Result

Search results for the GEO ID: GSE31678

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM786342

GPL1355

Control - NV, biological rep 1

Rat Lung - dorsal caudal quadrant

strain: Sprague-Dawley condition: Non-ventilated gender: Male

Sample_geo_accession	GSM786342
Sample_status	Public on Aug 27 2011
Sample_submission_date	Aug 26 2011
Sample_last_update_date	Aug 27 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Male Harlan Sprague-Dawley rats (340~400 g; Indianapolis, IN) were anesthetized and a tracheotomy and jugular cannulation performed. High Vt ventilation (HVt; 18 ml/Kg, RR 40 breaths/min, PEEP 0 cmH2O), in either the prone or supine position (PPV or SPV, respectively) was administered for up to 3 hours. Non-ventilated rats were used as controls.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Microarray targets were prepared and labeled from 300 ng total RNA using the MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin,TX) following the manufacturer’s instructions.
Sample_hyb_protocol	standard Affymetrix procedures
Sample_scan_protocol	standard Affymetrix procedures, using the Affy GCS3000
Sample_data_processing	Hybridization intensities were quantified and normalized across all arrays using GC-RMA as implemented by Partek Genomics Suite v6.5 software (St.Louis, MO). Non-expressed transcripts were eliminated if all values for a transcript were below background levels of expression (calculated at 3.5 log2 expression units). The remaining ‘present’ transcripts (20,242 of 31,099) were used for all subsequent statistical and visual analysis.
Sample_platform_id	GPL1355
Sample_contact_name	Michael,,Edwards
Sample_contact_email	michael.edwards@ucdenver.edu
Sample_contact_phone	303-724-6054
Sample_contact_fax	303-724-6042
Sample_contact_department	Pulmonary
Sample_contact_institute	UC Denver
Sample_contact_address	12700 East 19th Avenue, Box C272
Sample_contact_city	Aurora
Sample_contact_state	CO
Sample_contact_zip/postal_code	80045
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786342/suppl/GSM786342_Rat_Control_NV_R1.CEL.gz
Sample_series_id	GSE31678
Sample_data_row_count	20242

GSM786343

GPL1355

Control - NV, biological rep 2

Rat Lung - dorsal caudal quadrant

strain: Sprague-Dawley condition: Non-ventilated gender: Male

Sample_geo_accession	GSM786343
Sample_status	Public on Aug 27 2011
Sample_submission_date	Aug 26 2011
Sample_last_update_date	Aug 27 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Male Harlan Sprague-Dawley rats (340~400 g; Indianapolis, IN) were anesthetized and a tracheotomy and jugular cannulation performed. High Vt ventilation (HVt; 18 ml/Kg, RR 40 breaths/min, PEEP 0 cmH2O), in either the prone or supine position (PPV or SPV, respectively) was administered for up to 3 hours. Non-ventilated rats were used as controls.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Microarray targets were prepared and labeled from 300 ng total RNA using the MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin,TX) following the manufacturer’s instructions.
Sample_hyb_protocol	standard Affymetrix procedures
Sample_scan_protocol	standard Affymetrix procedures, using the Affy GCS3000
Sample_data_processing	Hybridization intensities were quantified and normalized across all arrays using GC-RMA as implemented by Partek Genomics Suite v6.5 software (St.Louis, MO). Non-expressed transcripts were eliminated if all values for a transcript were below background levels of expression (calculated at 3.5 log2 expression units). The remaining ‘present’ transcripts (20,242 of 31,099) were used for all subsequent statistical and visual analysis.
Sample_platform_id	GPL1355
Sample_contact_name	Michael,,Edwards
Sample_contact_email	michael.edwards@ucdenver.edu
Sample_contact_phone	303-724-6054
Sample_contact_fax	303-724-6042
Sample_contact_department	Pulmonary
Sample_contact_institute	UC Denver
Sample_contact_address	12700 East 19th Avenue, Box C272
Sample_contact_city	Aurora
Sample_contact_state	CO
Sample_contact_zip/postal_code	80045
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786343/suppl/GSM786343_Rat_Control_NV_R2.CEL.gz
Sample_series_id	GSE31678
Sample_data_row_count	20242

