Result

Search results for the GEO ID: GSE19315

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM479983

GPL570

Untreated replicate 1

THP-1 cells

cell type: Human myelogenous leukemia (macrophage-like) cells cell line: THP-1

The results visualized with a Gene Array scanner using Affymetrix software.

Sample_geo_accession	GSM479983
Sample_status	Public on Mar 31 2010
Sample_submission_date	Dec 03 2009
Sample_last_update_date	Mar 31 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	ATTC
Sample_treatment_protocol_ch1	Untreated
Sample_growth_protocol_ch1	The cells were maintained in RPMI 1640 (GIBCO-BRL, Grand Island, NY) supplemented with 10% fetal bovine serum (HyClone Laboratories, Logan, UT), penicillin (100 U/ml), and streptomycin (100 ug/ml) at 37°C in 5% CO2 in a humidified incubator.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from macrophage-like THP-1 cells was isolated using the RNAqueous kit (Ambion, Austin, TX), and 20 ug of total RNA was processed for microarray analysis. Briefly, cDNA synthesis, in vitro transcription, labeling and fragmentation to produce the oligonucleotide probes were performed following the GeneChip manufacturer’s instructions (Affymetrix, Santa Clara, CA). The probes were first hybridized to a test array (Affymetrix) and then to the GeneChip human genome HG-U133 Array (containing 54,675 probe sets representing more than 39,000 transcripts derived from ~33,000 well-substantiated human genes) using the GeneChip Hybridization Oven 640. The chips were washed in a GeneChip Fluidics Station 400 (Affymetrix), and the results visualized with a Gene Array scanner using Affymetrix software. The data were analyzed using the following software: GeneSifter (VizX Labs, Seattle, WA), Significance Analysis of Microarrays (SAM; Stanford University, Stanford, CA), and Spotfire DecisionSite 9.0 (Spotfire, Inc., Somerville, MA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Performed by UTMB microarray core per manufacturer's instructions
Sample_hyb_protocol	Performed by UTMB microarray core per manufacturer's instructions
Sample_scan_protocol	Performed by UTMB microarray core per manufacturer's instructions. The results visualized with a Gene Array scanner using Affymetrix software.
Sample_data_processing	RMA normalization was performed using GeneSifter (VizX Labs, Seattle, WA).
Sample_platform_id	GPL570
Sample_contact_name	Ashok,K,Chopra
Sample_contact_email	achopra@utmb.edu
Sample_contact_phone	409-747-0573
Sample_contact_fax	409-747-6869
Sample_contact_department	Microbiology & Immunology
Sample_contact_institute	University of Texas Medical Branch
Sample_contact_address	301 University Blvd.
Sample_contact_city	Galveston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77555
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479983/suppl/GSM479983.CEL.gz
Sample_series_id	GSE19315
Sample_data_row_count	54675

