Search results for the GEO ID: GSE30385  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM754022 | GPL201 |
|
SIDP10_blood_VAP_rep1
|
patients with VAP
|
tissue: blood
|
Gene expression data from critically-ill trauma patients following admission to the intensive care unit
|
| Sample_geo_accession | GSM754022
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Jul 05 2011
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times. Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS 3000 7G.
| | Sample_data_processing | The data were analyzed with RMA as the normalization method.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Joseph, ,Swanson
| | Sample_contact_email | jswanson@uthsc.edu
| | Sample_contact_phone | 901-448-1418
| | Sample_contact_department | Clinical Pharmacy
| | Sample_contact_institute | University of Tennessee
| | Sample_contact_address | 910 Madison Ave., Suite 308
| | Sample_contact_city | Memphis
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 38163
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM754nnn/GSM754022/suppl/GSM754022.CEL.gz
| | Sample_series_id | GSE30385
| | Sample_data_row_count | 8793
| | |
|
GSM754023 | GPL201 |
|
SIDP11_blood_NoVAP_rep1
|
patients without VAP
|
tissue: blood
|
Gene expression data from critically-ill trauma patients following admission to the intensive care unit
|
| Sample_geo_accession | GSM754023
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Jul 05 2011
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times. Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS 3000 7G.
| | Sample_data_processing | The data were analyzed with RMA as the normalization method.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Joseph, ,Swanson
| | Sample_contact_email | jswanson@uthsc.edu
| | Sample_contact_phone | 901-448-1418
| | Sample_contact_department | Clinical Pharmacy
| | Sample_contact_institute | University of Tennessee
| | Sample_contact_address | 910 Madison Ave., Suite 308
| | Sample_contact_city | Memphis
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 38163
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM754nnn/GSM754023/suppl/GSM754023.CEL.gz
| | Sample_series_id | GSE30385
| | Sample_data_row_count | 8793
| | |
|
GSM754024 | GPL201 |
|
SIDP12_blood_NoVAP_rep2
|
patients without VAP
|
tissue: blood
|
Gene expression data from critically-ill trauma patients following admission to the intensive care unit
|
| Sample_geo_accession | GSM754024
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Jul 05 2011
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times. Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS 3000 7G.
| | Sample_data_processing | The data were analyzed with RMA as the normalization method.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Joseph, ,Swanson
| | Sample_contact_email | jswanson@uthsc.edu
| | Sample_contact_phone | 901-448-1418
| | Sample_contact_department | Clinical Pharmacy
| | Sample_contact_institute | University of Tennessee
| | Sample_contact_address | 910 Madison Ave., Suite 308
| | Sample_contact_city | Memphis
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 38163
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM754nnn/GSM754024/suppl/GSM754024.CEL.gz
| | Sample_series_id | GSE30385
| | Sample_data_row_count | 8793
| | |
|
GSM754025 | GPL201 |
|
SIDP13_blood_VAP_rep2
|
patients with VAP
|
tissue: blood
|
Gene expression data from critically-ill trauma patients following admission to the intensive care unit
|
| Sample_geo_accession | GSM754025
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Jul 05 2011
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times. Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS 3000 7G.
| | Sample_data_processing | The data were analyzed with RMA as the normalization method.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Joseph, ,Swanson
| | Sample_contact_email | jswanson@uthsc.edu
| | Sample_contact_phone | 901-448-1418
| | Sample_contact_department | Clinical Pharmacy
| | Sample_contact_institute | University of Tennessee
| | Sample_contact_address | 910 Madison Ave., Suite 308
| | Sample_contact_city | Memphis
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 38163
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM754nnn/GSM754025/suppl/GSM754025.CEL.gz
| | Sample_series_id | GSE30385
| | Sample_data_row_count | 8793
| | |
|
GSM754026 | GPL201 |
|
SIDP14_blood_VAP_rep3
|
patients with VAP
|
tissue: blood
|
Gene expression data from critically-ill trauma patients following admission to the intensive care unit
|
| Sample_geo_accession | GSM754026
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Jul 05 2011
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times. Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS 3000 7G.
