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Search results for the GEO ID: GSE19345

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GSM480450

GPL570

mock-infected, biological rep1

Human neural stem cell culture

cell type: Post-mortem, fetal, human brain-derived neural stem cells genotype: Normal age: no more than passage 15

Gene expression data from mock-infected cells

Sample_geo_accession	GSM480450
Sample_status	Public on Dec 08 2009
Sample_submission_date	Dec 07 2009
Sample_last_update_date	Dec 07 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	HCMV Towne strain (ATCC#VR977) was used for all infections, and propagated and titrated on a monolayer of human foreskin fibroblasts (HFFs) as described previously (Tamashiro et al., 1982). Prior to virus infection, NPC monolayer cells were seeded onto poly-D-lysine-coated dishes or uncoated dishes containing poly-D-lysine-coated coverslips. Cells were seeded and allowed to attach overnight, infected with a multiplicity of infection (MOI) of 3 and incubated with virus for 2 h to allow for adsorption. The inoculum was then removed and cells were refed (Luo et al., 2008). Medium was refreshed by half every other day as necessary. Cells and coverslips were harvested at the indicated times post-infection (pi).
Sample_growth_protocol_ch1	Human neural stem cells were cultured in growth medium (GM) [DMEM-F12 containing L-glutamine (2mM Glutamax; Gibco/BRL), penicillin/streptomycin (100U/ml and 100µg/ml), gentamicin (50µg/ml), amphotericin B (Fungizone; Gibco/BRL, 2mg/ml), 10% BIT9500 (5mg/ml bovine serum albumin, 5µg/ml recombinant human insulin, 100 µg/ml human transferrin; Stem Cell Technologies), human basic fibroblast growth factor (bFGF; Invitrogen, 20ng/ml) and human epithelial growth factor (EGF; Invitrogen, 20ng/ml)]
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted using the SV Total RNA Isolation kit (Promega).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	First and second strand cDNA was synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and poly (T)-nucleotide primers containing a sequence recognized by T7 RNA polymerase. The resulting cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction, using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics). 15µg of the resulting biotin-tagged cRNA was fragmented to strands of 35-200 bases following prescribed protocols (Affymetrix).
Sample_hyb_protocol	Subsequently, 10 µg of this fragmented target cRNA was hybridized (at 45°C, rotating for 16 hours in an Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix HG-U133 2.0 PLUS array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner 7G.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL570
Sample_contact_name	Philip,Hitchins,Schwartz
Sample_contact_email	pschwartz@choc.org
Sample_contact_phone	7145164310
Sample_contact_fax	7142894531
Sample_contact_laboratory	Neuroscience
Sample_contact_department	Research Institute
Sample_contact_institute	Children's Hospital of Orange County
Sample_contact_address	455 South Main Street
Sample_contact_city	Orange
Sample_contact_state	CA
Sample_contact_zip/postal_code	92868-3874
Sample_contact_country	USA
Sample_contact_web_link	www.nhnscr.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM480nnn/GSM480450/suppl/GSM480450_0908A-03_12hp_Mock_RNA.CEL.gz
Sample_series_id	GSE19345
Sample_data_row_count	54613

GSM480451

GPL570

mock-infected, biological rep2

Human neural stem cell culture

cell type: Post-mortem, fetal, human brain-derived neural stem cells genotype: Normal age: no more than passage 15