GSM786344

GPL1355

Prone - HVt, biological rep 1

Rat Lung - dorsal caudal quadrant

strain: Sprague-Dawley condition: High Vt body position: Prone gender: Male

Sample_geo_accession	GSM786344
Sample_status	Public on Aug 27 2011
Sample_submission_date	Aug 26 2011
Sample_last_update_date	Aug 27 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Male Harlan Sprague-Dawley rats (340~400 g; Indianapolis, IN) were anesthetized and a tracheotomy and jugular cannulation performed. High Vt ventilation (HVt; 18 ml/Kg, RR 40 breaths/min, PEEP 0 cmH2O), in either the prone or supine position (PPV or SPV, respectively) was administered for up to 3 hours. Non-ventilated rats were used as controls.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Microarray targets were prepared and labeled from 300 ng total RNA using the MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin,TX) following the manufacturer’s instructions.
Sample_hyb_protocol	standard Affymetrix procedures
Sample_scan_protocol	standard Affymetrix procedures, using the Affy GCS3000
Sample_data_processing	Hybridization intensities were quantified and normalized across all arrays using GC-RMA as implemented by Partek Genomics Suite v6.5 software (St.Louis, MO). Non-expressed transcripts were eliminated if all values for a transcript were below background levels of expression (calculated at 3.5 log2 expression units). The remaining ‘present’ transcripts (20,242 of 31,099) were used for all subsequent statistical and visual analysis.
Sample_platform_id	GPL1355
Sample_contact_name	Michael,,Edwards
Sample_contact_email	michael.edwards@ucdenver.edu
Sample_contact_phone	303-724-6054
Sample_contact_fax	303-724-6042
Sample_contact_department	Pulmonary
Sample_contact_institute	UC Denver
Sample_contact_address	12700 East 19th Avenue, Box C272
Sample_contact_city	Aurora
Sample_contact_state	CO
Sample_contact_zip/postal_code	80045
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786344/suppl/GSM786344_Rat_Prone_HVt_R1.CEL.gz
Sample_series_id	GSE31678
Sample_data_row_count	20242

GSM786345

GPL1355

Prone - HVt, biological rep 2

Rat Lung - dorsal caudal quadrant

strain: Sprague-Dawley condition: High Vt body position: Prone gender: Male

Sample_geo_accession	GSM786345
Sample_status	Public on Aug 27 2011
Sample_submission_date	Aug 26 2011
Sample_last_update_date	Aug 27 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Male Harlan Sprague-Dawley rats (340~400 g; Indianapolis, IN) were anesthetized and a tracheotomy and jugular cannulation performed. High Vt ventilation (HVt; 18 ml/Kg, RR 40 breaths/min, PEEP 0 cmH2O), in either the prone or supine position (PPV or SPV, respectively) was administered for up to 3 hours. Non-ventilated rats were used as controls.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Microarray targets were prepared and labeled from 300 ng total RNA using the MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin,TX) following the manufacturer’s instructions.
Sample_hyb_protocol	standard Affymetrix procedures
Sample_scan_protocol	standard Affymetrix procedures, using the Affy GCS3000
Sample_data_processing	Hybridization intensities were quantified and normalized across all arrays using GC-RMA as implemented by Partek Genomics Suite v6.5 software (St.Louis, MO). Non-expressed transcripts were eliminated if all values for a transcript were below background levels of expression (calculated at 3.5 log2 expression units). The remaining ‘present’ transcripts (20,242 of 31,099) were used for all subsequent statistical and visual analysis.
Sample_platform_id	GPL1355
Sample_contact_name	Michael,,Edwards
Sample_contact_email	michael.edwards@ucdenver.edu
Sample_contact_phone	303-724-6054
Sample_contact_fax	303-724-6042
Sample_contact_department	Pulmonary
Sample_contact_institute	UC Denver
Sample_contact_address	12700 East 19th Avenue, Box C272
Sample_contact_city	Aurora
Sample_contact_state	CO
Sample_contact_zip/postal_code	80045
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786345/suppl/GSM786345_Rat_Prone_HVt_R2.CEL.gz
Sample_series_id	GSE31678
Sample_data_row_count	20242