GSM479985

GPL570

Untreated replicate 3

THP-1 cells

cell type: Human myelogenous leukemia (macrophage-like) cells cell line: THP-1

Performed by UTMB microarray core per manufacturer's instructions

Sample_geo_accession	GSM479985
Sample_status	Public on Mar 31 2010
Sample_submission_date	Dec 03 2009
Sample_last_update_date	Mar 31 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	ATTC
Sample_treatment_protocol_ch1	Untreated
Sample_growth_protocol_ch1	The cells were maintained in RPMI 1640 (GIBCO-BRL, Grand Island, NY) supplemented with 10% fetal bovine serum (HyClone Laboratories, Logan, UT), penicillin (100 U/ml), and streptomycin (100 ug/ml) at 37°C in 5% CO2 in a humidified incubator.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from macrophage-like THP-1 cells was isolated using the RNAqueous kit (Ambion, Austin, TX), and 20 ug of total RNA was processed for microarray analysis. Briefly, cDNA synthesis, in vitro transcription, labeling and fragmentation to produce the oligonucleotide probes were performed following the GeneChip manufacturer’s instructions (Affymetrix, Santa Clara, CA). The probes were first hybridized to a test array (Affymetrix) and then to the GeneChip human genome HG-U133 Array (containing 54,675 probe sets representing more than 39,000 transcripts derived from ~33,000 well-substantiated human genes) using the GeneChip Hybridization Oven 640. The chips were washed in a GeneChip Fluidics Station 400 (Affymetrix), and the results visualized with a Gene Array scanner using Affymetrix software. The data were analyzed using the following software: GeneSifter (VizX Labs, Seattle, WA), Significance Analysis of Microarrays (SAM; Stanford University, Stanford, CA), and Spotfire DecisionSite 9.0 (Spotfire, Inc., Somerville, MA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Performed by UTMB microarray core per manufacturer's instructions
Sample_hyb_protocol	Performed by UTMB microarray core per manufacturer's instructions
Sample_scan_protocol	Performed by UTMB microarray core per manufacturer's instructions. The results visualized with a Gene Array scanner using Affymetrix software.
Sample_data_processing	Data were RMA normalized using GeneSifter (VizX Labs, Seattle, WA).
Sample_platform_id	GPL570
Sample_contact_name	Ashok,K,Chopra
Sample_contact_email	achopra@utmb.edu
Sample_contact_phone	409-747-0573
Sample_contact_fax	409-747-6869
Sample_contact_department	Microbiology & Immunology
Sample_contact_institute	University of Texas Medical Branch
Sample_contact_address	301 University Blvd.
Sample_contact_city	Galveston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77555
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479985/suppl/GSM479985.CEL.gz
Sample_series_id	GSE19315
Sample_data_row_count	54675

GSM479986

GPL570

LPS-treated_6h replicate 1

THP-1 cells

cell type: Human myelogenous leukemia (macrophage-like) cells cell line: THP-1

Performed by UTMB microarray core per manufacturer's instructions

Sample_geo_accession	GSM479986
Sample_status	Public on Mar 31 2010
Sample_submission_date	Dec 03 2009
Sample_last_update_date	Mar 31 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	ATTC
Sample_treatment_protocol_ch1	Treated with LPS for 6h: Purified LPS derived from the enterohemorrhagic E. coli serotype O111 was purchased from Sigma Chemical Co (St. Louis, MO). Cells were washed with cold PBS before stimulation with LPS (200 ng/ml) in RPMI-1640 + 0.5% FBS for 6h
Sample_growth_protocol_ch1	The cells were maintained in RPMI 1640 (GIBCO-BRL, Grand Island, NY) supplemented with 10% fetal bovine serum (HyClone Laboratories, Logan, UT), penicillin (100 U/ml), and streptomycin (100 ug/ml) at 37°C in 5% CO2 in a humidified incubator.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from macrophage-like THP-1 cells was isolated using the RNAqueous kit (Ambion, Austin, TX), and 20 ug of total RNA was processed for microarray analysis. Briefly, cDNA synthesis, in vitro transcription, labeling and fragmentation to produce the oligonucleotide probes were performed following the GeneChip manufacturer’s instructions (Affymetrix, Santa Clara, CA). The probes were first hybridized to a test array (Affymetrix) and then to the GeneChip human genome HG-U133 Array (containing 54,675 probe sets representing more than 39,000 transcripts derived from ~33,000 well-substantiated human genes) using the GeneChip Hybridization Oven 640. The chips were washed in a GeneChip Fluidics Station 400 (Affymetrix), and the results visualized with a Gene Array scanner using Affymetrix software. The data were analyzed using the following software: GeneSifter (VizX Labs, Seattle, WA), Significance Analysis of Microarrays (SAM; Stanford University, Stanford, CA), and Spotfire DecisionSite 9.0 (Spotfire, Inc., Somerville, MA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Performed by UTMB microarray core per manufacturer's instructions
Sample_hyb_protocol	Performed by UTMB microarray core per manufacturer's instructions
Sample_scan_protocol	Performed by UTMB microarray core per manufacturer's instructions. The results visualized with a Gene Array scanner using Affymetrix software.
Sample_data_processing	Data were RMA normalized using GeneSifter (VizX Labs, Seattle, WA).
Sample_platform_id	GPL570
Sample_contact_name	Ashok,K,Chopra
Sample_contact_email	achopra@utmb.edu
Sample_contact_phone	409-747-0573
Sample_contact_fax	409-747-6869
Sample_contact_department	Microbiology & Immunology
Sample_contact_institute	University of Texas Medical Branch
Sample_contact_address	301 University Blvd.
Sample_contact_city	Galveston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77555
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479986/suppl/GSM479986.CEL.gz
Sample_series_id	GSE19315
Sample_data_row_count	54675

