before the conditioned media (DMEM + 1% FBS + BSA) was added to the cells at 72 h after siRNA transfection and incubated for another 24 h prior to harvest.
Sample_growth_protocol_ch1	Human hepatocarcinoma cells, Huh7, were maintained at approximately 70-80% confluence in the growing media consisting of high glucose DMEM (Invitrogen, Carlsbad, California), 10% fetal bovine serum (BSA, Sigma-Aldrich, St. Louis, Missouri), 2 mM L-glutamine (Invitrogen), 10mM hepes (Invitrogen) and 1% penicillin-streptomycin (Invitrogen) at 37C, 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from frozen cell pellet using standard Qiagen Rneasy kit by the vendor Gene Logic Incorporated.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized using 1-2 ug of high quality total RNA. Supercript II™ (Invitrogen) was used to reverse-transcribe the mRNA in the presence of a T7 containing oligo dT24 primer followed by second strand synthesis as recommended by Affymetrix. cDNA was purified using Agencourt RNAClean magnetic beads and used as a template for in vitro transcription using the GeneChip® One-Cycle Labeling Kit from Affymetrix. cRNA was purified using Agencourt magnetic beads and the quantity and purity of the cRNA was determined by absorbance at 260 nm and 260/280 absorbance ratio respectively. The quality of the cRNA was evaluated by assessing the size distribution of the cRNA using a 1.25% MOPS gel. This was performed by the vendor Gene Logic Incorporated.
Sample_hyb_protocol	The labeled cRNA was fragmented as recommended by Affymetrix and 10 µg was added to a hybridization cocktail prior to loading onto individual HG-U133_Plus_2 GeneChip®. The microarrays were hybridized at 45°C for 16- 24 hours and washed and stained on an Affymetrix FS450 fluidics station according to manufacturer recommendations. This was performed by the vendor Gene Logic Incorporated.
Sample_scan_protocol	The microarrays were scanned on a GeneChip® Scanner 3000. This was performed by the vendor Gene Logic Incorporated.
Sample_data_processing	All of the array files were normalized using the Robust Multi-Array Average (RMA) method and log2 transformed using the following Bioconductor and R programs: affy (1.18.2), affyio (1.8.1), annaffy (1.12.1), annotate (1.18.0), AnnotationDbi (1.2.2), base (2.7.2), Biobase (2.0.1), chron (2.3-32), contrast (0.11), datasets (2.7.2), DBI (0.2-4), Design (2.3-0), gcrma (2.12.1), genefilter (1.20.1), GO.db (2.2.0), graphics (2.7.2), grDevices (2.7.2), Hmisc (3.7-0), KEGG.db (2.2.0), lattice (0.17-13), limma (2.14.7), MASS (7.2-44), matchprobes (1.12.1), methods (2.7.2), multtest (2.0.0), nlme (3.1-89), odfWeave (0.7.11), preprocessCore (1.2.1), RSQLite (0.7-3), simpleaffy (2.16.1), splines (2.7.2), stats (2.7.2), survival (2.34-1), tools (2.7.2), utils (2.7.2), XML (2.6-0) and xtable (1.5-5).
Sample_platform_id	GPL570
Sample_contact_name	Wanida,,Ruangsiriluk
Sample_contact_email	wanida.ruangsiriluk@pfizer.com
Sample_contact_department	CVMED
Sample_contact_institute	Pfizer Inc.
Sample_contact_address	Eastern Point Road
Sample_contact_city	Groton
Sample_contact_state	CT
Sample_contact_zip/postal_code	06340
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM694nnn/GSM694038/suppl/GSM694038.CEL.gz
Sample_series_id	GSE28059
Sample_data_row_count	54675

