Search results for the GEO ID: GSE6332  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM146384 | GPL85 |
|
Sham Shock Biological replicate 1
|
Rat Lung
|
Sham Shock
|
Sham-shock animals underwent cannulation of the femoral artery and jugular vein followed by a laparotomy; however, no blood was withdrawn and the MAP was kept within normal limits.
|
| Sample_geo_accession | GSM146384
| | Sample_status | Public on Jul 25 2007
| | Sample_submission_date | Nov 20 2006
| | Sample_last_update_date | Jul 25 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Sham-shock animals (T/SS) underwent cannulation of the femoral artery and jugular vein followed by a laparotomy; however, no blood was withdrawn and the MAP was kept within normal limits. The temperature of the rats was maintained at 37ºC with the use of a heating pad as needed. Three hours after resuscitation, the animals were sacrificed and lung removed, snap-frozen in liquid nitrogen and stored at -80ºC until use.
| | Sample_growth_protocol_ch1 | Specific pathogen-free male Sprague-Dawley rats (Charles River Laboratories, Portage, MI) weighing 300-420 grams were housed for at least 1 week before use and were maintained according to the recommendations of the National Institutes of Health Guide for Care and Use of Laboratory Animals. The animals were fed standard chow and water. All experiments were approved by the New Jersey Medical School Animal Care and Use Committee.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRizol reagent (Invitrogen, Gaithersburg, MD).
| | Sample_label_ch1 | Biotin Label
| | Sample_label_protocol_ch1 | cDNA and cRNA synthesis were performed according to Affymetrix Expression Analysis protocols (see www.affymetrix.com). Briefly, double-stranded cDNA was synthesized from 5 ug of total RNA using the Superscript double-stranded cDNA synthesis kit (Invitrogen). Following phenol/chloroform extraction and ethanol precipitation, a biotin-labeled in vitro transcription reaction was carried out using the cDNA template (Enzo Life Sciences, Farmingdale, NY). Fifteen ug of cRNA was fragmented for hybridization to Affymetrix RG-U34A GeneChips (Santa Clara, CA), which contains ~8,800 known rat transcripts and EST’s.
| | Sample_hyb_protocol | Hybridization was done overnight at 45ºC for 16 hours using the Genechip Hybridization Oven 640 (Affymetrix). Washing and staining (Streptavidin Phycoerythrin) was performed using the Genechip Fluidics Station 450 (Affymetrix) using the EukGE-WS2v4 protocol.
| | Sample_scan_protocol | Images were acquired using the Affymetrix GeneArray Scanner 3000. Data was extracted using Affymetrix GeneChip Operating Software version 1.0.
| | Sample_data_processing | Data was extracted using Affymetrix GeneChip Operating Software version 1.0. Expression intensity values were extracted from the CEL files using the Robust Multi-Array Average algorithm in ArrayAssist version 3.2 (Stratagene). Quantile normalization was performed to normalize the distribution of probe intensities for all the arrays in a given set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Virginie,Marie,Aris
| | Sample_contact_email | arisvm@umdnj.edu
| | Sample_contact_phone | 973-854-3455
| | Sample_contact_fax | 973-854-3453
| | Sample_contact_laboratory | Soteropoulos
| | Sample_contact_department | Center For Applied Genomics
| | Sample_contact_institute | PHRI-UMNDJ
| | Sample_contact_address | W420M, 225 Warren St
| | Sample_contact_city | Newark
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07103
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.cag.icph.org/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM146nnn/GSM146384/suppl/GSM146384.CEL.gz
| | Sample_series_id | GSE6332
| | Sample_data_row_count | 8799
| | |
|
GSM146385 | GPL85 |
|
Sham Shock Biological replicate 2
|
Rat Lung
|
Sham Shock
|
Sham-shock animals underwent cannulation of the femoral artery and jugular vein followed by a laparotomy; however, no blood was withdrawn and the MAP was kept within normal limits.
|
| Sample_geo_accession | GSM146385
| | Sample_status | Public on Jul 25 2007
| | Sample_submission_date | Nov 20 2006
| | Sample_last_update_date | Jul 25 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Sham-shock animals (T/SS) underwent cannulation of the femoral artery and jugular vein followed by a laparotomy; however, no blood was withdrawn and the MAP was kept within normal limits. The temperature of the rats was maintained at 37ºC with the use of a heating pad as needed. Three hours after resuscitation, the animals were sacrificed and lung removed, snap-frozen in liquid nitrogen and stored at -80ºC until use.
| | Sample_growth_protocol_ch1 | Specific pathogen-free male Sprague-Dawley rats (Charles River Laboratories, Portage, MI) weighing 300-420 grams were housed for at least 1 week before use and were maintained according to the recommendations of the National Institutes of Health Guide for Care and Use of Laboratory Animals. The animals were fed standard chow and water. All experiments were approved by the New Jersey Medical School Animal Care and Use Committee.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRizol reagent (Invitrogen, Gaithersburg, MD).
| | Sample_label_ch1 | Biotin Label
| | Sample_label_protocol_ch1 | cDNA and cRNA synthesis were performed according to Affymetrix Expression Analysis protocols (see www.affymetrix.com). Briefly, double-stranded cDNA was synthesized from 5 ug of total RNA using the Superscript double-stranded cDNA synthesis kit (Invitrogen). Following phenol/chloroform extraction and ethanol precipitation, a biotin-labeled in vitro transcription reaction was carried out using the cDNA template (Enzo Life Sciences, Farmingdale, NY). Fifteen ug of cRNA was fragmented for hybridization to Affymetrix RG-U34A GeneChips (Santa Clara, CA), which contains ~8,800 known rat transcripts and EST’s.
| | Sample_hyb_protocol | Hybridization was done overnight at 45ºC for 16 hours using the Genechip Hybridization Oven 640 (Affymetrix). Washing and staining (Streptavidin Phycoerythrin) was performed using the Genechip Fluidics Station 450 (Affymetrix) using the EukGE-WS2v4 protocol.