Gene expression data from mock-infected cells

Sample_geo_accession	GSM480451
Sample_status	Public on Dec 08 2009
Sample_submission_date	Dec 07 2009
Sample_last_update_date	Dec 07 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	HCMV Towne strain (ATCC#VR977) was used for all infections, and propagated and titrated on a monolayer of human foreskin fibroblasts (HFFs) as described previously (Tamashiro et al., 1982). Prior to virus infection, NPC monolayer cells were seeded onto poly-D-lysine-coated dishes or uncoated dishes containing poly-D-lysine-coated coverslips. Cells were seeded and allowed to attach overnight, infected with a multiplicity of infection (MOI) of 3 and incubated with virus for 2 h to allow for adsorption. The inoculum was then removed and cells were refed (Luo et al., 2008). Medium was refreshed by half every other day as necessary. Cells and coverslips were harvested at the indicated times post-infection (pi).
Sample_growth_protocol_ch1	Human neural stem cells were cultured in growth medium (GM) [DMEM-F12 containing L-glutamine (2mM Glutamax; Gibco/BRL), penicillin/streptomycin (100U/ml and 100µg/ml), gentamicin (50µg/ml), amphotericin B (Fungizone; Gibco/BRL, 2mg/ml), 10% BIT9500 (5mg/ml bovine serum albumin, 5µg/ml recombinant human insulin, 100 µg/ml human transferrin; Stem Cell Technologies), human basic fibroblast growth factor (bFGF; Invitrogen, 20ng/ml) and human epithelial growth factor (EGF; Invitrogen, 20ng/ml)]
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted using the SV Total RNA Isolation kit (Promega).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	First and second strand cDNA was synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and poly (T)-nucleotide primers containing a sequence recognized by T7 RNA polymerase. The resulting cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction, using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics). 15µg of the resulting biotin-tagged cRNA was fragmented to strands of 35-200 bases following prescribed protocols (Affymetrix).
Sample_hyb_protocol	Subsequently, 10 µg of this fragmented target cRNA was hybridized (at 45°C, rotating for 16 hours in an Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix HG-U133 2.0 PLUS array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner 7G.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL570
Sample_contact_name	Philip,Hitchins,Schwartz
Sample_contact_email	pschwartz@choc.org
Sample_contact_phone	7145164310
Sample_contact_fax	7142894531
Sample_contact_laboratory	Neuroscience
Sample_contact_department	Research Institute
Sample_contact_institute	Children's Hospital of Orange County
Sample_contact_address	455 South Main Street
Sample_contact_city	Orange
Sample_contact_state	CA
Sample_contact_zip/postal_code	92868-3874
Sample_contact_country	USA
Sample_contact_web_link	www.nhnscr.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM480nnn/GSM480451/suppl/GSM480451_0908A-03_M12_SC27_RNA_8.14.08.CEL.gz
Sample_series_id	GSE19345
Sample_data_row_count	54613

GSM480452

GPL570

4 hours post-infection, biological rep1

Human neural stem cell culture

cell type: Post-mortem, fetal, human brain-derived neural stem cells genotype: Normal age: no more than passage 15

Gene expression data from cells 4 hours after HCMV infection

Sample_geo_accession	GSM480452
Sample_status	Public on Dec 08 2009
Sample_submission_date	Dec 07 2009
Sample_last_update_date	Dec 07 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	HCMV Towne strain (ATCC#VR977) was used for all infections, and propagated and titrated on a monolayer of human foreskin fibroblasts (HFFs) as described previously (Tamashiro et al., 1982). Prior to virus infection, NPC monolayer cells were seeded onto poly-D-lysine-coated dishes or uncoated dishes containing poly-D-lysine-coated coverslips. Cells were seeded and allowed to attach overnight, infected with a multiplicity of infection (MOI) of 3 and incubated with virus for 2 h to allow for adsorption. The inoculum was then removed and cells were refed (Luo et al., 2008). Medium was refreshed by half every other day as necessary. Cells and coverslips were harvested at the indicated times post-infection (pi).
Sample_growth_protocol_ch1	Human neural stem cells were cultured in growth medium (GM) [DMEM-F12 containing L-glutamine (2mM Glutamax; Gibco/BRL), penicillin/streptomycin (100U/ml and 100µg/ml), gentamicin (50µg/ml), amphotericin B (Fungizone; Gibco/BRL, 2mg/ml), 10% BIT9500 (5mg/ml bovine serum albumin, 5µg/ml recombinant human insulin, 100 µg/ml human transferrin; Stem Cell Technologies), human basic fibroblast growth factor (bFGF; Invitrogen, 20ng/ml) and human epithelial growth factor (EGF; Invitrogen, 20ng/ml)]
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted using the SV Total RNA Isolation kit (Promega).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	First and second strand cDNA was synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and poly (T)-nucleotide primers containing a sequence recognized by T7 RNA polymerase. The resulting cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction, using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics). 15µg of the resulting biotin-tagged cRNA was fragmented to strands of 35-200 bases following prescribed protocols (Affymetrix).
Sample_hyb_protocol	Subsequently, 10 µg of this fragmented target cRNA was hybridized (at 45°C, rotating for 16 hours in an Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix HG-U133 2.0 PLUS array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner 7G.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL570
Sample_contact_name	Philip,Hitchins,Schwartz
Sample_contact_email	pschwartz@choc.org
Sample_contact_phone	7145164310
Sample_contact_fax	7142894531
Sample_contact_laboratory	Neuroscience
Sample_contact_department	Research Institute
Sample_contact_institute	Children's Hospital of Orange County
Sample_contact_address	455 South Main Street
Sample_contact_city	Orange
Sample_contact_state	CA
Sample_contact_zip/postal_code	92868-3874
Sample_contact_country	USA
Sample_contact_web_link	www.nhnscr.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM480nnn/GSM480452/suppl/GSM480452_0908A-03_4hp_Towne_RNA.CEL.gz
Sample_series_id	GSE19345
Sample_data_row_count	54613