GSM479987

GPL570

LPS-treated_6h replicate 2

THP-1 cells

cell type: Human myelogenous leukemia (macrophage-like) cells cell line: THP-1

Performed by UTMB microarray core per manufacturer's instructions

Sample_geo_accession	GSM479987
Sample_status	Public on Mar 31 2010
Sample_submission_date	Dec 03 2009
Sample_last_update_date	Mar 31 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	ATTC
Sample_treatment_protocol_ch1	Treated with LPS for 6h: Purified LPS derived from the enterohemorrhagic E. coli serotype O111 was purchased from Sigma Chemical Co (St. Louis, MO). Cells were washed with cold PBS before stimulation with LPS (200 ng/ml) in RPMI-1640 + 0.5% FBS for 6h
Sample_growth_protocol_ch1	The cells were maintained in RPMI 1640 (GIBCO-BRL, Grand Island, NY) supplemented with 10% fetal bovine serum (HyClone Laboratories, Logan, UT), penicillin (100 U/ml), and streptomycin (100 ug/ml) at 37°C in 5% CO2 in a humidified incubator.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from macrophage-like THP-1 cells was isolated using the RNAqueous kit (Ambion, Austin, TX), and 20 ug of total RNA was processed for microarray analysis. Briefly, cDNA synthesis, in vitro transcription, labeling and fragmentation to produce the oligonucleotide probes were performed following the GeneChip manufacturer’s instructions (Affymetrix, Santa Clara, CA). The probes were first hybridized to a test array (Affymetrix) and then to the GeneChip human genome HG-U133 Array (containing 54,675 probe sets representing more than 39,000 transcripts derived from ~33,000 well-substantiated human genes) using the GeneChip Hybridization Oven 640. The chips were washed in a GeneChip Fluidics Station 400 (Affymetrix), and the results visualized with a Gene Array scanner using Affymetrix software. The data were analyzed using the following software: GeneSifter (VizX Labs, Seattle, WA), Significance Analysis of Microarrays (SAM; Stanford University, Stanford, CA), and Spotfire DecisionSite 9.0 (Spotfire, Inc., Somerville, MA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Performed by UTMB microarray core per manufacturer's instructions
Sample_hyb_protocol	Performed by UTMB microarray core per manufacturer's instructions
Sample_scan_protocol	Performed by UTMB microarray core per manufacturer's instructions. The results visualized with a Gene Array scanner using Affymetrix software.
Sample_data_processing	Data were RMA normalized using GeneSifter (VizX Labs, Seattle, WA).
Sample_platform_id	GPL570
Sample_contact_name	Ashok,K,Chopra
Sample_contact_email	achopra@utmb.edu
Sample_contact_phone	409-747-0573
Sample_contact_fax	409-747-6869
Sample_contact_department	Microbiology & Immunology
Sample_contact_institute	University of Texas Medical Branch
Sample_contact_address	301 University Blvd.
Sample_contact_city	Galveston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77555
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479987/suppl/GSM479987.CEL.gz
Sample_series_id	GSE19315
Sample_data_row_count	54675