GSM694039

GPL570

Huh7 scramble siRNA, biological rep3

Huh7 72 hours after scramble siRNA treatment, control

cell line: Huh7 hepatocarcinoma cell line

gene expression from Huh7 cells 72 hours after transfection with siRNA

Sample_geo_accession	GSM694039
Sample_status	Public on Jun 30 2011
Sample_submission_date	Mar 21 2011
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Huh7 cells were seeded at 60,000 cells/well in a 12-well plate or 6 millions cells/500 cm2 plate overnight. Next day, Silencer® Select siRNA (Applied Biosystem, Carlsbad, California) against SPTLC1, 2, 3 or DEGS1 gene and siLentFect™ lipid reagent (BIO-RAD, Hercules, California) was prepared in OptiMEM (Invitrogen) according to the manufacturer protocol. Silencer® Select scramble #1 was used as a control. Then, the siRNA-lipid complex was added to each well to yield the final concentration of 20 nM siRNA and incubated for 24 h at 37C, 5% CO2. Media was replaced with the fresh growing media and cells were incubated for another 24 h, before the conditioned media (DMEM + 1% FBS + BSA) was added to the cells at 72 h after siRNA transfection and incubated for another 24 h prior to harvest.
Sample_growth_protocol_ch1	Human hepatocarcinoma cells, Huh7, were maintained at approximately 70-80% confluence in the growing media consisting of high glucose DMEM (Invitrogen, Carlsbad, California), 10% fetal bovine serum (BSA, Sigma-Aldrich, St. Louis, Missouri), 2 mM L-glutamine (Invitrogen), 10mM hepes (Invitrogen) and 1% penicillin-streptomycin (Invitrogen) at 37C, 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from frozen cell pellet using standard Qiagen Rneasy kit by the vendor Gene Logic Incorporated.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized using 1-2 ug of high quality total RNA. Supercript II™ (Invitrogen) was used to reverse-transcribe the mRNA in the presence of a T7 containing oligo dT24 primer followed by second strand synthesis as recommended by Affymetrix. cDNA was purified using Agencourt RNAClean magnetic beads and used as a template for in vitro transcription using the GeneChip® One-Cycle Labeling Kit from Affymetrix. cRNA was purified using Agencourt magnetic beads and the quantity and purity of the cRNA was determined by absorbance at 260 nm and 260/280 absorbance ratio respectively. The quality of the cRNA was evaluated by assessing the size distribution of the cRNA using a 1.25% MOPS gel. This was performed by the vendor Gene Logic Incorporated.
Sample_hyb_protocol	The labeled cRNA was fragmented as recommended by Affymetrix and 10 µg was added to a hybridization cocktail prior to loading onto individual HG-U133_Plus_2 GeneChip®. The microarrays were hybridized at 45°C for 16- 24 hours and washed and stained on an Affymetrix FS450 fluidics station according to manufacturer recommendations. This was performed by the vendor Gene Logic Incorporated.
Sample_scan_protocol	The microarrays were scanned on a GeneChip® Scanner 3000. This was performed by the vendor Gene Logic Incorporated.
Sample_data_processing	All of the array files were normalized using the Robust Multi-Array Average (RMA) method and log2 transformed using the following Bioconductor and R programs: affy (1.18.2), affyio (1.8.1), annaffy (1.12.1), annotate (1.18.0), AnnotationDbi (1.2.2), base (2.7.2), Biobase (2.0.1), chron (2.3-32), contrast (0.11), datasets (2.7.2), DBI (0.2-4), Design (2.3-0), gcrma (2.12.1), genefilter (1.20.1), GO.db (2.2.0), graphics (2.7.2), grDevices (2.7.2), Hmisc (3.7-0), KEGG.db (2.2.0), lattice (0.17-13), limma (2.14.7), MASS (7.2-44), matchprobes (1.12.1), methods (2.7.2), multtest (2.0.0), nlme (3.1-89), odfWeave (0.7.11), preprocessCore (1.2.1), RSQLite (0.7-3), simpleaffy (2.16.1), splines (2.7.2), stats (2.7.2), survival (2.34-1), tools (2.7.2), utils (2.7.2), XML (2.6-0) and xtable (1.5-5).
Sample_platform_id	GPL570
Sample_contact_name	Wanida,,Ruangsiriluk
Sample_contact_email	wanida.ruangsiriluk@pfizer.com
Sample_contact_department	CVMED
Sample_contact_institute	Pfizer Inc.
Sample_contact_address	Eastern Point Road
Sample_contact_city	Groton
Sample_contact_state	CT
Sample_contact_zip/postal_code	06340
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM694nnn/GSM694039/suppl/GSM694039.CEL.gz
Sample_series_id	GSE28059
Sample_data_row_count	54675

