Result

Search results for the GEO ID: GSE19909

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Title

Source name

Description

Characteristics

GSM497586

GPL1355

JR1

Vascular smooth muscle cells

stress/flow condition: Static control sample pairing: 1

none

Sample_geo_accession	GSM497586
Sample_status	Public on Apr 01 2010
Sample_submission_date	Jan 15 2010
Sample_last_update_date	Jan 15 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Confluent rat SMC monolayers were exposed to arterial levels of fluid shear stress (14 dynes/cm2)14 for 24 h in a parallel-plate flow chamber. In brief, flow over the cell culture was obtained by a hydrostatic gradient created through differences in height position between two cell culture media reservoirs, one above and one below the chamber. The fluid level in the upper reservoir was maintained by a roller pump (323E/D, Watson-Marlow Alitea Pump, Wilmington, MA, USA). Shear stress was calculated from the volume flow through the chamber according to the formula (6 x Q x µ)/(b x h2). Q=flow (3 ml/s) µ=viscosity (0.01 dyne second/cm2) b=width of the flow channel (4.4 cm) and h=height of the flow channel (0.054 cm). Flow through the chamber was laminar with an approximate Reynolds number of 7.28 for a mean shear stress level of 14 dynes/cm2. Cells were inspected by phase-contrast microscopy before and after shear stress exposure and static incubation to ensure cell viability and to exclude significant cellular detachment. All experiments were carried out at 37°C in an atmosphere with 100% humidity and 5% CO2.
Sample_growth_protocol_ch1	Rat aortic SMCs of passage 3-5 were expanded in F-12 HAM/10% fetal calf serum (FCS) containing ascorbic acid (AA) and penicillin-streptomycin (PEST). Prior to all experiments, cells were synchronized for 24 h in F-12 HAM/0.1% bovine serum albumin (BSA) supplemented with AA and PEST.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell cultures were scraped from culture dishes, suspended in sterile phosphate-buffered saline (PBS) and transferred to centrifuge tubes. Rat carotid arteries were homogenized in Trizol using a Fastprep homogenizing device (Thermo Scientific, Waltham, MA, USA). Cell suspensions were centrifuged for 5 mins at 900 rpm, the supernatant removed, and the pellets resuspended in 1 ml of Trizol (Qiagen, Hilden, Germany). 200 µl phenol-chloroform was added to the suspensions, and RNA isolation proceeded according to protocol supplied by the manufacturer. Total RNA was eluted in 50 µl RNAse-free water, and RNA quality determined on a RNA Nano chip with an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA) and RNA quantity was assessed using a Nanodrop 1000 spectrophotometer (Thermo Scientific).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix one-cycle protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Standard protocol, Affymetrix Core center, BEA, Karolinska Institute, Sweden
Sample_scan_protocol	Standard protocol, Affymetrix Core center, BEA, Karolinska Institute, Sweden
Sample_data_processing	Microarray Suite version 5.0 (MAS 5.0).
Sample_platform_id	GPL1355
Sample_contact_name	Lasse,,Folkersen
Sample_contact_email	lassefolkersen@gmail.com
Sample_contact_phone	+4529936063
Sample_contact_department	Department of Medicine
Sample_contact_institute	Karolinska Institute
Sample_contact_address	L8:03
Sample_contact_city	Stockholm
Sample_contact_zip/postal_code	17176
Sample_contact_country	Sweden
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM497nnn/GSM497586/suppl/GSM497586.CEL.gz
Sample_series_id	GSE19909
Sample_data_row_count	31099