| | Sample_data_processing | The data were analyzed with RMA as the normalization method.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Joseph, ,Swanson
| | Sample_contact_email | jswanson@uthsc.edu
| | Sample_contact_phone | 901-448-1418
| | Sample_contact_department | Clinical Pharmacy
| | Sample_contact_institute | University of Tennessee
| | Sample_contact_address | 910 Madison Ave., Suite 308
| | Sample_contact_city | Memphis
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 38163
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM754nnn/GSM754026/suppl/GSM754026.CEL.gz
| | Sample_series_id | GSE30385
| | Sample_data_row_count | 8793
| | |
|
GSM754027 | GPL201 |
|
SIDP16_blood_VAP_rep4
|
patients with VAP
|
tissue: blood
|
Gene expression data from critically-ill trauma patients following admission to the intensive care unit
|
| Sample_geo_accession | GSM754027
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Jul 05 2011
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times. Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS 3000 7G.
| | Sample_data_processing | The data were analyzed with RMA as the normalization method.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Joseph, ,Swanson
| | Sample_contact_email | jswanson@uthsc.edu
| | Sample_contact_phone | 901-448-1418
| | Sample_contact_department | Clinical Pharmacy
| | Sample_contact_institute | University of Tennessee
| | Sample_contact_address | 910 Madison Ave., Suite 308
| | Sample_contact_city | Memphis
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 38163
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM754nnn/GSM754027/suppl/GSM754027.CEL.gz
| | Sample_series_id | GSE30385
| | Sample_data_row_count | 8793
| | |
|
GSM754028 | GPL201 |
|
SIDP17_blood_NoVAP_rep3
|
patients without VAP
|
tissue: blood
|
Gene expression data from critically-ill trauma patients following admission to the intensive care unit
|
| Sample_geo_accession | GSM754028
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Jul 05 2011
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times. Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS 3000 7G.
| | Sample_data_processing | The data were analyzed with RMA as the normalization method.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Joseph, ,Swanson
| | Sample_contact_email | jswanson@uthsc.edu
| | Sample_contact_phone | 901-448-1418
| | Sample_contact_department | Clinical Pharmacy
| | Sample_contact_institute | University of Tennessee
| | Sample_contact_address | 910 Madison Ave., Suite 308
| | Sample_contact_city | Memphis
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 38163
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM754nnn/GSM754028/suppl/GSM754028.CEL.gz
| | Sample_series_id | GSE30385
| | Sample_data_row_count | 8793
| | |
|
GSM754029 | GPL201 |
|
SIDP18_blood_VAP_rep5
|
patients with VAP
|
tissue: blood
|
Gene expression data from critically-ill trauma patients following admission to the intensive care unit
|
| Sample_geo_accession | GSM754029
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Jul 05 2011
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times. Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS 3000 7G.
| | Sample_data_processing | The data were analyzed with RMA as the normalization method.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Joseph, ,Swanson
| | Sample_contact_email | jswanson@uthsc.edu
| | Sample_contact_phone | 901-448-1418
| | Sample_contact_department | Clinical Pharmacy
| | Sample_contact_institute | University of Tennessee
| | Sample_contact_address | 910 Madison Ave., Suite 308
| | Sample_contact_city | Memphis
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 38163
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM754nnn/GSM754029/suppl/GSM754029.CEL.gz
| | Sample_series_id | GSE30385
| | Sample_data_row_count | 8793
| | |
|
GSM754030 | GPL201 |
|
SIDP19_blood_VAP_rep6
|
patients with VAP
|
tissue: blood
|
Gene expression data from critically-ill trauma patients following admission to the intensive care unit
|
| Sample_geo_accession | GSM754030
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Jul 05 2011
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times. Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS 3000 7G.