GSM694040

GPL570

Huh7 SPTLC123 siRNA, biological rep1

Huh7 72 hours after SPTLC123 siRNA treatment

cell line: Huh7 hepatocarcinoma cell line

gene expression from Huh7 cells 72 hours after transfection with siRNA

Sample_geo_accession	GSM694040
Sample_status	Public on Jun 30 2011
Sample_submission_date	Mar 21 2011
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Huh7 cells were seeded at 60,000 cells/well in a 12-well plate or 6 millions cells/500 cm2 plate overnight. Next day, Silencer® Select siRNA (Applied Biosystem, Carlsbad, California) against SPTLC1, 2, 3 or DEGS1 gene and siLentFect™ lipid reagent (BIO-RAD, Hercules, California) was prepared in OptiMEM (Invitrogen) according to the manufacturer protocol. Silencer® Select scramble #1 was used as a control. Then, the siRNA-lipid complex was added to each well to yield the final concentration of 20 nM siRNA and incubated for 24 h at 37C, 5% CO2. Media was replaced with the fresh growing media and cells were incubated for another 24 h, before the conditioned media (DMEM + 1% FBS + BSA) was added to the cells at 72 h after siRNA transfection and incubated for another 24 h prior to harvest.
Sample_growth_protocol_ch1	Human hepatocarcinoma cells, Huh7, were maintained at approximately 70-80% confluence in the growing media consisting of high glucose DMEM (Invitrogen, Carlsbad, California), 10% fetal bovine serum (BSA, Sigma-Aldrich, St. Louis, Missouri), 2 mM L-glutamine (Invitrogen), 10mM hepes (Invitrogen) and 1% penicillin-streptomycin (Invitrogen) at 37C, 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from frozen cell pellet using standard Qiagen Rneasy kit by the vendor Gene Logic Incorporated.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized using 1-2 ug of high quality total RNA. Supercript II™ (Invitrogen) was used to reverse-transcribe the mRNA in the presence of a T7 containing oligo dT24 primer followed by second strand synthesis as recommended by Affymetrix. cDNA was purified using Agencourt RNAClean magnetic beads and used as a template for in vitro transcription using the GeneChip® One-Cycle Labeling Kit from Affymetrix. cRNA was purified using Agencourt magnetic beads and the quantity and purity of the cRNA was determined by absorbance at 260 nm and 260/280 absorbance ratio respectively. The quality of the cRNA was evaluated by assessing the size distribution of the cRNA using a 1.25% MOPS gel. This was performed by the vendor Gene Logic Incorporated.
Sample_hyb_protocol	The labeled cRNA was fragmented as recommended by Affymetrix and 10 µg was added to a hybridization cocktail prior to loading onto individual HG-U133_Plus_2 GeneChip®. The microarrays were hybridized at 45°C for 16- 24 hours and washed and stained on an Affymetrix FS450 fluidics station according to manufacturer recommendations. This was performed by the vendor Gene Logic Incorporated.
Sample_scan_protocol	The microarrays were scanned on a GeneChip® Scanner 3000. This was performed by the vendor Gene Logic Incorporated.
Sample_data_processing	All of the array files were normalized using the Robust Multi-Array Average (RMA) method and log2 transformed using the following Bioconductor and R programs: affy (1.18.2), affyio (1.8.1), annaffy (1.12.1), annotate (1.18.0), AnnotationDbi (1.2.2), base (2.7.2), Biobase (2.0.1), chron (2.3-32), contrast (0.11), datasets (2.7.2), DBI (0.2-4), Design (2.3-0), gcrma (2.12.1), genefilter (1.20.1), GO.db (2.2.0), graphics (2.7.2), grDevices (2.7.2), Hmisc (3.7-0), KEGG.db (2.2.0), lattice (0.17-13), limma (2.14.7), MASS (7.2-44), matchprobes (1.12.1), methods (2.7.2), multtest (2.0.0), nlme (3.1-89), odfWeave (0.7.11), preprocessCore (1.2.1), RSQLite (0.7-3), simpleaffy (2.16.1), splines (2.7.2), stats (2.7.2), survival (2.34-1), tools (2.7.2), utils (2.7.2), XML (2.6-0) and xtable (1.5-5).
Sample_platform_id	GPL570
Sample_contact_name	Wanida,,Ruangsiriluk
Sample_contact_email	wanida.ruangsiriluk@pfizer.com
Sample_contact_department	CVMED
Sample_contact_institute	Pfizer Inc.
Sample_contact_address	Eastern Point Road
Sample_contact_city	Groton
Sample_contact_state	CT
Sample_contact_zip/postal_code	06340
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM694nnn/GSM694040/suppl/GSM694040.CEL.gz
Sample_series_id	GSE28059
Sample_data_row_count	54675