| | Sample_scan_protocol | Images were acquired using the Affymetrix GeneArray Scanner 3000. Data was extracted using Affymetrix GeneChip Operating Software version 1.0.
| | Sample_data_processing | Data was extracted using Affymetrix GeneChip Operating Software version 1.0. Expression intensity values were extracted from the CEL files using the Robust Multi-Array Average algorithm in ArrayAssist version 3.2 (Stratagene). Quantile normalization was performed to normalize the distribution of probe intensities for all the arrays in a given set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Virginie,Marie,Aris
| | Sample_contact_email | arisvm@umdnj.edu
| | Sample_contact_phone | 973-854-3455
| | Sample_contact_fax | 973-854-3453
| | Sample_contact_laboratory | Soteropoulos
| | Sample_contact_department | Center For Applied Genomics
| | Sample_contact_institute | PHRI-UMNDJ
| | Sample_contact_address | W420M, 225 Warren St
| | Sample_contact_city | Newark
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07103
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.cag.icph.org/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM146nnn/GSM146385/suppl/GSM146385.CEL.gz
| | Sample_series_id | GSE6332
| | Sample_data_row_count | 8799
| | |
|
GSM146386 | GPL85 |
|
Sham Shock Biological replicate 3
|
Rat Lung
|
Sham Shock
|
Sham-shock animals underwent cannulation of the femoral artery and jugular vein followed by a laparotomy; however, no blood was withdrawn and the MAP was kept within normal limits.
|
| Sample_geo_accession | GSM146386
| | Sample_status | Public on Jul 25 2007
| | Sample_submission_date | Nov 20 2006
| | Sample_last_update_date | Jul 25 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Sham-shock animals (T/SS) underwent cannulation of the femoral artery and jugular vein followed by a laparotomy; however, no blood was withdrawn and the MAP was kept within normal limits. The temperature of the rats was maintained at 37ºC with the use of a heating pad as needed. Three hours after resuscitation, the animals were sacrificed and lung removed, snap-frozen in liquid nitrogen and stored at -80ºC until use.
| | Sample_growth_protocol_ch1 | Specific pathogen-free male Sprague-Dawley rats (Charles River Laboratories, Portage, MI) weighing 300-420 grams were housed for at least 1 week before use and were maintained according to the recommendations of the National Institutes of Health Guide for Care and Use of Laboratory Animals. The animals were fed standard chow and water. All experiments were approved by the New Jersey Medical School Animal Care and Use Committee.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRizol reagent (Invitrogen, Gaithersburg, MD).
| | Sample_label_ch1 | Biotin Label
| | Sample_label_protocol_ch1 | cDNA and cRNA synthesis were performed according to Affymetrix Expression Analysis protocols (see www.affymetrix.com). Briefly, double-stranded cDNA was synthesized from 5 ug of total RNA using the Superscript double-stranded cDNA synthesis kit (Invitrogen). Following phenol/chloroform extraction and ethanol precipitation, a biotin-labeled in vitro transcription reaction was carried out using the cDNA template (Enzo Life Sciences, Farmingdale, NY). Fifteen ug of cRNA was fragmented for hybridization to Affymetrix RG-U34A GeneChips (Santa Clara, CA), which contains ~8,800 known rat transcripts and EST’s.
| | Sample_hyb_protocol | Hybridization was done overnight at 45ºC for 16 hours using the Genechip Hybridization Oven 640 (Affymetrix). Washing and staining (Streptavidin Phycoerythrin) was performed using the Genechip Fluidics Station 450 (Affymetrix) using the EukGE-WS2v4 protocol.
| | Sample_scan_protocol | Images were acquired using the Affymetrix GeneArray Scanner 3000. Data was extracted using Affymetrix GeneChip Operating Software version 1.0.
| | Sample_data_processing | Data was extracted using Affymetrix GeneChip Operating Software version 1.0. Expression intensity values were extracted from the CEL files using the Robust Multi-Array Average algorithm in ArrayAssist version 3.2 (Stratagene). Quantile normalization was performed to normalize the distribution of probe intensities for all the arrays in a given set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Virginie,Marie,Aris
| | Sample_contact_email | arisvm@umdnj.edu
| | Sample_contact_phone | 973-854-3455
| | Sample_contact_fax | 973-854-3453
| | Sample_contact_laboratory | Soteropoulos
| | Sample_contact_department | Center For Applied Genomics
| | Sample_contact_institute | PHRI-UMNDJ
| | Sample_contact_address | W420M, 225 Warren St
| | Sample_contact_city | Newark
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07103
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.cag.icph.org/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM146nnn/GSM146386/suppl/GSM146386.CEL.gz
| | Sample_series_id | GSE6332
| | Sample_data_row_count | 8799
| | |
|
GSM146387 | GPL85 |
|
Hemoragic Shock Biological replicate 1
|
Rat Lung
|
Hemoragic Shock
|
Hemoragic shock animals underwent cannulation of the femoral artery and jugular vein followed by a laparotomy in which blood was withdrawn and a mean arterial pressure of 30 mmHg was kept for 90 min.
|
| Sample_geo_accession | GSM146387
| | Sample_status | Public on Jul 25 2007
| | Sample_submission_date | Nov 20 2006
| | Sample_last_update_date | Jul 25 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Male rats were anesthetized with intraperitoneal (IP) pentobarbital (50mg/kg) and under strict asepsis, the femoral artery and jugular vein were cannulated, and a 5cm laparotomy was performed to mimic tissue injury. Blood was withdrawn from the jugular vein into a syringe containing 100 units of heparin in 0.3 ml of 0.9% saline until a mean arterial pressure (MAP) of 30 mmHg was obtained. This MAP was maintained for 90 minutes by withdrawing or reinfusing blood as needed. At the end of the shock period, all the shed blood was returned. Return of the shed blood restored the MAP to pre-shock levels. The temperature of the rats was maintained at 37ºC with the use of a heating pad as needed. Three hours after resuscitation, the animals were sacrificed and lung removed, snap-frozen in liquid nitrogen and stored at -80ºC until use.