| | Sample_data_processing | The data were analyzed with RMA as the normalization method.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Joseph, ,Swanson
| | Sample_contact_email | jswanson@uthsc.edu
| | Sample_contact_phone | 901-448-1418
| | Sample_contact_department | Clinical Pharmacy
| | Sample_contact_institute | University of Tennessee
| | Sample_contact_address | 910 Madison Ave., Suite 308
| | Sample_contact_city | Memphis
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 38163
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM754nnn/GSM754030/suppl/GSM754030.CEL.gz
| | Sample_series_id | GSE30385
| | Sample_data_row_count | 8793
| | |
|
GSM754031 | GPL201 |
|
SIDP20_blood_VAP_rep7
|
patients with VAP
|
tissue: blood
|
Gene expression data from critically-ill trauma patients following admission to the intensive care unit
|
| Sample_geo_accession | GSM754031
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Jul 05 2011
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times. Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS 3000 7G.
| | Sample_data_processing | The data were analyzed with RMA as the normalization method.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Joseph, ,Swanson
| | Sample_contact_email | jswanson@uthsc.edu
| | Sample_contact_phone | 901-448-1418
| | Sample_contact_department | Clinical Pharmacy
| | Sample_contact_institute | University of Tennessee
| | Sample_contact_address | 910 Madison Ave., Suite 308
| | Sample_contact_city | Memphis
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 38163
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM754nnn/GSM754031/suppl/GSM754031.CEL.gz
| | Sample_series_id | GSE30385
| | Sample_data_row_count | 8793
| | |
|
GSM754032 | GPL201 |
|
SIDP21_blood_NoVAP_rep4
|
patients without VAP
|
tissue: blood
|
Gene expression data from critically-ill trauma patients following admission to the intensive care unit
|
| Sample_geo_accession | GSM754032
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Jul 05 2011
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times. Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS 3000 7G.
| | Sample_data_processing | The data were analyzed with RMA as the normalization method.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Joseph, ,Swanson
| | Sample_contact_email | jswanson@uthsc.edu
| | Sample_contact_phone | 901-448-1418
| | Sample_contact_department | Clinical Pharmacy
| | Sample_contact_institute | University of Tennessee
| | Sample_contact_address | 910 Madison Ave., Suite 308
| | Sample_contact_city | Memphis
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 38163
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM754nnn/GSM754032/suppl/GSM754032.CEL.gz
| | Sample_series_id | GSE30385
| | Sample_data_row_count | 8793
| | |
|
GSM754033 | GPL201 |
|
SIDP22_blood_VAP_rep8
|
patients with VAP
|
tissue: blood
|
Gene expression data from critically-ill trauma patients following admission to the intensive care unit
|
| Sample_geo_accession | GSM754033
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Jul 05 2011
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times. Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS 3000 7G.
| | Sample_data_processing | The data were analyzed with RMA as the normalization method.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Joseph, ,Swanson
| | Sample_contact_email | jswanson@uthsc.edu
| | Sample_contact_phone | 901-448-1418
| | Sample_contact_department | Clinical Pharmacy
| | Sample_contact_institute | University of Tennessee
| | Sample_contact_address | 910 Madison Ave., Suite 308
| | Sample_contact_city | Memphis
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 38163
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM754nnn/GSM754033/suppl/GSM754033.CEL.gz
| | Sample_series_id | GSE30385
| | Sample_data_row_count | 8793
| | |
|
GSM754034 | GPL201 |
|
SIDP23_blood_VAP_rep9
|
patients with VAP
|
tissue: blood
|
Gene expression data from critically-ill trauma patients following admission to the intensive care unit
|
| Sample_geo_accession | GSM754034
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Jul 05 2011
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times. Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS 3000 7G.
| | Sample_data_processing | The data were analyzed with RMA as the normalization method.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Joseph, ,Swanson
| | Sample_contact_email | jswanson@uthsc.edu
| | Sample_contact_phone | 901-448-1418
| | Sample_contact_department | Clinical Pharmacy
| | Sample_contact_institute | University of Tennessee
| | Sample_contact_address | 910 Madison Ave., Suite 308
| | Sample_contact_city | Memphis
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 38163
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM754nnn/GSM754034/suppl/GSM754034.CEL.gz
| | Sample_series_id | GSE30385
| | Sample_data_row_count | 8793
| | |
|
GSM754035 | GPL201 |
|
SIDP24_blood_VAP_rep10
|
patients with VAP
|
tissue: blood
|
Gene expression data from critically-ill trauma patients following admission to the intensive care unit
|
| Sample_geo_accession | GSM754035
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Jul 05 2011
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times. Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS 3000 7G.