GSM480453

GPL570

4 hours post-infection, biological rep2

Human neural stem cell culture

cell type: Post-mortem, fetal, human brain-derived neural stem cells genotype: Normal age: no more than passage 15

Gene expression data from cells 4 hours after HCMV infection

Sample_geo_accession	GSM480453
Sample_status	Public on Dec 08 2009
Sample_submission_date	Dec 07 2009
Sample_last_update_date	Dec 07 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	HCMV Towne strain (ATCC#VR977) was used for all infections, and propagated and titrated on a monolayer of human foreskin fibroblasts (HFFs) as described previously (Tamashiro et al., 1982). Prior to virus infection, NPC monolayer cells were seeded onto poly-D-lysine-coated dishes or uncoated dishes containing poly-D-lysine-coated coverslips. Cells were seeded and allowed to attach overnight, infected with a multiplicity of infection (MOI) of 3 and incubated with virus for 2 h to allow for adsorption. The inoculum was then removed and cells were refed (Luo et al., 2008). Medium was refreshed by half every other day as necessary. Cells and coverslips were harvested at the indicated times post-infection (pi).
Sample_growth_protocol_ch1	Human neural stem cells were cultured in growth medium (GM) [DMEM-F12 containing L-glutamine (2mM Glutamax; Gibco/BRL), penicillin/streptomycin (100U/ml and 100µg/ml), gentamicin (50µg/ml), amphotericin B (Fungizone; Gibco/BRL, 2mg/ml), 10% BIT9500 (5mg/ml bovine serum albumin, 5µg/ml recombinant human insulin, 100 µg/ml human transferrin; Stem Cell Technologies), human basic fibroblast growth factor (bFGF; Invitrogen, 20ng/ml) and human epithelial growth factor (EGF; Invitrogen, 20ng/ml)]
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted using the SV Total RNA Isolation kit (Promega).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	First and second strand cDNA was synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and poly (T)-nucleotide primers containing a sequence recognized by T7 RNA polymerase. The resulting cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction, using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics). 15µg of the resulting biotin-tagged cRNA was fragmented to strands of 35-200 bases following prescribed protocols (Affymetrix).
Sample_hyb_protocol	Subsequently, 10 µg of this fragmented target cRNA was hybridized (at 45°C, rotating for 16 hours in an Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix HG-U133 2.0 PLUS array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner 7G.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL570
Sample_contact_name	Philip,Hitchins,Schwartz
Sample_contact_email	pschwartz@choc.org
Sample_contact_phone	7145164310
Sample_contact_fax	7142894531
Sample_contact_laboratory	Neuroscience
Sample_contact_department	Research Institute
Sample_contact_institute	Children's Hospital of Orange County
Sample_contact_address	455 South Main Street
Sample_contact_city	Orange
Sample_contact_state	CA
Sample_contact_zip/postal_code	92868-3874
Sample_contact_country	USA
Sample_contact_web_link	www.nhnscr.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM480nnn/GSM480453/suppl/GSM480453_0908A-03_V4_SC27_RNA_8.14.08.CEL.gz
Sample_series_id	GSE19345
Sample_data_row_count	54613