| | Sample_growth_protocol_ch1 | Specific pathogen-free male Sprague-Dawley rats (Charles River Laboratories, Portage, MI) weighing 300-420 grams were housed for at least 1 week before use and were maintained according to the recommendations of the National Institutes of Health Guide for Care and Use of Laboratory Animals. The animals were fed standard chow and water. All experiments were approved by the New Jersey Medical School Animal Care and Use Committee.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRizol reagent (Invitrogen, Gaithersburg, MD).
| | Sample_label_ch1 | Biotin Label
| | Sample_label_protocol_ch1 | cDNA and cRNA synthesis were performed according to Affymetrix Expression Analysis protocols (see www.affymetrix.com). Briefly, double-stranded cDNA was synthesized from 5 ug of total RNA using the Superscript double-stranded cDNA synthesis kit (Invitrogen). Following phenol/chloroform extraction and ethanol precipitation, a biotin-labeled in vitro transcription reaction was carried out using the cDNA template (Enzo Life Sciences, Farmingdale, NY). Fifteen ug of cRNA was fragmented for hybridization to Affymetrix RG-U34A GeneChips (Santa Clara, CA), which contains ~8,800 known rat transcripts and EST’s.
| | Sample_hyb_protocol | Hybridization was done overnight at 45ºC for 16 hours using the Genechip Hybridization Oven 640 (Affymetrix). Washing and staining (Streptavidin Phycoerythrin) was performed using the Genechip Fluidics Station 450 (Affymetrix) using the EukGE-WS2v4 protocol.
| | Sample_scan_protocol | Images were acquired using the Affymetrix GeneArray Scanner 3000. Data was extracted using Affymetrix GeneChip Operating Software version 1.0.
| | Sample_data_processing | Data was extracted using Affymetrix GeneChip Operating Software version 1.0. Expression intensity values were extracted from the CEL files using the Robust Multi-Array Average algorithm in ArrayAssist version 3.2 (Stratagene). Quantile normalization was performed to normalize the distribution of probe intensities for all the arrays in a given set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Virginie,Marie,Aris
| | Sample_contact_email | arisvm@umdnj.edu
| | Sample_contact_phone | 973-854-3455
| | Sample_contact_fax | 973-854-3453
| | Sample_contact_laboratory | Soteropoulos
| | Sample_contact_department | Center For Applied Genomics
| | Sample_contact_institute | PHRI-UMNDJ
| | Sample_contact_address | W420M, 225 Warren St
| | Sample_contact_city | Newark
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07103
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.cag.icph.org/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM146nnn/GSM146387/suppl/GSM146387.CEL.gz
| | Sample_series_id | GSE6332
| | Sample_data_row_count | 8799
| | |
|
GSM146388 | GPL85 |
|
Hemoragic Shock Biological replicate 2
|
Rat Lung
|
Hemoragic Shock
|
Hemoragic shock animals underwent cannulation of the femoral artery and jugular vein followed by a laparotomy in which blood was withdrawn and a mean arterial pressure of 30 mmHg was kept for 90 min.
|
| Sample_geo_accession | GSM146388
| | Sample_status | Public on Jul 25 2007
| | Sample_submission_date | Nov 20 2006
| | Sample_last_update_date | Jul 25 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Male rats were anesthetized with intraperitoneal (IP) pentobarbital (50mg/kg) and under strict asepsis, the femoral artery and jugular vein were cannulated, and a 5cm laparotomy was performed to mimic tissue injury. Blood was withdrawn from the jugular vein into a syringe containing 100 units of heparin in 0.3 ml of 0.9% saline until a mean arterial pressure (MAP) of 30 mmHg was obtained. This MAP was maintained for 90 minutes by withdrawing or reinfusing blood as needed. At the end of the shock period, all the shed blood was returned. Return of the shed blood restored the MAP to pre-shock levels. The temperature of the rats was maintained at 37ºC with the use of a heating pad as needed. Three hours after resuscitation, the animals were sacrificed and lung removed, snap-frozen in liquid nitrogen and stored at -80ºC until use.
| | Sample_growth_protocol_ch1 | Specific pathogen-free male Sprague-Dawley rats (Charles River Laboratories, Portage, MI) weighing 300-420 grams were housed for at least 1 week before use and were maintained according to the recommendations of the National Institutes of Health Guide for Care and Use of Laboratory Animals. The animals were fed standard chow and water. All experiments were approved by the New Jersey Medical School Animal Care and Use Committee.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRizol reagent (Invitrogen, Gaithersburg, MD).
| | Sample_label_ch1 | Biotin Label
| | Sample_label_protocol_ch1 | cDNA and cRNA synthesis were performed according to Affymetrix Expression Analysis protocols (see www.affymetrix.com). Briefly, double-stranded cDNA was synthesized from 5 ug of total RNA using the Superscript double-stranded cDNA synthesis kit (Invitrogen). Following phenol/chloroform extraction and ethanol precipitation, a biotin-labeled in vitro transcription reaction was carried out using the cDNA template (Enzo Life Sciences, Farmingdale, NY). Fifteen ug of cRNA was fragmented for hybridization to Affymetrix RG-U34A GeneChips (Santa Clara, CA), which contains ~8,800 known rat transcripts and EST’s.
| | Sample_hyb_protocol | Hybridization was done overnight at 45ºC for 16 hours using the Genechip Hybridization Oven 640 (Affymetrix). Washing and staining (Streptavidin Phycoerythrin) was performed using the Genechip Fluidics Station 450 (Affymetrix) using the EukGE-WS2v4 protocol.
| | Sample_scan_protocol | Images were acquired using the Affymetrix GeneArray Scanner 3000. Data was extracted using Affymetrix GeneChip Operating Software version 1.0.