GSM497587

GPL1355

JR2

Vascular smooth muscle cells

stress/flow condition: Static control sample pairing: 2

none

Sample_geo_accession	GSM497587
Sample_status	Public on Apr 01 2010
Sample_submission_date	Jan 15 2010
Sample_last_update_date	Jan 15 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Confluent rat SMC monolayers were exposed to arterial levels of fluid shear stress (14 dynes/cm2)14 for 24 h in a parallel-plate flow chamber. In brief, flow over the cell culture was obtained by a hydrostatic gradient created through differences in height position between two cell culture media reservoirs, one above and one below the chamber. The fluid level in the upper reservoir was maintained by a roller pump (323E/D, Watson-Marlow Alitea Pump, Wilmington, MA, USA). Shear stress was calculated from the volume flow through the chamber according to the formula (6 x Q x µ)/(b x h2). Q=flow (3 ml/s) µ=viscosity (0.01 dyne second/cm2) b=width of the flow channel (4.4 cm) and h=height of the flow channel (0.054 cm). Flow through the chamber was laminar with an approximate Reynolds number of 7.28 for a mean shear stress level of 14 dynes/cm2. Cells were inspected by phase-contrast microscopy before and after shear stress exposure and static incubation to ensure cell viability and to exclude significant cellular detachment. All experiments were carried out at 37°C in an atmosphere with 100% humidity and 5% CO2.
Sample_growth_protocol_ch1	Rat aortic SMCs of passage 3-5 were expanded in F-12 HAM/10% fetal calf serum (FCS) containing ascorbic acid (AA) and penicillin-streptomycin (PEST). Prior to all experiments, cells were synchronized for 24 h in F-12 HAM/0.1% bovine serum albumin (BSA) supplemented with AA and PEST.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell cultures were scraped from culture dishes, suspended in sterile phosphate-buffered saline (PBS) and transferred to centrifuge tubes. Rat carotid arteries were homogenized in Trizol using a Fastprep homogenizing device (Thermo Scientific, Waltham, MA, USA). Cell suspensions were centrifuged for 5 mins at 900 rpm, the supernatant removed, and the pellets resuspended in 1 ml of Trizol (Qiagen, Hilden, Germany). 200 µl phenol-chloroform was added to the suspensions, and RNA isolation proceeded according to protocol supplied by the manufacturer. Total RNA was eluted in 50 µl RNAse-free water, and RNA quality determined on a RNA Nano chip with an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA) and RNA quantity was assessed using a Nanodrop 1000 spectrophotometer (Thermo Scientific).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix one-cycle protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Standard protocol, Affymetrix Core center, BEA, Karolinska Institute, Sweden
Sample_scan_protocol	Standard protocol, Affymetrix Core center, BEA, Karolinska Institute, Sweden
Sample_data_processing	Microarray Suite version 5.0 (MAS 5.0).
Sample_platform_id	GPL1355
Sample_contact_name	Lasse,,Folkersen
Sample_contact_email	lassefolkersen@gmail.com
Sample_contact_phone	+4529936063
Sample_contact_department	Department of Medicine
Sample_contact_institute	Karolinska Institute
Sample_contact_address	L8:03
Sample_contact_city	Stockholm
Sample_contact_zip/postal_code	17176
Sample_contact_country	Sweden
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM497nnn/GSM497587/suppl/GSM497587.CEL.gz
Sample_series_id	GSE19909
Sample_data_row_count	31099