GSM480454

GPL570

12 hours post-infection, biological rep1

Human neural stem cell culture

cell type: Post-mortem, fetal, human brain-derived neural stem cells genotype: Normal age: no more than passage 15

Gene expression data from cells 12 hours after HCMV infection

Sample_geo_accession	GSM480454
Sample_status	Public on Dec 08 2009
Sample_submission_date	Dec 07 2009
Sample_last_update_date	Dec 07 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	HCMV Towne strain (ATCC#VR977) was used for all infections, and propagated and titrated on a monolayer of human foreskin fibroblasts (HFFs) as described previously (Tamashiro et al., 1982). Prior to virus infection, NPC monolayer cells were seeded onto poly-D-lysine-coated dishes or uncoated dishes containing poly-D-lysine-coated coverslips. Cells were seeded and allowed to attach overnight, infected with a multiplicity of infection (MOI) of 3 and incubated with virus for 2 h to allow for adsorption. The inoculum was then removed and cells were refed (Luo et al., 2008). Medium was refreshed by half every other day as necessary. Cells and coverslips were harvested at the indicated times post-infection (pi).
Sample_growth_protocol_ch1	Human neural stem cells were cultured in growth medium (GM) [DMEM-F12 containing L-glutamine (2mM Glutamax; Gibco/BRL), penicillin/streptomycin (100U/ml and 100µg/ml), gentamicin (50µg/ml), amphotericin B (Fungizone; Gibco/BRL, 2mg/ml), 10% BIT9500 (5mg/ml bovine serum albumin, 5µg/ml recombinant human insulin, 100 µg/ml human transferrin; Stem Cell Technologies), human basic fibroblast growth factor (bFGF; Invitrogen, 20ng/ml) and human epithelial growth factor (EGF; Invitrogen, 20ng/ml)]
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted using the SV Total RNA Isolation kit (Promega).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	First and second strand cDNA was synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and poly (T)-nucleotide primers containing a sequence recognized by T7 RNA polymerase. The resulting cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction, using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics). 15µg of the resulting biotin-tagged cRNA was fragmented to strands of 35-200 bases following prescribed protocols (Affymetrix).
Sample_hyb_protocol	Subsequently, 10 µg of this fragmented target cRNA was hybridized (at 45°C, rotating for 16 hours in an Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix HG-U133 2.0 PLUS array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner 7G.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL570
Sample_contact_name	Philip,Hitchins,Schwartz
Sample_contact_email	pschwartz@choc.org
Sample_contact_phone	7145164310
Sample_contact_fax	7142894531
Sample_contact_laboratory	Neuroscience
Sample_contact_department	Research Institute
Sample_contact_institute	Children's Hospital of Orange County
Sample_contact_address	455 South Main Street
Sample_contact_city	Orange
Sample_contact_state	CA
Sample_contact_zip/postal_code	92868-3874
Sample_contact_country	USA
Sample_contact_web_link	www.nhnscr.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM480nnn/GSM480454/suppl/GSM480454_0908A-03_12hp_Towne_RNA.CEL.gz
Sample_series_id	GSE19345
Sample_data_row_count	54613

GSM480455

GPL570

12 hours post-infection, biological rep2

Human neural stem cell culture

cell type: Post-mortem, fetal, human brain-derived neural stem cells genotype: Normal age: no more than passage 15