| | Sample_data_processing | Data was extracted using Affymetrix GeneChip Operating Software version 1.0. Expression intensity values were extracted from the CEL files using the Robust Multi-Array Average algorithm in ArrayAssist version 3.2 (Stratagene). Quantile normalization was performed to normalize the distribution of probe intensities for all the arrays in a given set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Virginie,Marie,Aris
| | Sample_contact_email | arisvm@umdnj.edu
| | Sample_contact_phone | 973-854-3455
| | Sample_contact_fax | 973-854-3453
| | Sample_contact_laboratory | Soteropoulos
| | Sample_contact_department | Center For Applied Genomics
| | Sample_contact_institute | PHRI-UMNDJ
| | Sample_contact_address | W420M, 225 Warren St
| | Sample_contact_city | Newark
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07103
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.cag.icph.org/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM146nnn/GSM146388/suppl/GSM146388.CEL.gz
| | Sample_series_id | GSE6332
| | Sample_data_row_count | 8799
| | |
|
GSM146389 | GPL85 |
|
Hemoragic Shock Biological replicate 3
|
Rat Lung
|
Hemoragic Shock
|
Hemoragic shock animals underwent cannulation of the femoral artery and jugular vein followed by a laparotomy in which blood was withdrawn and a mean arterial pressure of 30 mmHg was kept for 90 min.
|
| Sample_geo_accession | GSM146389
| | Sample_status | Public on Jul 25 2007
| | Sample_submission_date | Nov 20 2006
| | Sample_last_update_date | Jul 25 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Male rats were anesthetized with intraperitoneal (IP) pentobarbital (50mg/kg) and under strict asepsis, the femoral artery and jugular vein were cannulated, and a 5cm laparotomy was performed to mimic tissue injury. Blood was withdrawn from the jugular vein into a syringe containing 100 units of heparin in 0.3 ml of 0.9% saline until a mean arterial pressure (MAP) of 30 mmHg was obtained. This MAP was maintained for 90 minutes by withdrawing or reinfusing blood as needed. At the end of the shock period, all the shed blood was returned. Return of the shed blood restored the MAP to pre-shock levels. The temperature of the rats was maintained at 37ºC with the use of a heating pad as needed. Three hours after resuscitation, the animals were sacrificed and lung removed, snap-frozen in liquid nitrogen and stored at -80ºC until use.
| | Sample_growth_protocol_ch1 | Specific pathogen-free male Sprague-Dawley rats (Charles River Laboratories, Portage, MI) weighing 300-420 grams were housed for at least 1 week before use and were maintained according to the recommendations of the National Institutes of Health Guide for Care and Use of Laboratory Animals. The animals were fed standard chow and water. All experiments were approved by the New Jersey Medical School Animal Care and Use Committee.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRizol reagent (Invitrogen, Gaithersburg, MD).
| | Sample_label_ch1 | Biotin Label
| | Sample_label_protocol_ch1 | cDNA and cRNA synthesis were performed according to Affymetrix Expression Analysis protocols (see www.affymetrix.com). Briefly, double-stranded cDNA was synthesized from 5 ug of total RNA using the Superscript double-stranded cDNA synthesis kit (Invitrogen). Following phenol/chloroform extraction and ethanol precipitation, a biotin-labeled in vitro transcription reaction was carried out using the cDNA template (Enzo Life Sciences, Farmingdale, NY). Fifteen ug of cRNA was fragmented for hybridization to Affymetrix RG-U34A GeneChips (Santa Clara, CA), which contains ~8,800 known rat transcripts and EST’s.
| | Sample_hyb_protocol | Hybridization was done overnight at 45ºC for 16 hours using the Genechip Hybridization Oven 640 (Affymetrix). Washing and staining (Streptavidin Phycoerythrin) was performed using the Genechip Fluidics Station 450 (Affymetrix) using the EukGE-WS2v4 protocol.
| | Sample_scan_protocol | Images were acquired using the Affymetrix GeneArray Scanner 3000. Data was extracted using Affymetrix GeneChip Operating Software version 1.0.
| | Sample_data_processing | Data was extracted using Affymetrix GeneChip Operating Software version 1.0. Expression intensity values were extracted from the CEL files using the Robust Multi-Array Average algorithm in ArrayAssist version 3.2 (Stratagene). Quantile normalization was performed to normalize the distribution of probe intensities for all the arrays in a given set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Virginie,Marie,Aris
| | Sample_contact_email | arisvm@umdnj.edu
| | Sample_contact_phone | 973-854-3455
| | Sample_contact_fax | 973-854-3453
| | Sample_contact_laboratory | Soteropoulos
| | Sample_contact_department | Center For Applied Genomics
| | Sample_contact_institute | PHRI-UMNDJ
| | Sample_contact_address | W420M, 225 Warren St
| | Sample_contact_city | Newark
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07103
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.cag.icph.org/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM146nnn/GSM146389/suppl/GSM146389.CEL.gz
| | Sample_series_id | GSE6332
| | Sample_data_row_count | 8799
| | |
|
GSM146390 | GPL85 |
|
Sham Shock Lymph Duct Ligation Biological replicate 1
|
Rat Lung
|
Sham Shock Lymph Duct Ligation
|
Sham-shock Lymph Duc Liagted animals underwent ligation of the lymphatic vessels, and then cannulation of the femoral artery and jugular vein followed by a laparotomy, no blood was withdrawn and the MAP was kept within normal limits.
|
| Sample_geo_accession | GSM146390
| | Sample_status | Public on Jul 25 2007
| | Sample_submission_date | Nov 20 2006
| | Sample_last_update_date | Jul 25 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were anesthetized as described above and a midline celiotomy was performed. The efferent mesenteric lymphatic vessel was identified adjacent to the superior mesenteric artery by reflecting the intestinal loops to the left. The lymphatic vessels were bluntly dissected free, following which they were ligated and subsequently divided. Then animals underwent cannulation of the femoral artery and jugular vein followed by a laparotomy; however, no blood was withdrawn and the MAP was kept within normal limits. The temperature of the rats was maintained at 37ºC with the use of a heating pad as needed. Three hours after resuscitation, the animals were sacrificed and lung removed, snap-frozen in liquid nitrogen and stored at -80ºC until use.
