Search results for the GEO ID: GSE22779  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM563241 | GPL570 |
|
Epilepsy patient E3, untreated sample
|
Mononuclear cells, epilepsy patient E3, before administration of GC
|
tissue: peripheral blood
cell type: mononuclear cells
disease state: epilepsy, non-leukemic
treatment: untreated
treatment_time: 0 hrs
patient: E3
|
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E3 before administration of GC.
E3-0h
|
| Sample_geo_accession | GSM563241
| | Sample_status | Public on Feb 01 2011
| | Sample_submission_date | Jul 06 2010
| | Sample_last_update_date | Feb 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Single administration of the glucocorticoid dexamethasone (20 mg/m2).
| | Sample_growth_protocol_ch1 | None.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH, USA) was used according to the manufacturer’s protocol. Briefly, mononuclear cells isolated from peripheral blood (Lymphoprep) were lysed with TRIreagent, 200ul of chloroform was added, the mixture was centrifuged, and the RNA from the aqueous phase was precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA was further processed with the RNeasy Cleanup Kit (Qiagen), and quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA). Only high quality RNA was further processed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS (version 1.4.0.036) software.
| | Sample_data_processing | The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's GCRMA package version 2.18.1).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM563nnn/GSM563241/suppl/GSM563241.CEL.gz
| | Sample_series_id | GSE22779
| | Sample_data_row_count | 54675
| | |
|
GSM563242 | GPL570 |
|
Epilepsy patient E3, 2 hours GC treatment
|
Mononuclear cells, epilepsy patient E3, 2 hours after GC administration
|
tissue: peripheral blood
cell type: mononuclear cells
disease state: epilepsy, non-leukemic
treatment: dexamethasone
treatment_time: 2 hrs
patient: E3
|
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E3 taken 2 hours after GC administration.
E3-2h
|
| Sample_geo_accession | GSM563242
| | Sample_status | Public on Feb 01 2011
| | Sample_submission_date | Jul 06 2010
| | Sample_last_update_date | Feb 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Single administration of the glucocorticoid dexamethasone (20 mg/m2).
| | Sample_growth_protocol_ch1 | None.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH, USA) was used according to the manufacturer’s protocol. Briefly, mononuclear cells isolated from peripheral blood (Lymphoprep) were lysed with TRIreagent, 200ul of chloroform was added, the mixture was centrifuged, and the RNA from the aqueous phase was precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA was further processed with the RNeasy Cleanup Kit (Qiagen), and quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA). Only high quality RNA was further processed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS (version 1.4.0.036) software.
| | Sample_data_processing | The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's GCRMA package version 2.18.1).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM563nnn/GSM563242/suppl/GSM563242.CEL.gz
| | Sample_series_id | GSE22779
| | Sample_data_row_count | 54675
| | |
|
GSM563243 | GPL570 |
|
Epilepsy patient E3, 6 hours GC treatment
|
Mononuclear cells, epilepsy patient E3, 6 hours after GC administration
|
tissue: peripheral blood
cell type: mononuclear cells
disease state: epilepsy, non-leukemic
treatment: dexamethasone
treatment_time: 6 hrs
patient: E3
|
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E3 taken 6 hours after GC administration.
E3-6h
|
| Sample_geo_accession | GSM563243
| | Sample_status | Public on Feb 01 2011
| | Sample_submission_date | Jul 06 2010
| | Sample_last_update_date | Feb 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Single administration of the glucocorticoid dexamethasone (20 mg/m2).
| | Sample_growth_protocol_ch1 | None.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH, USA) was used according to the manufacturer’s protocol. Briefly, mononuclear cells isolated from peripheral blood (Lymphoprep) were lysed with TRIreagent, 200ul of chloroform was added, the mixture was centrifuged, and the RNA from the aqueous phase was precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA was further processed with the RNeasy Cleanup Kit (Qiagen), and quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA). Only high quality RNA was further processed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS (version 1.4.0.036) software.
| | Sample_data_processing | The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's GCRMA package version 2.18.1).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM563nnn/GSM563243/suppl/GSM563243.CEL.gz
| | Sample_series_id | GSE22779
| | Sample_data_row_count | 54675
| | |
|
GSM563244 | GPL570 |
|
Epilepsy patient E3, 24 hours GC treatment
|
Mononuclear cells, epilepsy patient E3, 24 hours after GC administration
|
tissue: peripheral blood
cell type: mononuclear cells
disease state: epilepsy, non-leukemic
treatment: dexamethasone
treatment_time: 24 hrs
patient: E3
|
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E3 taken 24 hours after GC administration.