| | Sample_data_processing | The data were analyzed with RMA as the normalization method.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Joseph, ,Swanson
| | Sample_contact_email | jswanson@uthsc.edu
| | Sample_contact_phone | 901-448-1418
| | Sample_contact_department | Clinical Pharmacy
| | Sample_contact_institute | University of Tennessee
| | Sample_contact_address | 910 Madison Ave., Suite 308
| | Sample_contact_city | Memphis
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 38163
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM754nnn/GSM754035/suppl/GSM754035.CEL.gz
| | Sample_series_id | GSE30385
| | Sample_data_row_count | 8793
| | |
|
GSM754036 | GPL201 |
|
SIDP25_blood_NoVAP_rep5
|
patients without VAP
|
tissue: blood
|
Gene expression data from critically-ill trauma patients following admission to the intensive care unit
|
| Sample_geo_accession | GSM754036
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Jul 05 2011
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times. Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS 3000 7G.
| | Sample_data_processing | The data were analyzed with RMA as the normalization method.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Joseph, ,Swanson
| | Sample_contact_email | jswanson@uthsc.edu
| | Sample_contact_phone | 901-448-1418
| | Sample_contact_department | Clinical Pharmacy
| | Sample_contact_institute | University of Tennessee
| | Sample_contact_address | 910 Madison Ave., Suite 308
| | Sample_contact_city | Memphis
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 38163
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM754nnn/GSM754036/suppl/GSM754036.CEL.gz
| | Sample_series_id | GSE30385
| | Sample_data_row_count | 8793
| | |
|
GSM754037 | GPL201 |
|
SIDP27_blood_NoVAP_rep6
|
patients without VAP
|
tissue: blood
|
Gene expression data from critically-ill trauma patients following admission to the intensive care unit
|
| Sample_geo_accession | GSM754037
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Jul 05 2011
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times. Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS 3000 7G.
| | Sample_data_processing | The data were analyzed with RMA as the normalization method.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Joseph, ,Swanson
| | Sample_contact_email | jswanson@uthsc.edu
| | Sample_contact_phone | 901-448-1418
| | Sample_contact_department | Clinical Pharmacy
| | Sample_contact_institute | University of Tennessee
| | Sample_contact_address | 910 Madison Ave., Suite 308
| | Sample_contact_city | Memphis
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 38163
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM754nnn/GSM754037/suppl/GSM754037.CEL.gz
| | Sample_series_id | GSE30385
| | Sample_data_row_count | 8793
| | |
|
GSM754038 | GPL201 |
|
SIDP28_blood_NoVAP_rep7
|
patients without VAP
|
tissue: blood
|
Gene expression data from critically-ill trauma patients following admission to the intensive care unit
|
| Sample_geo_accession | GSM754038
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Jul 05 2011
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times. Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS 3000 7G.
| | Sample_data_processing | The data were analyzed with RMA as the normalization method.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Joseph, ,Swanson
| | Sample_contact_email | jswanson@uthsc.edu
| | Sample_contact_phone | 901-448-1418
| | Sample_contact_department | Clinical Pharmacy
| | Sample_contact_institute | University of Tennessee
| | Sample_contact_address | 910 Madison Ave., Suite 308
| | Sample_contact_city | Memphis
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 38163
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM754nnn/GSM754038/suppl/GSM754038.CEL.gz
| | Sample_series_id | GSE30385
| | Sample_data_row_count | 8793
| | |
|
GSM754039 | GPL201 |
|
SIDP29_blood_NoVAP_rep8
|
patients without VAP
|
tissue: blood
|
Gene expression data from critically-ill trauma patients following admission to the intensive care unit
|
| Sample_geo_accession | GSM754039
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Jul 05 2011
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times. Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS 3000 7G.