| | Sample_growth_protocol_ch1 | Specific pathogen-free male Sprague-Dawley rats (Charles River Laboratories, Portage, MI) weighing 300-420 grams were housed for at least 1 week before use and were maintained according to the recommendations of the National Institutes of Health Guide for Care and Use of Laboratory Animals. The animals were fed standard chow and water. All experiments were approved by the New Jersey Medical School Animal Care and Use Committee.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRizol reagent (Invitrogen, Gaithersburg, MD).
| | Sample_label_ch1 | Biotin Label
| | Sample_label_protocol_ch1 | cDNA and cRNA synthesis were performed according to Affymetrix Expression Analysis protocols (see www.affymetrix.com). Briefly, double-stranded cDNA was synthesized from 5 ug of total RNA using the Superscript double-stranded cDNA synthesis kit (Invitrogen). Following phenol/chloroform extraction and ethanol precipitation, a biotin-labeled in vitro transcription reaction was carried out using the cDNA template (Enzo Life Sciences, Farmingdale, NY). Fifteen ug of cRNA was fragmented for hybridization to Affymetrix RG-U34A GeneChips (Santa Clara, CA), which contains ~8,800 known rat transcripts and EST’s.
| | Sample_hyb_protocol | Hybridization was done overnight at 45ºC for 16 hours using the Genechip Hybridization Oven 640 (Affymetrix). Washing and staining (Streptavidin Phycoerythrin) was performed using the Genechip Fluidics Station 450 (Affymetrix) using the EukGE-WS2v4 protocol.
| | Sample_scan_protocol | Images were acquired using the Affymetrix GeneArray Scanner 3000. Data was extracted using Affymetrix GeneChip Operating Software version 1.0.
| | Sample_data_processing | Data was extracted using Affymetrix GeneChip Operating Software version 1.0. Expression intensity values were extracted from the CEL files using the Robust Multi-Array Average algorithm in ArrayAssist version 3.2 (Stratagene). Quantile normalization was performed to normalize the distribution of probe intensities for all the arrays in a given set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Virginie,Marie,Aris
| | Sample_contact_email | arisvm@umdnj.edu
| | Sample_contact_phone | 973-854-3455
| | Sample_contact_fax | 973-854-3453
| | Sample_contact_laboratory | Soteropoulos
| | Sample_contact_department | Center For Applied Genomics
| | Sample_contact_institute | PHRI-UMNDJ
| | Sample_contact_address | W420M, 225 Warren St
| | Sample_contact_city | Newark
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07103
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.cag.icph.org/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM146nnn/GSM146390/suppl/GSM146390.CEL.gz
| | Sample_series_id | GSE6332
| | Sample_data_row_count | 8799
| | |
|
GSM146391 | GPL85 |
|
Sham Shock Lymph Duct Ligation Biological replicate 2
|
Rat Lung
|
Sham Shock Lymph Duct Ligation
|
Sham-shock Lymph Duc Liagted animals underwent ligation of the lymphatic vessels, and then cannulation of the femoral artery and jugular vein followed by a laparotomy, no blood was withdrawn and the MAP was kept within normal limits.
|
| Sample_geo_accession | GSM146391
| | Sample_status | Public on Jul 25 2007
| | Sample_submission_date | Nov 20 2006
| | Sample_last_update_date | Jul 25 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were anesthetized as described above and a midline celiotomy was performed. The efferent mesenteric lymphatic vessel was identified adjacent to the superior mesenteric artery by reflecting the intestinal loops to the left. The lymphatic vessels were bluntly dissected free, following which they were ligated and subsequently divided. Then animals underwent cannulation of the femoral artery and jugular vein followed by a laparotomy; however, no blood was withdrawn and the MAP was kept within normal limits. The temperature of the rats was maintained at 37ºC with the use of a heating pad as needed. Three hours after resuscitation, the animals were sacrificed and lung removed, snap-frozen in liquid nitrogen and stored at -80ºC until use.
| | Sample_growth_protocol_ch1 | Specific pathogen-free male Sprague-Dawley rats (Charles River Laboratories, Portage, MI) weighing 300-420 grams were housed for at least 1 week before use and were maintained according to the recommendations of the National Institutes of Health Guide for Care and Use of Laboratory Animals. The animals were fed standard chow and water. All experiments were approved by the New Jersey Medical School Animal Care and Use Committee.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRizol reagent (Invitrogen, Gaithersburg, MD).
| | Sample_label_ch1 | Biotin Label
| | Sample_label_protocol_ch1 | cDNA and cRNA synthesis were performed according to Affymetrix Expression Analysis protocols (see www.affymetrix.com). Briefly, double-stranded cDNA was synthesized from 5 ug of total RNA using the Superscript double-stranded cDNA synthesis kit (Invitrogen). Following phenol/chloroform extraction and ethanol precipitation, a biotin-labeled in vitro transcription reaction was carried out using the cDNA template (Enzo Life Sciences, Farmingdale, NY). Fifteen ug of cRNA was fragmented for hybridization to Affymetrix RG-U34A GeneChips (Santa Clara, CA), which contains ~8,800 known rat transcripts and EST’s.
| | Sample_hyb_protocol | Hybridization was done overnight at 45ºC for 16 hours using the Genechip Hybridization Oven 640 (Affymetrix). Washing and staining (Streptavidin Phycoerythrin) was performed using the Genechip Fluidics Station 450 (Affymetrix) using the EukGE-WS2v4 protocol.
| | Sample_scan_protocol | Images were acquired using the Affymetrix GeneArray Scanner 3000. Data was extracted using Affymetrix GeneChip Operating Software version 1.0.