GSM786346

GPL1355

Prone - HVt, biological rep 3

Rat Lung - dorsal caudal quadrant

strain: Sprague-Dawley condition: High Vt body position: Prone gender: Male

Sample_geo_accession	GSM786346
Sample_status	Public on Aug 27 2011
Sample_submission_date	Aug 26 2011
Sample_last_update_date	Aug 27 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Male Harlan Sprague-Dawley rats (340~400 g; Indianapolis, IN) were anesthetized and a tracheotomy and jugular cannulation performed. High Vt ventilation (HVt; 18 ml/Kg, RR 40 breaths/min, PEEP 0 cmH2O), in either the prone or supine position (PPV or SPV, respectively) was administered for up to 3 hours. Non-ventilated rats were used as controls.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Microarray targets were prepared and labeled from 300 ng total RNA using the MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin,TX) following the manufacturer’s instructions.
Sample_hyb_protocol	standard Affymetrix procedures
Sample_scan_protocol	standard Affymetrix procedures, using the Affy GCS3000
Sample_data_processing	Hybridization intensities were quantified and normalized across all arrays using GC-RMA as implemented by Partek Genomics Suite v6.5 software (St.Louis, MO). Non-expressed transcripts were eliminated if all values for a transcript were below background levels of expression (calculated at 3.5 log2 expression units). The remaining ‘present’ transcripts (20,242 of 31,099) were used for all subsequent statistical and visual analysis.
Sample_platform_id	GPL1355
Sample_contact_name	Michael,,Edwards
Sample_contact_email	michael.edwards@ucdenver.edu
Sample_contact_phone	303-724-6054
Sample_contact_fax	303-724-6042
Sample_contact_department	Pulmonary
Sample_contact_institute	UC Denver
Sample_contact_address	12700 East 19th Avenue, Box C272
Sample_contact_city	Aurora
Sample_contact_state	CO
Sample_contact_zip/postal_code	80045
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786346/suppl/GSM786346_Rat_Prone_HVt_R3.CEL.gz
Sample_series_id	GSE31678
Sample_data_row_count	20242

GSM786347

GPL1355

Supine - SVt, biological rep 1

Rat Lung - dorsal caudal quadrant

strain: Sprague-Dawley condition: High Vt body position: Supine gender: Male

Sample_geo_accession	GSM786347
Sample_status	Public on Aug 27 2011
Sample_submission_date	Aug 26 2011
Sample_last_update_date	Aug 27 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Male Harlan Sprague-Dawley rats (340~400 g; Indianapolis, IN) were anesthetized and a tracheotomy and jugular cannulation performed. High Vt ventilation (HVt; 18 ml/Kg, RR 40 breaths/min, PEEP 0 cmH2O), in either the prone or supine position (PPV or SPV, respectively) was administered for up to 3 hours. Non-ventilated rats were used as controls.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Microarray targets were prepared and labeled from 300 ng total RNA using the MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin,TX) following the manufacturer’s instructions.
Sample_hyb_protocol	standard Affymetrix procedures
Sample_scan_protocol	standard Affymetrix procedures, using the Affy GCS3000
Sample_data_processing	Hybridization intensities were quantified and normalized across all arrays using GC-RMA as implemented by Partek Genomics Suite v6.5 software (St.Louis, MO). Non-expressed transcripts were eliminated if all values for a transcript were below background levels of expression (calculated at 3.5 log2 expression units). The remaining ‘present’ transcripts (20,242 of 31,099) were used for all subsequent statistical and visual analysis.
Sample_platform_id	GPL1355
Sample_contact_name	Michael,,Edwards
Sample_contact_email	michael.edwards@ucdenver.edu
Sample_contact_phone	303-724-6054
Sample_contact_fax	303-724-6042
Sample_contact_department	Pulmonary
Sample_contact_institute	UC Denver
Sample_contact_address	12700 East 19th Avenue, Box C272
Sample_contact_city	Aurora
Sample_contact_state	CO
Sample_contact_zip/postal_code	80045
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786347/suppl/GSM786347_Rat_Supine_HVt_R1.CEL.gz
Sample_series_id	GSE31678
Sample_data_row_count	20242