GSM479988

GPL570

LPS-treated_6h replicate 3

THP-1 cells

cell type: Human myelogenous leukemia (macrophage-like) cells cell line: THP-1

Performed by UTMB microarray core per manufacturer's instructions

Sample_geo_accession	GSM479988
Sample_status	Public on Mar 31 2010
Sample_submission_date	Dec 03 2009
Sample_last_update_date	Mar 31 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	ATTC
Sample_treatment_protocol_ch1	Treated with LPS for 6h: Purified LPS derived from the enterohemorrhagic E. coli serotype O111 was purchased from Sigma Chemical Co (St. Louis, MO). Cells were washed with cold PBS before stimulation with LPS (200 ng/ml) in RPMI-1640 + 0.5% FBS for 6h
Sample_growth_protocol_ch1	The cells were maintained in RPMI 1640 (GIBCO-BRL, Grand Island, NY) supplemented with 10% fetal bovine serum (HyClone Laboratories, Logan, UT), penicillin (100 U/ml), and streptomycin (100 ug/ml) at 37°C in 5% CO2 in a humidified incubator.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from macrophage-like THP-1 cells was isolated using the RNAqueous kit (Ambion, Austin, TX), and 20 ug of total RNA was processed for microarray analysis. Briefly, cDNA synthesis, in vitro transcription, labeling and fragmentation to produce the oligonucleotide probes were performed following the GeneChip manufacturer’s instructions (Affymetrix, Santa Clara, CA). The probes were first hybridized to a test array (Affymetrix) and then to the GeneChip human genome HG-U133 Array (containing 54,675 probe sets representing more than 39,000 transcripts derived from ~33,000 well-substantiated human genes) using the GeneChip Hybridization Oven 640. The chips were washed in a GeneChip Fluidics Station 400 (Affymetrix), and the results visualized with a Gene Array scanner using Affymetrix software. The data were analyzed using the following software: GeneSifter (VizX Labs, Seattle, WA), Significance Analysis of Microarrays (SAM; Stanford University, Stanford, CA), and Spotfire DecisionSite 9.0 (Spotfire, Inc., Somerville, MA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Performed by UTMB microarray core per manufacturer's instructions
Sample_hyb_protocol	Performed by UTMB microarray core per manufacturer's instructions
Sample_scan_protocol	Performed by UTMB microarray core per manufacturer's instructions. The results visualized with a Gene Array scanner using Affymetrix software.
Sample_data_processing	Data were RMA normalized using GeneSifter (VizX Labs, Seattle, WA).
Sample_platform_id	GPL570
Sample_contact_name	Ashok,K,Chopra
Sample_contact_email	achopra@utmb.edu
Sample_contact_phone	409-747-0573
Sample_contact_fax	409-747-6869
Sample_contact_department	Microbiology & Immunology
Sample_contact_institute	University of Texas Medical Branch
Sample_contact_address	301 University Blvd.
Sample_contact_city	Galveston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77555
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479988/suppl/GSM479988.CEL.gz
Sample_series_id	GSE19315
Sample_data_row_count	54675