| | Sample_data_processing | Data was extracted using Affymetrix GeneChip Operating Software version 1.0. Expression intensity values were extracted from the CEL files using the Robust Multi-Array Average algorithm in ArrayAssist version 3.2 (Stratagene). Quantile normalization was performed to normalize the distribution of probe intensities for all the arrays in a given set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Virginie,Marie,Aris
| | Sample_contact_email | arisvm@umdnj.edu
| | Sample_contact_phone | 973-854-3455
| | Sample_contact_fax | 973-854-3453
| | Sample_contact_laboratory | Soteropoulos
| | Sample_contact_department | Center For Applied Genomics
| | Sample_contact_institute | PHRI-UMNDJ
| | Sample_contact_address | W420M, 225 Warren St
| | Sample_contact_city | Newark
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07103
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.cag.icph.org/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM146nnn/GSM146391/suppl/GSM146391.CEL.gz
| | Sample_series_id | GSE6332
| | Sample_data_row_count | 8799
| | |
|
GSM146392 | GPL85 |
|
Sham Shock Lymph Duct Ligation Biological replicate 3
|
Rat Lung
|
Sham Shock Lymph Duct Ligation
|
Sham-shock Lymph Duc Liagted animals underwent ligation of the lymphatic vessels, and then cannulation of the femoral artery and jugular vein followed by a laparotomy, no blood was withdrawn and the MAP was kept within normal limits.
|
| Sample_geo_accession | GSM146392
| | Sample_status | Public on Jul 25 2007
| | Sample_submission_date | Nov 20 2006
| | Sample_last_update_date | Jul 25 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were anesthetized as described above and a midline celiotomy was performed. The efferent mesenteric lymphatic vessel was identified adjacent to the superior mesenteric artery by reflecting the intestinal loops to the left. The lymphatic vessels were bluntly dissected free, following which they were ligated and subsequently divided. Then animals underwent cannulation of the femoral artery and jugular vein followed by a laparotomy; however, no blood was withdrawn and the MAP was kept within normal limits. The temperature of the rats was maintained at 37ºC with the use of a heating pad as needed. Three hours after resuscitation, the animals were sacrificed and lung removed, snap-frozen in liquid nitrogen and stored at -80ºC until use.
| | Sample_growth_protocol_ch1 | Specific pathogen-free male Sprague-Dawley rats (Charles River Laboratories, Portage, MI) weighing 300-420 grams were housed for at least 1 week before use and were maintained according to the recommendations of the National Institutes of Health Guide for Care and Use of Laboratory Animals. The animals were fed standard chow and water. All experiments were approved by the New Jersey Medical School Animal Care and Use Committee.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRizol reagent (Invitrogen, Gaithersburg, MD).
| | Sample_label_ch1 | Biotin Label
| | Sample_label_protocol_ch1 | cDNA and cRNA synthesis were performed according to Affymetrix Expression Analysis protocols (see www.affymetrix.com). Briefly, double-stranded cDNA was synthesized from 5 ug of total RNA using the Superscript double-stranded cDNA synthesis kit (Invitrogen). Following phenol/chloroform extraction and ethanol precipitation, a biotin-labeled in vitro transcription reaction was carried out using the cDNA template (Enzo Life Sciences, Farmingdale, NY). Fifteen ug of cRNA was fragmented for hybridization to Affymetrix RG-U34A GeneChips (Santa Clara, CA), which contains ~8,800 known rat transcripts and EST’s.
| | Sample_hyb_protocol | Hybridization was done overnight at 45ºC for 16 hours using the Genechip Hybridization Oven 640 (Affymetrix). Washing and staining (Streptavidin Phycoerythrin) was performed using the Genechip Fluidics Station 450 (Affymetrix) using the EukGE-WS2v4 protocol.
| | Sample_scan_protocol | Images were acquired using the Affymetrix GeneArray Scanner 3000. Data was extracted using Affymetrix GeneChip Operating Software version 1.0.
| | Sample_data_processing | Data was extracted using Affymetrix GeneChip Operating Software version 1.0. Expression intensity values were extracted from the CEL files using the Robust Multi-Array Average algorithm in ArrayAssist version 3.2 (Stratagene). Quantile normalization was performed to normalize the distribution of probe intensities for all the arrays in a given set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Virginie,Marie,Aris
| | Sample_contact_email | arisvm@umdnj.edu
| | Sample_contact_phone | 973-854-3455
| | Sample_contact_fax | 973-854-3453
| | Sample_contact_laboratory | Soteropoulos
| | Sample_contact_department | Center For Applied Genomics
| | Sample_contact_institute | PHRI-UMNDJ
| | Sample_contact_address | W420M, 225 Warren St
| | Sample_contact_city | Newark
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07103
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.cag.icph.org/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM146nnn/GSM146392/suppl/GSM146392.CEL.gz
| | Sample_series_id | GSE6332
| | Sample_data_row_count | 8799
| | |
|
GSM146393 | GPL85 |
|
Hemoragic Shock Lymph Duct Ligation Biological replicate 1
|
Rat Lung
|
Hemoragic Shock Lymph Duct Ligation
|
Hemoragic shock Lymph Duc Liagted animals underwent liagtion of the lymphatic vessels, and then cannulation of the femoral artery and jugular vein followed by a laparotomyin in which blood was withdrawn and a mean arterial pressure of 30 mmHg was kept for 90 min.
|
| Sample_geo_accession | GSM146393
| | Sample_status | Public on Jul 25 2007
| | Sample_submission_date | Nov 20 2006
| | Sample_last_update_date | Jul 25 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were anesthetized as described above and a midline celiotomy was performed. The efferent mesenteric lymphatic vessel was identified adjacent to the superior mesenteric artery by reflecting the intestinal loops to the left. The lymphatic vessels were bluntly dissected free, following which they were ligated and subsequently divided. Then the femoral artery and jugular vein were cannulated, and a 5cm laparotomy was performed to mimic tissue injury. Blood was withdrawn from the jugular vein into a syringe containing 100 units of heparin in 0.3 ml of 0.9% saline until a mean arterial pressure (MAP) of 30 mmHg was obtained. This MAP was maintained for 90 minutes by withdrawing or reinfusing blood as needed. At the end of the shock period, all the shed blood was returned. Return of the shed blood restored the MAP to pre-shock levels. The temperature of the rats was maintained at 37ºC with the use of a heating pad as needed. Three hours after resuscitation, the animals were sacrificed and lung removed, snap-frozen in liquid nitrogen and stored at -80ºC until use.