GSM694041

GPL570

Huh7 SPTLC123 siRNA, biological rep2

Huh7 72 hours after SPTLC123 siRNA treatment

cell line: Huh7 hepatocarcinoma cell line

gene expression from Huh7 cells 72 hours after transfection with siRNA

Sample_geo_accession	GSM694041
Sample_status	Public on Jun 30 2011
Sample_submission_date	Mar 21 2011
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Huh7 cells were seeded at 60,000 cells/well in a 12-well plate or 6 millions cells/500 cm2 plate overnight. Next day, Silencer® Select siRNA (Applied Biosystem, Carlsbad, California) against SPTLC1, 2, 3 or DEGS1 gene and siLentFect™ lipid reagent (BIO-RAD, Hercules, California) was prepared in OptiMEM (Invitrogen) according to the manufacturer protocol. Silencer® Select scramble #1 was used as a control. Then, the siRNA-lipid complex was added to each well to yield the final concentration of 20 nM siRNA and incubated for 24 h at 37C, 5% CO2. Media was replaced with the fresh growing media and cells were incubated for another 24 h, before the conditioned media (DMEM + 1% FBS + BSA) was added to the cells at 72 h after siRNA transfection and incubated for another 24 h prior to harvest.
Sample_growth_protocol_ch1	Human hepatocarcinoma cells, Huh7, were maintained at approximately 70-80% confluence in the growing media consisting of high glucose DMEM (Invitrogen, Carlsbad, California), 10% fetal bovine serum (BSA, Sigma-Aldrich, St. Louis, Missouri), 2 mM L-glutamine (Invitrogen), 10mM hepes (Invitrogen) and 1% penicillin-streptomycin (Invitrogen) at 37C, 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from frozen cell pellet using standard Qiagen Rneasy kit by the vendor Gene Logic Incorporated.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized using 1-2 ug of high quality total RNA. Supercript II™ (Invitrogen) was used to reverse-transcribe the mRNA in the presence of a T7 containing oligo dT24 primer followed by second strand synthesis as recommended by Affymetrix. cDNA was purified using Agencourt RNAClean magnetic beads and used as a template for in vitro transcription using the GeneChip® One-Cycle Labeling Kit from Affymetrix. cRNA was purified using Agencourt magnetic beads and the quantity and purity of the cRNA was determined by absorbance at 260 nm and 260/280 absorbance ratio respectively. The quality of the cRNA was evaluated by assessing the size distribution of the cRNA using a 1.25% MOPS gel. This was performed by the vendor Gene Logic Incorporated.
Sample_hyb_protocol	The labeled cRNA was fragmented as recommended by Affymetrix and 10 µg was added to a hybridization cocktail prior to loading onto individual HG-U133_Plus_2 GeneChip®. The microarrays were hybridized at 45°C for 16- 24 hours and washed and stained on an Affymetrix FS450 fluidics station according to manufacturer recommendations. This was performed by the vendor Gene Logic Incorporated.
Sample_scan_protocol	The microarrays were scanned on a GeneChip® Scanner 3000. This was performed by the vendor Gene Logic Incorporated.
Sample_data_processing	All of the array files were normalized using the Robust Multi-Array Average (RMA) method and log2 transformed using the following Bioconductor and R programs: affy (1.18.2), affyio (1.8.1), annaffy (1.12.1), annotate (1.18.0), AnnotationDbi (1.2.2), base (2.7.2), Biobase (2.0.1), chron (2.3-32), contrast (0.11), datasets (2.7.2), DBI (0.2-4), Design (2.3-0), gcrma (2.12.1), genefilter (1.20.1), GO.db (2.2.0), graphics (2.7.2), grDevices (2.7.2), Hmisc (3.7-0), KEGG.db (2.2.0), lattice (0.17-13), limma (2.14.7), MASS (7.2-44), matchprobes (1.12.1), methods (2.7.2), multtest (2.0.0), nlme (3.1-89), odfWeave (0.7.11), preprocessCore (1.2.1), RSQLite (0.7-3), simpleaffy (2.16.1), splines (2.7.2), stats (2.7.2), survival (2.34-1), tools (2.7.2), utils (2.7.2), XML (2.6-0) and xtable (1.5-5).
Sample_platform_id	GPL570
Sample_contact_name	Wanida,,Ruangsiriluk
Sample_contact_email	wanida.ruangsiriluk@pfizer.com
Sample_contact_department	CVMED
Sample_contact_institute	Pfizer Inc.
Sample_contact_address	Eastern Point Road
Sample_contact_city	Groton
Sample_contact_state	CT
Sample_contact_zip/postal_code	06340
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM694nnn/GSM694041/suppl/GSM694041.CEL.gz
Sample_series_id	GSE28059
Sample_data_row_count	54675