GSM479989

GPL570

ST-treated_6h replicate 1

THP-1 cells

cell type: Human myelogenous leukemia (macrophage-like) cells cell line: THP-1

Performed by UTMB microarray core per manufacturer's instructions

Sample_geo_accession	GSM479989
Sample_status	Public on Mar 31 2010
Sample_submission_date	Dec 03 2009
Sample_last_update_date	Mar 31 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	ATTC
Sample_treatment_protocol_ch1	Treated with LPS for 6h: Purified LPS derived from the enterohemorrhagic E. coli serotype O111 was purchased from Sigma Chemical Co (St. Louis, MO). Cells were washed with cold PBS before stimulation with Stx1 (400 ng/ml) in RPMI-1640 + 0.5% FBS for 6h
Sample_growth_protocol_ch1	The cells were maintained in RPMI 1640 (GIBCO-BRL, Grand Island, NY) supplemented with 10% fetal bovine serum (HyClone Laboratories, Logan, UT), penicillin (100 U/ml), and streptomycin (100 ug/ml) at 37°C in 5% CO2 in a humidified incubator.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from macrophage-like THP-1 cells was isolated using the RNAqueous kit (Ambion, Austin, TX), and 20 ug of total RNA was processed for microarray analysis. Briefly, cDNA synthesis, in vitro transcription, labeling and fragmentation to produce the oligonucleotide probes were performed following the GeneChip manufacturer’s instructions (Affymetrix, Santa Clara, CA). The probes were first hybridized to a test array (Affymetrix) and then to the GeneChip human genome HG-U133 Array (containing 54,675 probe sets representing more than 39,000 transcripts derived from ~33,000 well-substantiated human genes) using the GeneChip Hybridization Oven 640. The chips were washed in a GeneChip Fluidics Station 400 (Affymetrix), and the results visualized with a Gene Array scanner using Affymetrix software. The data were analyzed using the following software: GeneSifter (VizX Labs, Seattle, WA), Significance Analysis of Microarrays (SAM; Stanford University, Stanford, CA), and Spotfire DecisionSite 9.0 (Spotfire, Inc., Somerville, MA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Performed by UTMB microarray core per manufacturer's instructions
Sample_hyb_protocol	Performed by UTMB microarray core per manufacturer's instructions
Sample_scan_protocol	Performed by UTMB microarray core per manufacturer's instructions. The results visualized with a Gene Array scanner using Affymetrix software.
Sample_data_processing	Data were RMA normalized using GeneSifter (VizX Labs, Seattle, WA).
Sample_platform_id	GPL570
Sample_contact_name	Ashok,K,Chopra
Sample_contact_email	achopra@utmb.edu
Sample_contact_phone	409-747-0573
Sample_contact_fax	409-747-6869
Sample_contact_department	Microbiology & Immunology
Sample_contact_institute	University of Texas Medical Branch
Sample_contact_address	301 University Blvd.
Sample_contact_city	Galveston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77555
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479989/suppl/GSM479989.CEL.gz
Sample_series_id	GSE19315
Sample_data_row_count	54675

GSM479990

GPL570

ST-treated_6h replicate 2

THP-1 cells

cell type: Human myelogenous leukemia (macrophage-like) cells cell line: THP-1

Performed by UTMB microarray core per manufacturer's instructions

Sample_geo_accession	GSM479990
Sample_status	Public on Mar 31 2010
Sample_submission_date	Dec 03 2009
Sample_last_update_date	Mar 31 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	ATTC
Sample_treatment_protocol_ch1	Treated with LPS for 6h: Purified LPS derived from the enterohemorrhagic E. coli serotype O111 was purchased from Sigma Chemical Co (St. Louis, MO). Cells were washed with cold PBS before stimulation with Stx1 (400 ng/ml) in RPMI-1640 + 0.5% FBS for 6h
Sample_growth_protocol_ch1	The cells were maintained in RPMI 1640 (GIBCO-BRL, Grand Island, NY) supplemented with 10% fetal bovine serum (HyClone Laboratories, Logan, UT), penicillin (100 U/ml), and streptomycin (100 ug/ml) at 37°C in 5% CO2 in a humidified incubator.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from macrophage-like THP-1 cells was isolated using the RNAqueous kit (Ambion, Austin, TX), and 20 ug of total RNA was processed for microarray analysis. Briefly, cDNA synthesis, in vitro transcription, labeling and fragmentation to produce the oligonucleotide probes were performed following the GeneChip manufacturer’s instructions (Affymetrix, Santa Clara, CA). The probes were first hybridized to a test array (Affymetrix) and then to the GeneChip human genome HG-U133 Array (containing 54,675 probe sets representing more than 39,000 transcripts derived from ~33,000 well-substantiated human genes) using the GeneChip Hybridization Oven 640. The chips were washed in a GeneChip Fluidics Station 400 (Affymetrix), and the results visualized with a Gene Array scanner using Affymetrix software. The data were analyzed using the following software: GeneSifter (VizX Labs, Seattle, WA), Significance Analysis of Microarrays (SAM; Stanford University, Stanford, CA), and Spotfire DecisionSite 9.0 (Spotfire, Inc., Somerville, MA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Performed by UTMB microarray core per manufacturer's instructions
Sample_hyb_protocol	Performed by UTMB microarray core per manufacturer's instructions
Sample_scan_protocol	Performed by UTMB microarray core per manufacturer's instructions. The results visualized with a Gene Array scanner using Affymetrix software.
Sample_data_processing	Data were RMA normalized using GeneSifter (VizX Labs, Seattle, WA).
Sample_platform_id	GPL570
Sample_contact_name	Ashok,K,Chopra
Sample_contact_email	achopra@utmb.edu
Sample_contact_phone	409-747-0573
Sample_contact_fax	409-747-6869
Sample_contact_department	Microbiology & Immunology
Sample_contact_institute	University of Texas Medical Branch
Sample_contact_address	301 University Blvd.
Sample_contact_city	Galveston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77555
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479990/suppl/GSM479990.CEL.gz
Sample_series_id	GSE19315
Sample_data_row_count	54675