E3-24h
|
| Sample_geo_accession | GSM563244
| | Sample_status | Public on Feb 01 2011
| | Sample_submission_date | Jul 06 2010
| | Sample_last_update_date | Feb 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Single administration of the glucocorticoid dexamethasone (20 mg/m2).
| | Sample_growth_protocol_ch1 | None.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH, USA) was used according to the manufacturer’s protocol. Briefly, mononuclear cells isolated from peripheral blood (Lymphoprep) were lysed with TRIreagent, 200ul of chloroform was added, the mixture was centrifuged, and the RNA from the aqueous phase was precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA was further processed with the RNeasy Cleanup Kit (Qiagen), and quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA). Only high quality RNA was further processed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS (version 1.4.0.036) software.
| | Sample_data_processing | The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's GCRMA package version 2.18.1).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM563nnn/GSM563244/suppl/GSM563244.CEL.gz
| | Sample_series_id | GSE22779
| | Sample_data_row_count | 54675
| | |
|
GSM563245 | GPL570 |
|
Epilepsy patient E4, untreated sample
|
Mononuclear cells, epilepsy patient E4, before administration of GC
|
tissue: peripheral blood
cell type: mononuclear cells
disease state: epilepsy, non-leukemic
treatment: untreated
treatment_time: 0 hrs
patient: E4
|
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E4 before administration of GC.
E4-0h
|
| Sample_geo_accession | GSM563245
| | Sample_status | Public on Feb 01 2011
| | Sample_submission_date | Jul 06 2010
| | Sample_last_update_date | Feb 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Single administration of the glucocorticoid dexamethasone (20 mg/m2).
| | Sample_growth_protocol_ch1 | None.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH, USA) was used according to the manufacturer’s protocol. Briefly, mononuclear cells isolated from peripheral blood (Lymphoprep) were lysed with TRIreagent, 200ul of chloroform was added, the mixture was centrifuged, and the RNA from the aqueous phase was precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA was further processed with the RNeasy Cleanup Kit (Qiagen), and quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA). Only high quality RNA was further processed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS (version 1.4.0.036) software.
| | Sample_data_processing | The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's GCRMA package version 2.18.1).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM563nnn/GSM563245/suppl/GSM563245.CEL.gz
| | Sample_series_id | GSE22779
| | Sample_data_row_count | 54675
| | |
|
GSM563246 | GPL570 |
|
Epilepsy patient E4, 2 hours GC treatment
|
Mononuclear cells, epilepsy patient E4, 2 hours after GC administration
|
tissue: peripheral blood
cell type: mononuclear cells
disease state: epilepsy, non-leukemic
treatment: dexamethasone
treatment_time: 2 hrs
patient: E4
|
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E4 taken 2 hours after GC administration.
E4-2h
|
| Sample_geo_accession | GSM563246
| | Sample_status | Public on Feb 01 2011
| | Sample_submission_date | Jul 06 2010
| | Sample_last_update_date | Feb 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Single administration of the glucocorticoid dexamethasone (20 mg/m2).
| | Sample_growth_protocol_ch1 | None.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH, USA) was used according to the manufacturer’s protocol. Briefly, mononuclear cells isolated from peripheral blood (Lymphoprep) were lysed with TRIreagent, 200ul of chloroform was added, the mixture was centrifuged, and the RNA from the aqueous phase was precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA was further processed with the RNeasy Cleanup Kit (Qiagen), and quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA). Only high quality RNA was further processed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS (version 1.4.0.036) software.
| | Sample_data_processing | The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's GCRMA package version 2.18.1).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM563nnn/GSM563246/suppl/GSM563246.CEL.gz
| | Sample_series_id | GSE22779
| | Sample_data_row_count | 54675
| | |
|
GSM563247 | GPL570 |
|
Epilepsy patient E4, 6 hours GC treatment
|
Mononuclear cells, epilepsy patient E4, 6 hours after GC administration
|
tissue: peripheral blood
cell type: mononuclear cells
disease state: epilepsy, non-leukemic
treatment: dexamethasone
treatment_time: 6 hrs
patient: E4
|
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E4 taken 6 hours after GC administration.
E4-6h
|
| Sample_geo_accession | GSM563247
| | Sample_status | Public on Feb 01 2011
| | Sample_submission_date | Jul 06 2010
| | Sample_last_update_date | Feb 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Single administration of the glucocorticoid dexamethasone (20 mg/m2).
| | Sample_growth_protocol_ch1 | None.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH, USA) was used according to the manufacturer’s protocol. Briefly, mononuclear cells isolated from peripheral blood (Lymphoprep) were lysed with TRIreagent, 200ul of chloroform was added, the mixture was centrifuged, and the RNA from the aqueous phase was precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA was further processed with the RNeasy Cleanup Kit (Qiagen), and quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA). Only high quality RNA was further processed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS (version 1.4.0.036) software.
| | Sample_data_processing | The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's GCRMA package version 2.18.1).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM563nnn/GSM563247/suppl/GSM563247.CEL.gz
| | Sample_series_id | GSE22779
| | Sample_data_row_count | 54675
| | |
|
GSM563248 | GPL570 |
|
Epilepsy patient E4, 24 hours GC treatment
|
Mononuclear cells, epilepsy patient E4, 24 hours after GC administration
|
tissue: peripheral blood
cell type: mononuclear cells
disease state: epilepsy, non-leukemic
treatment: dexamethasone
treatment_time: 24 hrs
patient: E4
|
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E4 taken 24 hours after GC administration.