| | Sample_growth_protocol_ch1 | Specific pathogen-free male Sprague-Dawley rats (Charles River Laboratories, Portage, MI) weighing 300-420 grams were housed for at least 1 week before use and were maintained according to the recommendations of the National Institutes of Health Guide for Care and Use of Laboratory Animals. The animals were fed standard chow and water. All experiments were approved by the New Jersey Medical School Animal Care and Use Committee.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRizol reagent (Invitrogen, Gaithersburg, MD).
| | Sample_label_ch1 | Biotin Label
| | Sample_label_protocol_ch1 | cDNA and cRNA synthesis were performed according to Affymetrix Expression Analysis protocols (see www.affymetrix.com). Briefly, double-stranded cDNA was synthesized from 5 ug of total RNA using the Superscript double-stranded cDNA synthesis kit (Invitrogen). Following phenol/chloroform extraction and ethanol precipitation, a biotin-labeled in vitro transcription reaction was carried out using the cDNA template (Enzo Life Sciences, Farmingdale, NY). Fifteen ug of cRNA was fragmented for hybridization to Affymetrix RG-U34A GeneChips (Santa Clara, CA), which contains ~8,800 known rat transcripts and EST’s.
| | Sample_hyb_protocol | Hybridization was done overnight at 45ºC for 16 hours using the Genechip Hybridization Oven 640 (Affymetrix). Washing and staining (Streptavidin Phycoerythrin) was performed using the Genechip Fluidics Station 450 (Affymetrix) using the EukGE-WS2v4 protocol.
| | Sample_scan_protocol | Images were acquired using the Affymetrix GeneArray Scanner 3000. Data was extracted using Affymetrix GeneChip Operating Software version 1.0.
| | Sample_data_processing | Data was extracted using Affymetrix GeneChip Operating Software version 1.0. Expression intensity values were extracted from the CEL files using the Robust Multi-Array Average algorithm in ArrayAssist version 3.2 (Stratagene). Quantile normalization was performed to normalize the distribution of probe intensities for all the arrays in a given set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Virginie,Marie,Aris
| | Sample_contact_email | arisvm@umdnj.edu
| | Sample_contact_phone | 973-854-3455
| | Sample_contact_fax | 973-854-3453
| | Sample_contact_laboratory | Soteropoulos
| | Sample_contact_department | Center For Applied Genomics
| | Sample_contact_institute | PHRI-UMNDJ
| | Sample_contact_address | W420M, 225 Warren St
| | Sample_contact_city | Newark
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07103
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.cag.icph.org/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM146nnn/GSM146393/suppl/GSM146393.CEL.gz
| | Sample_series_id | GSE6332
| | Sample_data_row_count | 8799
| | |
|
GSM146394 | GPL85 |
|
Hemoragic Shock Lymph Duct Ligation Biological replicate 2
|
Rat Lung
|
Hemoragic Shock Lymph Duct Ligation
|
Hemoragic shock Lymph Duc Liagted animals underwent liagtion of the lymphatic vessels, and then cannulation of the femoral artery and jugular vein followed by a laparotomyin in which blood was withdrawn and a mean arterial pressure of 30 mmHg was kept for 90 min.
|
| Sample_geo_accession | GSM146394
| | Sample_status | Public on Jul 25 2007
| | Sample_submission_date | Nov 20 2006
| | Sample_last_update_date | Jul 25 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were anesthetized as described above and a midline celiotomy was performed. The efferent mesenteric lymphatic vessel was identified adjacent to the superior mesenteric artery by reflecting the intestinal loops to the left. The lymphatic vessels were bluntly dissected free, following which they were ligated and subsequently divided. Then the femoral artery and jugular vein were cannulated, and a 5cm laparotomy was performed to mimic tissue injury. Blood was withdrawn from the jugular vein into a syringe containing 100 units of heparin in 0.3 ml of 0.9% saline until a mean arterial pressure (MAP) of 30 mmHg was obtained. This MAP was maintained for 90 minutes by withdrawing or reinfusing blood as needed. At the end of the shock period, all the shed blood was returned. Return of the shed blood restored the MAP to pre-shock levels. The temperature of the rats was maintained at 37ºC with the use of a heating pad as needed. Three hours after resuscitation, the animals were sacrificed and lung removed, snap-frozen in liquid nitrogen and stored at -80ºC until use.
| | Sample_growth_protocol_ch1 | Specific pathogen-free male Sprague-Dawley rats (Charles River Laboratories, Portage, MI) weighing 300-420 grams were housed for at least 1 week before use and were maintained according to the recommendations of the National Institutes of Health Guide for Care and Use of Laboratory Animals. The animals were fed standard chow and water. All experiments were approved by the New Jersey Medical School Animal Care and Use Committee.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRizol reagent (Invitrogen, Gaithersburg, MD).
| | Sample_label_ch1 | Biotin Label
| | Sample_label_protocol_ch1 | cDNA and cRNA synthesis were performed according to Affymetrix Expression Analysis protocols (see www.affymetrix.com). Briefly, double-stranded cDNA was synthesized from 5 ug of total RNA using the Superscript double-stranded cDNA synthesis kit (Invitrogen). Following phenol/chloroform extraction and ethanol precipitation, a biotin-labeled in vitro transcription reaction was carried out using the cDNA template (Enzo Life Sciences, Farmingdale, NY). Fifteen ug of cRNA was fragmented for hybridization to Affymetrix RG-U34A GeneChips (Santa Clara, CA), which contains ~8,800 known rat transcripts and EST’s.