GSM694042

GPL570

Huh7 SPTLC123 siRNA, biological rep3

Huh7 72 hours after SPTLC123 siRNA treatment

cell line: Huh7 hepatocarcinoma cell line

gene expression from Huh7 cells 72 hours after transfection with siRNA

Sample_geo_accession	GSM694042
Sample_status	Public on Jun 30 2011
Sample_submission_date	Mar 21 2011
Sample_last_update_date	Jun 30 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Huh7 cells were seeded at 60,000 cells/well in a 12-well plate or 6 millions cells/500 cm2 plate overnight. Next day, Silencer® Select siRNA (Applied Biosystem, Carlsbad, California) against SPTLC1, 2, 3 or DEGS1 gene and siLentFect™ lipid reagent (BIO-RAD, Hercules, California) was prepared in OptiMEM (Invitrogen) according to the manufacturer protocol. Silencer® Select scramble #1 was used as a control. Then, the siRNA-lipid complex was added to each well to yield the final concentration of 20 nM siRNA and incubated for 24 h at 37C, 5% CO2. Media was replaced with the fresh growing media and cells were incubated for another 24 h, before the conditioned media (DMEM + 1% FBS + BSA) was added to the cells at 72 h after siRNA transfection and incubated for another 24 h prior to harvest.
Sample_growth_protocol_ch1	Human hepatocarcinoma cells, Huh7, were maintained at approximately 70-80% confluence in the growing media consisting of high glucose DMEM (Invitrogen, Carlsbad, California), 10% fetal bovine serum (BSA, Sigma-Aldrich, St. Louis, Missouri), 2 mM L-glutamine (Invitrogen), 10mM hepes (Invitrogen) and 1% penicillin-streptomycin (Invitrogen) at 37C, 5% CO2.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from frozen cell pellet using standard Qiagen Rneasy kit by the vendor Gene Logic Incorporated.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	cDNA was synthesized using 1-2 ug of high quality total RNA. Supercript II™ (Invitrogen) was used to reverse-transcribe the mRNA in the presence of a T7 containing oligo dT24 primer followed by second strand synthesis as recommended by Affymetrix. cDNA was purified using Agencourt RNAClean magnetic beads and used as a template for in vitro transcription using the GeneChip® One-Cycle Labeling Kit from Affymetrix. cRNA was purified using Agencourt magnetic beads and the quantity and purity of the cRNA was determined by absorbance at 260 nm and 260/280 absorbance ratio respectively. The quality of the cRNA was evaluated by assessing the size distribution of the cRNA using a 1.25% MOPS gel. This was performed by the vendor Gene Logic Incorporated.
Sample_hyb_protocol	The labeled cRNA was fragmented as recommended by Affymetrix and 10 µg was added to a hybridization cocktail prior to loading onto individual HG-U133_Plus_2 GeneChip®. The microarrays were hybridized at 45°C for 16- 24 hours and washed and stained on an Affymetrix FS450 fluidics station according to manufacturer recommendations. This was performed by the vendor Gene Logic Incorporated.
Sample_scan_protocol	The microarrays were scanned on a GeneChip® Scanner 3000. This was performed by the vendor Gene Logic Incorporated.
Sample_data_processing	All of the array files were normalized using the Robust Multi-Array Average (RMA) method and log2 transformed using the following Bioconductor and R programs: affy (1.18.2), affyio (1.8.1), annaffy (1.12.1), annotate (1.18.0), AnnotationDbi (1.2.2), base (2.7.2), Biobase (2.0.1), chron (2.3-32), contrast (0.11), datasets (2.7.2), DBI (0.2-4), Design (2.3-0), gcrma (2.12.1), genefilter (1.20.1), GO.db (2.2.0), graphics (2.7.2), grDevices (2.7.2), Hmisc (3.7-0), KEGG.db (2.2.0), lattice (0.17-13), limma (2.14.7), MASS (7.2-44), matchprobes (1.12.1), methods (2.7.2), multtest (2.0.0), nlme (3.1-89), odfWeave (0.7.11), preprocessCore (1.2.1), RSQLite (0.7-3), simpleaffy (2.16.1), splines (2.7.2), stats (2.7.2), survival (2.34-1), tools (2.7.2), utils (2.7.2), XML (2.6-0) and xtable (1.5-5).
Sample_platform_id	GPL570
Sample_contact_name	Wanida,,Ruangsiriluk
Sample_contact_email	wanida.ruangsiriluk@pfizer.com
Sample_contact_department	CVMED
Sample_contact_institute	Pfizer Inc.
Sample_contact_address	Eastern Point Road
Sample_contact_city	Groton
Sample_contact_state	CT
Sample_contact_zip/postal_code	06340
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM694nnn/GSM694042/suppl/GSM694042.CEL.gz
Sample_series_id	GSE28059
Sample_data_row_count	54675

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