GSM786348

GPL1355

Supine - SVt, biological rep 2

Rat Lung - dorsal caudal quadrant

strain: Sprague-Dawley condition: High Vt body position: Supine gender: Male

Sample_geo_accession	GSM786348
Sample_status	Public on Aug 27 2011
Sample_submission_date	Aug 26 2011
Sample_last_update_date	Aug 27 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Male Harlan Sprague-Dawley rats (340~400 g; Indianapolis, IN) were anesthetized and a tracheotomy and jugular cannulation performed. High Vt ventilation (HVt; 18 ml/Kg, RR 40 breaths/min, PEEP 0 cmH2O), in either the prone or supine position (PPV or SPV, respectively) was administered for up to 3 hours. Non-ventilated rats were used as controls.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Microarray targets were prepared and labeled from 300 ng total RNA using the MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin,TX) following the manufacturer’s instructions.
Sample_hyb_protocol	standard Affymetrix procedures
Sample_scan_protocol	standard Affymetrix procedures, using the Affy GCS3000
Sample_data_processing	Hybridization intensities were quantified and normalized across all arrays using GC-RMA as implemented by Partek Genomics Suite v6.5 software (St.Louis, MO). Non-expressed transcripts were eliminated if all values for a transcript were below background levels of expression (calculated at 3.5 log2 expression units). The remaining ‘present’ transcripts (20,242 of 31,099) were used for all subsequent statistical and visual analysis.
Sample_platform_id	GPL1355
Sample_contact_name	Michael,,Edwards
Sample_contact_email	michael.edwards@ucdenver.edu
Sample_contact_phone	303-724-6054
Sample_contact_fax	303-724-6042
Sample_contact_department	Pulmonary
Sample_contact_institute	UC Denver
Sample_contact_address	12700 East 19th Avenue, Box C272
Sample_contact_city	Aurora
Sample_contact_state	CO
Sample_contact_zip/postal_code	80045
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786348/suppl/GSM786348_Rat_Supine_HVt_R2.CEL.gz
Sample_series_id	GSE31678
Sample_data_row_count	20242

GSM786349

GPL1355

Supine - SVt, biological rep 3

Rat Lung - dorsal caudal quadrant

strain: Sprague-Dawley condition: High Vt body position: Supine gender: Male

Sample_geo_accession	GSM786349
Sample_status	Public on Aug 27 2011
Sample_submission_date	Aug 26 2011
Sample_last_update_date	Aug 27 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Male Harlan Sprague-Dawley rats (340~400 g; Indianapolis, IN) were anesthetized and a tracheotomy and jugular cannulation performed. High Vt ventilation (HVt; 18 ml/Kg, RR 40 breaths/min, PEEP 0 cmH2O), in either the prone or supine position (PPV or SPV, respectively) was administered for up to 3 hours. Non-ventilated rats were used as controls.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Microarray targets were prepared and labeled from 300 ng total RNA using the MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin,TX) following the manufacturer’s instructions.
Sample_hyb_protocol	standard Affymetrix procedures
Sample_scan_protocol	standard Affymetrix procedures, using the Affy GCS3000
Sample_data_processing	Hybridization intensities were quantified and normalized across all arrays using GC-RMA as implemented by Partek Genomics Suite v6.5 software (St.Louis, MO). Non-expressed transcripts were eliminated if all values for a transcript were below background levels of expression (calculated at 3.5 log2 expression units). The remaining ‘present’ transcripts (20,242 of 31,099) were used for all subsequent statistical and visual analysis.
Sample_platform_id	GPL1355
Sample_contact_name	Michael,,Edwards
Sample_contact_email	michael.edwards@ucdenver.edu
Sample_contact_phone	303-724-6054
Sample_contact_fax	303-724-6042
Sample_contact_department	Pulmonary
Sample_contact_institute	UC Denver
Sample_contact_address	12700 East 19th Avenue, Box C272
Sample_contact_city	Aurora
Sample_contact_state	CO
Sample_contact_zip/postal_code	80045
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM786nnn/GSM786349/suppl/GSM786349_Rat_Supine_HVt_R3.CEL.gz
Sample_series_id	GSE31678
Sample_data_row_count	20242

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