| | Sample_hyb_protocol | Hybridization was done overnight at 45ºC for 16 hours using the Genechip Hybridization Oven 640 (Affymetrix). Washing and staining (Streptavidin Phycoerythrin) was performed using the Genechip Fluidics Station 450 (Affymetrix) using the EukGE-WS2v4 protocol.
| | Sample_scan_protocol | Images were acquired using the Affymetrix GeneArray Scanner 3000. Data was extracted using Affymetrix GeneChip Operating Software version 1.0.
| | Sample_data_processing | Data was extracted using Affymetrix GeneChip Operating Software version 1.0. Expression intensity values were extracted from the CEL files using the Robust Multi-Array Average algorithm in ArrayAssist version 3.2 (Stratagene). Quantile normalization was performed to normalize the distribution of probe intensities for all the arrays in a given set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Virginie,Marie,Aris
| | Sample_contact_email | arisvm@umdnj.edu
| | Sample_contact_phone | 973-854-3455
| | Sample_contact_fax | 973-854-3453
| | Sample_contact_laboratory | Soteropoulos
| | Sample_contact_department | Center For Applied Genomics
| | Sample_contact_institute | PHRI-UMNDJ
| | Sample_contact_address | W420M, 225 Warren St
| | Sample_contact_city | Newark
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07103
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.cag.icph.org/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM146nnn/GSM146394/suppl/GSM146394.CEL.gz
| | Sample_series_id | GSE6332
| | Sample_data_row_count | 8799
| | |
|
GSM146395 | GPL85 |
|
Hemoragic Shock Lymph Duct Ligation Biological replicate 3
|
Rat Lung
|
Hemoragic Shock Lymph Duct Ligation
|
Hemoragic shock Lymph Duc Liagted animals underwent liagtion of the lymphatic vessels, and then cannulation of the femoral artery and jugular vein followed by a laparotomyin in which blood was withdrawn and a mean arterial pressure of 30 mmHg was kept for 90 min.
|
| Sample_geo_accession | GSM146395
| | Sample_status | Public on Jul 25 2007
| | Sample_submission_date | Nov 20 2006
| | Sample_last_update_date | Jul 25 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The rats were anesthetized as described above and a midline celiotomy was performed. The efferent mesenteric lymphatic vessel was identified adjacent to the superior mesenteric artery by reflecting the intestinal loops to the left. The lymphatic vessels were bluntly dissected free, following which they were ligated and subsequently divided. Then the femoral artery and jugular vein were cannulated, and a 5cm laparotomy was performed to mimic tissue injury. Blood was withdrawn from the jugular vein into a syringe containing 100 units of heparin in 0.3 ml of 0.9% saline until a mean arterial pressure (MAP) of 30 mmHg was obtained. This MAP was maintained for 90 minutes by withdrawing or reinfusing blood as needed. At the end of the shock period, all the shed blood was returned. Return of the shed blood restored the MAP to pre-shock levels. The temperature of the rats was maintained at 37ºC with the use of a heating pad as needed. Three hours after resuscitation, the animals were sacrificed and lung removed, snap-frozen in liquid nitrogen and stored at -80ºC until use.
| | Sample_growth_protocol_ch1 | Specific pathogen-free male Sprague-Dawley rats (Charles River Laboratories, Portage, MI) weighing 300-420 grams were housed for at least 1 week before use and were maintained according to the recommendations of the National Institutes of Health Guide for Care and Use of Laboratory Animals. The animals were fed standard chow and water. All experiments were approved by the New Jersey Medical School Animal Care and Use Committee.
| | Sample_molecule_ch1 | polyA RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using TRizol reagent (Invitrogen, Gaithersburg, MD).
| | Sample_label_ch1 | Biotin Label
| | Sample_label_protocol_ch1 | cDNA and cRNA synthesis were performed according to Affymetrix Expression Analysis protocols (see www.affymetrix.com). Briefly, double-stranded cDNA was synthesized from 5 ug of total RNA using the Superscript double-stranded cDNA synthesis kit (Invitrogen). Following phenol/chloroform extraction and ethanol precipitation, a biotin-labeled in vitro transcription reaction was carried out using the cDNA template (Enzo Life Sciences, Farmingdale, NY). Fifteen ug of cRNA was fragmented for hybridization to Affymetrix RG-U34A GeneChips (Santa Clara, CA), which contains ~8,800 known rat transcripts and EST’s.
| | Sample_hyb_protocol | Hybridization was done overnight at 45ºC for 16 hours using the Genechip Hybridization Oven 640 (Affymetrix). Washing and staining (Streptavidin Phycoerythrin) was performed using the Genechip Fluidics Station 450 (Affymetrix) using the EukGE-WS2v4 protocol.
| | Sample_scan_protocol | Images were acquired using the Affymetrix GeneArray Scanner 3000. Data was extracted using Affymetrix GeneChip Operating Software version 1.0.
| | Sample_data_processing | Data was extracted using Affymetrix GeneChip Operating Software version 1.0. Expression intensity values were extracted from the CEL files using the Robust Multi-Array Average algorithm in ArrayAssist version 3.2 (Stratagene). Quantile normalization was performed to normalize the distribution of probe intensities for all the arrays in a given set.
| | Sample_platform_id | GPL85
| | Sample_contact_name | Virginie,Marie,Aris
| | Sample_contact_email | arisvm@umdnj.edu
| | Sample_contact_phone | 973-854-3455
| | Sample_contact_fax | 973-854-3453
| | Sample_contact_laboratory | Soteropoulos
| | Sample_contact_department | Center For Applied Genomics
| | Sample_contact_institute | PHRI-UMNDJ
| | Sample_contact_address | W420M, 225 Warren St
| | Sample_contact_city | Newark
| | Sample_contact_state | NJ
| | Sample_contact_zip/postal_code | 07103
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.cag.icph.org/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM146nnn/GSM146395/suppl/GSM146395.CEL.gz
| | Sample_series_id | GSE6332
| | Sample_data_row_count | 8799
| | |
|
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