GSM497588

GPL1355

JR3

Vascular smooth muscle cells

stress/flow condition: Static control sample pairing: 3

none

Sample_geo_accession	GSM497588
Sample_status	Public on Apr 01 2010
Sample_submission_date	Jan 15 2010
Sample_last_update_date	Jan 15 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Confluent rat SMC monolayers were exposed to arterial levels of fluid shear stress (14 dynes/cm2)14 for 24 h in a parallel-plate flow chamber. In brief, flow over the cell culture was obtained by a hydrostatic gradient created through differences in height position between two cell culture media reservoirs, one above and one below the chamber. The fluid level in the upper reservoir was maintained by a roller pump (323E/D, Watson-Marlow Alitea Pump, Wilmington, MA, USA). Shear stress was calculated from the volume flow through the chamber according to the formula (6 x Q x µ)/(b x h2). Q=flow (3 ml/s) µ=viscosity (0.01 dyne second/cm2) b=width of the flow channel (4.4 cm) and h=height of the flow channel (0.054 cm). Flow through the chamber was laminar with an approximate Reynolds number of 7.28 for a mean shear stress level of 14 dynes/cm2. Cells were inspected by phase-contrast microscopy before and after shear stress exposure and static incubation to ensure cell viability and to exclude significant cellular detachment. All experiments were carried out at 37°C in an atmosphere with 100% humidity and 5% CO2.
Sample_growth_protocol_ch1	Rat aortic SMCs of passage 3-5 were expanded in F-12 HAM/10% fetal calf serum (FCS) containing ascorbic acid (AA) and penicillin-streptomycin (PEST). Prior to all experiments, cells were synchronized for 24 h in F-12 HAM/0.1% bovine serum albumin (BSA) supplemented with AA and PEST.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell cultures were scraped from culture dishes, suspended in sterile phosphate-buffered saline (PBS) and transferred to centrifuge tubes. Rat carotid arteries were homogenized in Trizol using a Fastprep homogenizing device (Thermo Scientific, Waltham, MA, USA). Cell suspensions were centrifuged for 5 mins at 900 rpm, the supernatant removed, and the pellets resuspended in 1 ml of Trizol (Qiagen, Hilden, Germany). 200 µl phenol-chloroform was added to the suspensions, and RNA isolation proceeded according to protocol supplied by the manufacturer. Total RNA was eluted in 50 µl RNAse-free water, and RNA quality determined on a RNA Nano chip with an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA) and RNA quantity was assessed using a Nanodrop 1000 spectrophotometer (Thermo Scientific).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix one-cycle protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Standard protocol, Affymetrix Core center, BEA, Karolinska Institute, Sweden
Sample_scan_protocol	Standard protocol, Affymetrix Core center, BEA, Karolinska Institute, Sweden
Sample_data_processing	Microarray Suite version 5.0 (MAS 5.0).
Sample_platform_id	GPL1355
Sample_contact_name	Lasse,,Folkersen
Sample_contact_email	lassefolkersen@gmail.com
Sample_contact_phone	+4529936063
Sample_contact_department	Department of Medicine
Sample_contact_institute	Karolinska Institute
Sample_contact_address	L8:03
Sample_contact_city	Stockholm
Sample_contact_zip/postal_code	17176
Sample_contact_country	Sweden
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM497nnn/GSM497588/suppl/GSM497588.CEL.gz
Sample_series_id	GSE19909
Sample_data_row_count	31099

GSM497589

GPL1355

JR4

Vascular smooth muscle cells

stress/flow condition: Fluid shear stress sample pairing: 1

none

Sample_geo_accession	GSM497589
Sample_status	Public on Apr 01 2010
Sample_submission_date	Jan 15 2010
Sample_last_update_date	Jan 15 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Confluent rat SMC monolayers were exposed to arterial levels of fluid shear stress (14 dynes/cm2)14 for 24 h in a parallel-plate flow chamber. In brief, flow over the cell culture was obtained by a hydrostatic gradient created through differences in height position between two cell culture media reservoirs, one above and one below the chamber. The fluid level in the upper reservoir was maintained by a roller pump (323E/D, Watson-Marlow Alitea Pump, Wilmington, MA, USA). Shear stress was calculated from the volume flow through the chamber according to the formula (6 x Q x µ)/(b x h2). Q=flow (3 ml/s) µ=viscosity (0.01 dyne second/cm2) b=width of the flow channel (4.4 cm) and h=height of the flow channel (0.054 cm). Flow through the chamber was laminar with an approximate Reynolds number of 7.28 for a mean shear stress level of 14 dynes/cm2. Cells were inspected by phase-contrast microscopy before and after shear stress exposure and static incubation to ensure cell viability and to exclude significant cellular detachment. All experiments were carried out at 37°C in an atmosphere with 100% humidity and 5% CO2.
Sample_growth_protocol_ch1	Rat aortic SMCs of passage 3-5 were expanded in F-12 HAM/10% fetal calf serum (FCS) containing ascorbic acid (AA) and penicillin-streptomycin (PEST). Prior to all experiments, cells were synchronized for 24 h in F-12 HAM/0.1% bovine serum albumin (BSA) supplemented with AA and PEST.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell cultures were scraped from culture dishes, suspended in sterile phosphate-buffered saline (PBS) and transferred to centrifuge tubes. Rat carotid arteries were homogenized in Trizol using a Fastprep homogenizing device (Thermo Scientific, Waltham, MA, USA). Cell suspensions were centrifuged for 5 mins at 900 rpm, the supernatant removed, and the pellets resuspended in 1 ml of Trizol (Qiagen, Hilden, Germany). 200 µl phenol-chloroform was added to the suspensions, and RNA isolation proceeded according to protocol supplied by the manufacturer. Total RNA was eluted in 50 µl RNAse-free water, and RNA quality determined on a RNA Nano chip with an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA) and RNA quantity was assessed using a Nanodrop 1000 spectrophotometer (Thermo Scientific).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix one-cycle protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Standard protocol, Affymetrix Core center, BEA, Karolinska Institute, Sweden
Sample_scan_protocol	Standard protocol, Affymetrix Core center, BEA, Karolinska Institute, Sweden
Sample_data_processing	Microarray Suite version 5.0 (MAS 5.0).
Sample_platform_id	GPL1355
Sample_contact_name	Lasse,,Folkersen
Sample_contact_email	lassefolkersen@gmail.com
Sample_contact_phone	+4529936063
Sample_contact_department	Department of Medicine
Sample_contact_institute	Karolinska Institute
Sample_contact_address	L8:03
Sample_contact_city	Stockholm
Sample_contact_zip/postal_code	17176
Sample_contact_country	Sweden
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM497nnn/GSM497589/suppl/GSM497589.CEL.gz
Sample_series_id	GSE19909
Sample_data_row_count	31099