Gene expression data from cells 12 hours after HCMV infection

Sample_geo_accession	GSM480455
Sample_status	Public on Dec 08 2009
Sample_submission_date	Dec 07 2009
Sample_last_update_date	Dec 07 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	HCMV Towne strain (ATCC#VR977) was used for all infections, and propagated and titrated on a monolayer of human foreskin fibroblasts (HFFs) as described previously (Tamashiro et al., 1982). Prior to virus infection, NPC monolayer cells were seeded onto poly-D-lysine-coated dishes or uncoated dishes containing poly-D-lysine-coated coverslips. Cells were seeded and allowed to attach overnight, infected with a multiplicity of infection (MOI) of 3 and incubated with virus for 2 h to allow for adsorption. The inoculum was then removed and cells were refed (Luo et al., 2008). Medium was refreshed by half every other day as necessary. Cells and coverslips were harvested at the indicated times post-infection (pi).
Sample_growth_protocol_ch1	Human neural stem cells were cultured in growth medium (GM) [DMEM-F12 containing L-glutamine (2mM Glutamax; Gibco/BRL), penicillin/streptomycin (100U/ml and 100µg/ml), gentamicin (50µg/ml), amphotericin B (Fungizone; Gibco/BRL, 2mg/ml), 10% BIT9500 (5mg/ml bovine serum albumin, 5µg/ml recombinant human insulin, 100 µg/ml human transferrin; Stem Cell Technologies), human basic fibroblast growth factor (bFGF; Invitrogen, 20ng/ml) and human epithelial growth factor (EGF; Invitrogen, 20ng/ml)]
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted using the SV Total RNA Isolation kit (Promega).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	First and second strand cDNA was synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and poly (T)-nucleotide primers containing a sequence recognized by T7 RNA polymerase. The resulting cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction, using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics). 15µg of the resulting biotin-tagged cRNA was fragmented to strands of 35-200 bases following prescribed protocols (Affymetrix).
Sample_hyb_protocol	Subsequently, 10 µg of this fragmented target cRNA was hybridized (at 45°C, rotating for 16 hours in an Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix HG-U133 2.0 PLUS array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner 7G.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL570
Sample_contact_name	Philip,Hitchins,Schwartz
Sample_contact_email	pschwartz@choc.org
Sample_contact_phone	7145164310
Sample_contact_fax	7142894531
Sample_contact_laboratory	Neuroscience
Sample_contact_department	Research Institute
Sample_contact_institute	Children's Hospital of Orange County
Sample_contact_address	455 South Main Street
Sample_contact_city	Orange
Sample_contact_state	CA
Sample_contact_zip/postal_code	92868-3874
Sample_contact_country	USA
Sample_contact_web_link	www.nhnscr.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM480nnn/GSM480455/suppl/GSM480455_0908A-03_V12_SC27_RNA_8.14.08.CEL.gz
Sample_series_id	GSE19345
Sample_data_row_count	54613

GSM480456

GPL570

24 hours post-infection, biological rep1

Human neural stem cell culture

cell type: Post-mortem, fetal, human brain-derived neural stem cells genotype: Normal age: no more than passage 15

Gene expression data from cells 24 hours after HCMV infection

Sample_geo_accession	GSM480456
Sample_status	Public on Dec 08 2009
Sample_submission_date	Dec 07 2009
Sample_last_update_date	Dec 07 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	HCMV Towne strain (ATCC#VR977) was used for all infections, and propagated and titrated on a monolayer of human foreskin fibroblasts (HFFs) as described previously (Tamashiro et al., 1982). Prior to virus infection, NPC monolayer cells were seeded onto poly-D-lysine-coated dishes or uncoated dishes containing poly-D-lysine-coated coverslips. Cells were seeded and allowed to attach overnight, infected with a multiplicity of infection (MOI) of 3 and incubated with virus for 2 h to allow for adsorption. The inoculum was then removed and cells were refed (Luo et al., 2008). Medium was refreshed by half every other day as necessary. Cells and coverslips were harvested at the indicated times post-infection (pi).
Sample_growth_protocol_ch1	Human neural stem cells were cultured in growth medium (GM) [DMEM-F12 containing L-glutamine (2mM Glutamax; Gibco/BRL), penicillin/streptomycin (100U/ml and 100µg/ml), gentamicin (50µg/ml), amphotericin B (Fungizone; Gibco/BRL, 2mg/ml), 10% BIT9500 (5mg/ml bovine serum albumin, 5µg/ml recombinant human insulin, 100 µg/ml human transferrin; Stem Cell Technologies), human basic fibroblast growth factor (bFGF; Invitrogen, 20ng/ml) and human epithelial growth factor (EGF; Invitrogen, 20ng/ml)]
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted using the SV Total RNA Isolation kit (Promega).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	First and second strand cDNA was synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and poly (T)-nucleotide primers containing a sequence recognized by T7 RNA polymerase. The resulting cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction, using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics). 15µg of the resulting biotin-tagged cRNA was fragmented to strands of 35-200 bases following prescribed protocols (Affymetrix).
Sample_hyb_protocol	Subsequently, 10 µg of this fragmented target cRNA was hybridized (at 45°C, rotating for 16 hours in an Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix HG-U133 2.0 PLUS array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner 7G.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL570
Sample_contact_name	Philip,Hitchins,Schwartz
Sample_contact_email	pschwartz@choc.org
Sample_contact_phone	7145164310
Sample_contact_fax	7142894531
Sample_contact_laboratory	Neuroscience
Sample_contact_department	Research Institute
Sample_contact_institute	Children's Hospital of Orange County
Sample_contact_address	455 South Main Street
Sample_contact_city	Orange
Sample_contact_state	CA
Sample_contact_zip/postal_code	92868-3874
Sample_contact_country	USA
Sample_contact_web_link	www.nhnscr.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM480nnn/GSM480456/suppl/GSM480456_0908A-03_24hp_Towne_RNA.CEL.gz
Sample_series_id	GSE19345
Sample_data_row_count	54613