| | Sample_data_processing | The data were analyzed with RMA as the normalization method.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Joseph, ,Swanson
| | Sample_contact_email | jswanson@uthsc.edu
| | Sample_contact_phone | 901-448-1418
| | Sample_contact_department | Clinical Pharmacy
| | Sample_contact_institute | University of Tennessee
| | Sample_contact_address | 910 Madison Ave., Suite 308
| | Sample_contact_city | Memphis
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 38163
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM754nnn/GSM754039/suppl/GSM754039.CEL.gz
| | Sample_series_id | GSE30385
| | Sample_data_row_count | 8793
| | |
|
GSM754040 | GPL201 |
|
SIDP31_blood_NoVAP_rep9
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patients without VAP
|
tissue: blood
|
Gene expression data from critically-ill trauma patients following admission to the intensive care unit
|
| Sample_geo_accession | GSM754040
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Jul 05 2011
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times. Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS 3000 7G.
| | Sample_data_processing | The data were analyzed with RMA as the normalization method.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Joseph, ,Swanson
| | Sample_contact_email | jswanson@uthsc.edu
| | Sample_contact_phone | 901-448-1418
| | Sample_contact_department | Clinical Pharmacy
| | Sample_contact_institute | University of Tennessee
| | Sample_contact_address | 910 Madison Ave., Suite 308
| | Sample_contact_city | Memphis
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 38163
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM754nnn/GSM754040/suppl/GSM754040.CEL.gz
| | Sample_series_id | GSE30385
| | Sample_data_row_count | 8793
| | |
|
GSM754041 | GPL201 |
|
SIDP32_blood_NoVAP_rep10
|
patients without VAP
|
tissue: blood
|
Gene expression data from critically-ill trauma patients following admission to the intensive care unit
|
| Sample_geo_accession | GSM754041
| | Sample_status | Public on Jan 01 2013
| | Sample_submission_date | Jul 05 2011
| | Sample_last_update_date | Jan 01 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 40 mL of whole blood was collected. Blood samples were immediately stimulated with 1000 ng/mL of lipopolysaccharide (LPS) solution (E. coli 011B4 LPS in RPMI 1640 culture medium - 10% fetal bovine serum and 100 U/mL penicillin-streptomycin). Samples were incubated for 3 hours in a water bath at 37C.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Immediately following incubation, samples were centrifuged for 10 minutes at 4C. The plasma layer was decanted. The white blood cell layer was removed and incubated in 30 mL of RBC lysis buffer (Tris HCL/TRIZMA HCl/NH4Cl) at 37C for 15 minutes then centrifuged for 15 minutes at 4C. The supernatant was decanted and the pellet resuspended and washed with D-PBS two times. Total RNA was isolated using phenol-chloroform extraction per the RNAgents Total RNA isolation kit protocol (Promega, Madison, WI). RNA concentration was initially estimated by comparing the ultraviolet absorbance (A260/A280) ratio of the sample. The integrity and concentration of the RNA sample was subsequently assessed using the RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer (Agilent Technologies).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared by a modified Eberwine RT-IVT procedure using the Bioarray HighYield™ RNA Transcript Labeling Kit (Enzo), according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome Focus arrays (Affymetrix; catalog no. 510637). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GCS 3000 7G.
| | Sample_data_processing | The data were analyzed with RMA as the normalization method.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Joseph, ,Swanson
| | Sample_contact_email | jswanson@uthsc.edu
| | Sample_contact_phone | 901-448-1418
| | Sample_contact_department | Clinical Pharmacy
| | Sample_contact_institute | University of Tennessee
| | Sample_contact_address | 910 Madison Ave., Suite 308
| | Sample_contact_city | Memphis
| | Sample_contact_state | TN
| | Sample_contact_zip/postal_code | 38163
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM754nnn/GSM754041/suppl/GSM754041.CEL.gz
| | Sample_series_id | GSE30385
| | Sample_data_row_count | 8793
| | |
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