GSM497590

GPL1355

JR5

Vascular smooth muscle cells

stress/flow condition: Fluid shear stress sample pairing: 2

none

Sample_geo_accession	GSM497590
Sample_status	Public on Apr 01 2010
Sample_submission_date	Jan 15 2010
Sample_last_update_date	Jan 15 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Confluent rat SMC monolayers were exposed to arterial levels of fluid shear stress (14 dynes/cm2)14 for 24 h in a parallel-plate flow chamber. In brief, flow over the cell culture was obtained by a hydrostatic gradient created through differences in height position between two cell culture media reservoirs, one above and one below the chamber. The fluid level in the upper reservoir was maintained by a roller pump (323E/D, Watson-Marlow Alitea Pump, Wilmington, MA, USA). Shear stress was calculated from the volume flow through the chamber according to the formula (6 x Q x µ)/(b x h2). Q=flow (3 ml/s) µ=viscosity (0.01 dyne second/cm2) b=width of the flow channel (4.4 cm) and h=height of the flow channel (0.054 cm). Flow through the chamber was laminar with an approximate Reynolds number of 7.28 for a mean shear stress level of 14 dynes/cm2. Cells were inspected by phase-contrast microscopy before and after shear stress exposure and static incubation to ensure cell viability and to exclude significant cellular detachment. All experiments were carried out at 37°C in an atmosphere with 100% humidity and 5% CO2.
Sample_growth_protocol_ch1	Rat aortic SMCs of passage 3-5 were expanded in F-12 HAM/10% fetal calf serum (FCS) containing ascorbic acid (AA) and penicillin-streptomycin (PEST). Prior to all experiments, cells were synchronized for 24 h in F-12 HAM/0.1% bovine serum albumin (BSA) supplemented with AA and PEST.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell cultures were scraped from culture dishes, suspended in sterile phosphate-buffered saline (PBS) and transferred to centrifuge tubes. Rat carotid arteries were homogenized in Trizol using a Fastprep homogenizing device (Thermo Scientific, Waltham, MA, USA). Cell suspensions were centrifuged for 5 mins at 900 rpm, the supernatant removed, and the pellets resuspended in 1 ml of Trizol (Qiagen, Hilden, Germany). 200 µl phenol-chloroform was added to the suspensions, and RNA isolation proceeded according to protocol supplied by the manufacturer. Total RNA was eluted in 50 µl RNAse-free water, and RNA quality determined on a RNA Nano chip with an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA) and RNA quantity was assessed using a Nanodrop 1000 spectrophotometer (Thermo Scientific).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix one-cycle protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Standard protocol, Affymetrix Core center, BEA, Karolinska Institute, Sweden
Sample_scan_protocol	Standard protocol, Affymetrix Core center, BEA, Karolinska Institute, Sweden
Sample_data_processing	Microarray Suite version 5.0 (MAS 5.0).
Sample_platform_id	GPL1355
Sample_contact_name	Lasse,,Folkersen
Sample_contact_email	lassefolkersen@gmail.com
Sample_contact_phone	+4529936063
Sample_contact_department	Department of Medicine
Sample_contact_institute	Karolinska Institute
Sample_contact_address	L8:03
Sample_contact_city	Stockholm
Sample_contact_zip/postal_code	17176
Sample_contact_country	Sweden
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM497nnn/GSM497590/suppl/GSM497590.CEL.gz
Sample_series_id	GSE19909
Sample_data_row_count	31099