GSM480457

GPL570

24 hours post-infection, biological rep2

Human neural stem cell culture

cell type: Post-mortem, fetal, human brain-derived neural stem cells genotype: Normal age: no more than passage 15

Gene expression data from cells 24 hours after HCMV infection

Sample_geo_accession	GSM480457
Sample_status	Public on Dec 08 2009
Sample_submission_date	Dec 07 2009
Sample_last_update_date	Dec 07 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	HCMV Towne strain (ATCC#VR977) was used for all infections, and propagated and titrated on a monolayer of human foreskin fibroblasts (HFFs) as described previously (Tamashiro et al., 1982). Prior to virus infection, NPC monolayer cells were seeded onto poly-D-lysine-coated dishes or uncoated dishes containing poly-D-lysine-coated coverslips. Cells were seeded and allowed to attach overnight, infected with a multiplicity of infection (MOI) of 3 and incubated with virus for 2 h to allow for adsorption. The inoculum was then removed and cells were refed (Luo et al., 2008). Medium was refreshed by half every other day as necessary. Cells and coverslips were harvested at the indicated times post-infection (pi).
Sample_growth_protocol_ch1	Human neural stem cells were cultured in growth medium (GM) [DMEM-F12 containing L-glutamine (2mM Glutamax; Gibco/BRL), penicillin/streptomycin (100U/ml and 100µg/ml), gentamicin (50µg/ml), amphotericin B (Fungizone; Gibco/BRL, 2mg/ml), 10% BIT9500 (5mg/ml bovine serum albumin, 5µg/ml recombinant human insulin, 100 µg/ml human transferrin; Stem Cell Technologies), human basic fibroblast growth factor (bFGF; Invitrogen, 20ng/ml) and human epithelial growth factor (EGF; Invitrogen, 20ng/ml)]
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted using the SV Total RNA Isolation kit (Promega).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	First and second strand cDNA was synthesized using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and poly (T)-nucleotide primers containing a sequence recognized by T7 RNA polymerase. The resulting cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction, using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics). 15µg of the resulting biotin-tagged cRNA was fragmented to strands of 35-200 bases following prescribed protocols (Affymetrix).
Sample_hyb_protocol	Subsequently, 10 µg of this fragmented target cRNA was hybridized (at 45°C, rotating for 16 hours in an Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix HG-U133 2.0 PLUS array. The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip 3000 Scanner 7G.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL570
Sample_contact_name	Philip,Hitchins,Schwartz
Sample_contact_email	pschwartz@choc.org
Sample_contact_phone	7145164310
Sample_contact_fax	7142894531
Sample_contact_laboratory	Neuroscience
Sample_contact_department	Research Institute
Sample_contact_institute	Children's Hospital of Orange County
Sample_contact_address	455 South Main Street
Sample_contact_city	Orange
Sample_contact_state	CA
Sample_contact_zip/postal_code	92868-3874
Sample_contact_country	USA
Sample_contact_web_link	www.nhnscr.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM480nnn/GSM480457/suppl/GSM480457_0908A-03_V24_SC27_RNA_8.14.08.CEL.gz
Sample_series_id	GSE19345
Sample_data_row_count	54613

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