GSM479991

GPL570

ST-treated_6h replicate 3

THP-1 cells

cell type: Human myelogenous leukemia (macrophage-like) cells cell line: THP-1

Performed by UTMB microarray core per manufacturer's instructions

Sample_geo_accession	GSM479991
Sample_status	Public on Mar 31 2010
Sample_submission_date	Dec 03 2009
Sample_last_update_date	Mar 31 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	ATTC
Sample_treatment_protocol_ch1	Treated with LPS for 6h: Purified LPS derived from the enterohemorrhagic E. coli serotype O111 was purchased from Sigma Chemical Co (St. Louis, MO). Cells were washed with cold PBS before stimulation with Stx1 (400 ng/ml) in RPMI-1640 + 0.5% FBS for 6h
Sample_growth_protocol_ch1	The cells were maintained in RPMI 1640 (GIBCO-BRL, Grand Island, NY) supplemented with 10% fetal bovine serum (HyClone Laboratories, Logan, UT), penicillin (100 U/ml), and streptomycin (100 ug/ml) at 37°C in 5% CO2 in a humidified incubator.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from macrophage-like THP-1 cells was isolated using the RNAqueous kit (Ambion, Austin, TX), and 20 ug of total RNA was processed for microarray analysis. Briefly, cDNA synthesis, in vitro transcription, labeling and fragmentation to produce the oligonucleotide probes were performed following the GeneChip manufacturer’s instructions (Affymetrix, Santa Clara, CA). The probes were first hybridized to a test array (Affymetrix) and then to the GeneChip human genome HG-U133 Array (containing 54,675 probe sets representing more than 39,000 transcripts derived from ~33,000 well-substantiated human genes) using the GeneChip Hybridization Oven 640. The chips were washed in a GeneChip Fluidics Station 400 (Affymetrix), and the results visualized with a Gene Array scanner using Affymetrix software. The data were analyzed using the following software: GeneSifter (VizX Labs, Seattle, WA), Significance Analysis of Microarrays (SAM; Stanford University, Stanford, CA), and Spotfire DecisionSite 9.0 (Spotfire, Inc., Somerville, MA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Performed by UTMB microarray core per manufacturer's instructions
Sample_hyb_protocol	Performed by UTMB microarray core per manufacturer's instructions
Sample_scan_protocol	Performed by UTMB microarray core per manufacturer's instructions. The results visualized with a Gene Array scanner using Affymetrix software.
Sample_data_processing	Data were RMA normalized using GeneSifter (VizX Labs, Seattle, WA).
Sample_platform_id	GPL570
Sample_contact_name	Ashok,K,Chopra
Sample_contact_email	achopra@utmb.edu
Sample_contact_phone	409-747-0573
Sample_contact_fax	409-747-6869
Sample_contact_department	Microbiology & Immunology
Sample_contact_institute	University of Texas Medical Branch
Sample_contact_address	301 University Blvd.
Sample_contact_city	Galveston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77555
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM479nnn/GSM479991/suppl/GSM479991.CEL.gz
Sample_series_id	GSE19315
Sample_data_row_count	54675

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