GSM497591

GPL1355

JR6

Vascular smooth muscle cells

stress/flow condition: Fluid shear stress sample pairing: 3

none

Sample_geo_accession	GSM497591
Sample_status	Public on Apr 01 2010
Sample_submission_date	Jan 15 2010
Sample_last_update_date	Jan 15 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Confluent rat SMC monolayers were exposed to arterial levels of fluid shear stress (14 dynes/cm2)14 for 24 h in a parallel-plate flow chamber. In brief, flow over the cell culture was obtained by a hydrostatic gradient created through differences in height position between two cell culture media reservoirs, one above and one below the chamber. The fluid level in the upper reservoir was maintained by a roller pump (323E/D, Watson-Marlow Alitea Pump, Wilmington, MA, USA). Shear stress was calculated from the volume flow through the chamber according to the formula (6 x Q x µ)/(b x h2). Q=flow (3 ml/s) µ=viscosity (0.01 dyne second/cm2) b=width of the flow channel (4.4 cm) and h=height of the flow channel (0.054 cm). Flow through the chamber was laminar with an approximate Reynolds number of 7.28 for a mean shear stress level of 14 dynes/cm2. Cells were inspected by phase-contrast microscopy before and after shear stress exposure and static incubation to ensure cell viability and to exclude significant cellular detachment. All experiments were carried out at 37°C in an atmosphere with 100% humidity and 5% CO2.
Sample_growth_protocol_ch1	Rat aortic SMCs of passage 3-5 were expanded in F-12 HAM/10% fetal calf serum (FCS) containing ascorbic acid (AA) and penicillin-streptomycin (PEST). Prior to all experiments, cells were synchronized for 24 h in F-12 HAM/0.1% bovine serum albumin (BSA) supplemented with AA and PEST.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Cell cultures were scraped from culture dishes, suspended in sterile phosphate-buffered saline (PBS) and transferred to centrifuge tubes. Rat carotid arteries were homogenized in Trizol using a Fastprep homogenizing device (Thermo Scientific, Waltham, MA, USA). Cell suspensions were centrifuged for 5 mins at 900 rpm, the supernatant removed, and the pellets resuspended in 1 ml of Trizol (Qiagen, Hilden, Germany). 200 µl phenol-chloroform was added to the suspensions, and RNA isolation proceeded according to protocol supplied by the manufacturer. Total RNA was eluted in 50 µl RNAse-free water, and RNA quality determined on a RNA Nano chip with an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA) and RNA quantity was assessed using a Nanodrop 1000 spectrophotometer (Thermo Scientific).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix one-cycle protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Standard protocol, Affymetrix Core center, BEA, Karolinska Institute, Sweden
Sample_scan_protocol	Standard protocol, Affymetrix Core center, BEA, Karolinska Institute, Sweden
Sample_data_processing	Microarray Suite version 5.0 (MAS 5.0).
Sample_platform_id	GPL1355
Sample_contact_name	Lasse,,Folkersen
Sample_contact_email	lassefolkersen@gmail.com
Sample_contact_phone	+4529936063
Sample_contact_department	Department of Medicine
Sample_contact_institute	Karolinska Institute
Sample_contact_address	L8:03
Sample_contact_city	Stockholm
Sample_contact_zip/postal_code	17176
Sample_contact_country	Sweden
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM497nnn/GSM497591/suppl/GSM497591.CEL.gz
Sample_series_id	GSE19909
Sample_data_row_count	31099

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