E4-24h
|
| Sample_geo_accession | GSM563248
| | Sample_status | Public on Feb 01 2011
| | Sample_submission_date | Jul 06 2010
| | Sample_last_update_date | Feb 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Single administration of the glucocorticoid dexamethasone (20 mg/m2).
| | Sample_growth_protocol_ch1 | None.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH, USA) was used according to the manufacturer’s protocol. Briefly, mononuclear cells isolated from peripheral blood (Lymphoprep) were lysed with TRIreagent, 200ul of chloroform was added, the mixture was centrifuged, and the RNA from the aqueous phase was precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA was further processed with the RNeasy Cleanup Kit (Qiagen), and quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA). Only high quality RNA was further processed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS (version 1.4.0.036) software.
| | Sample_data_processing | The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's GCRMA package version 2.18.1).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM563nnn/GSM563248/suppl/GSM563248.CEL.gz
| | Sample_series_id | GSE22779
| | Sample_data_row_count | 54675
| | |
|
GSM563249 | GPL570 |
|
Epilepsy patient E5, untreated sample
|
Mononuclear cells, epilepsy patient E5, before administration of GC
|
tissue: peripheral blood
cell type: mononuclear cells
disease state: epilepsy, non-leukemic
treatment: untreated
treatment_time: 0 hrs
patient: E5
|
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E5 before administration of GC.
E5-0h
|
| Sample_geo_accession | GSM563249
| | Sample_status | Public on Feb 01 2011
| | Sample_submission_date | Jul 06 2010
| | Sample_last_update_date | Feb 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Single administration of the glucocorticoid dexamethasone (20 mg/m2).
| | Sample_growth_protocol_ch1 | None.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH, USA) was used according to the manufacturer’s protocol. Briefly, mononuclear cells isolated from peripheral blood (Lymphoprep) were lysed with TRIreagent, 200ul of chloroform was added, the mixture was centrifuged, and the RNA from the aqueous phase was precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA was further processed with the RNeasy Cleanup Kit (Qiagen), and quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA). Only high quality RNA was further processed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS (version 1.4.0.036) software.
| | Sample_data_processing | The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's GCRMA package version 2.18.1).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM563nnn/GSM563249/suppl/GSM563249.CEL.gz
| | Sample_series_id | GSE22779
| | Sample_data_row_count | 54675
| | |
|
GSM563250 | GPL570 |
|
Epilepsy patient E5, 2 hours GC treatment
|
Mononuclear cells, epilepsy patient E5, 2 hours after GC administration
|
tissue: peripheral blood
cell type: mononuclear cells
disease state: epilepsy, non-leukemic
treatment: dexamethasone
treatment_time: 2 hrs
patient: E5
|
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E5 taken 2 hours after GC administration.
E5-2h
|
| Sample_geo_accession | GSM563250
| | Sample_status | Public on Feb 01 2011
| | Sample_submission_date | Jul 06 2010
| | Sample_last_update_date | Feb 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Single administration of the glucocorticoid dexamethasone (20 mg/m2).
| | Sample_growth_protocol_ch1 | None.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH, USA) was used according to the manufacturer’s protocol. Briefly, mononuclear cells isolated from peripheral blood (Lymphoprep) were lysed with TRIreagent, 200ul of chloroform was added, the mixture was centrifuged, and the RNA from the aqueous phase was precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA was further processed with the RNeasy Cleanup Kit (Qiagen), and quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA). Only high quality RNA was further processed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS (version 1.4.0.036) software.
| | Sample_data_processing | The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's GCRMA package version 2.18.1).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM563nnn/GSM563250/suppl/GSM563250.CEL.gz
| | Sample_series_id | GSE22779
| | Sample_data_row_count | 54675
| | |
|
GSM563251 | GPL570 |
|
Epilepsy patient E5, 6 hours GC treatment
|
Mononuclear cells, epilepsy patient E5, 6 hours after GC administration
|
tissue: peripheral blood
cell type: mononuclear cells
disease state: epilepsy, non-leukemic
treatment: dexamethasone
treatment_time: 6 hrs
patient: E5
|
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E5 taken 6 hours after GC administration.
E5-6h
|
| Sample_geo_accession | GSM563251
| | Sample_status | Public on Feb 01 2011
| | Sample_submission_date | Jul 06 2010
| | Sample_last_update_date | Feb 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Single administration of the glucocorticoid dexamethasone (20 mg/m2).
| | Sample_growth_protocol_ch1 | None.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH, USA) was used according to the manufacturer’s protocol. Briefly, mononuclear cells isolated from peripheral blood (Lymphoprep) were lysed with TRIreagent, 200ul of chloroform was added, the mixture was centrifuged, and the RNA from the aqueous phase was precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA was further processed with the RNeasy Cleanup Kit (Qiagen), and quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA). Only high quality RNA was further processed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS (version 1.4.0.036) software.
| | Sample_data_processing | The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's GCRMA package version 2.18.1).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM563nnn/GSM563251/suppl/GSM563251.CEL.gz
| | Sample_series_id | GSE22779
| | Sample_data_row_count | 54675
| | |
|
GSM563252 | GPL570 |
|
Epilepsy patient E5, 24 hours GC treatment
|
Mononuclear cells, epilepsy patient E5, 24 hours after GC administration
|
tissue: peripheral blood
cell type: mononuclear cells
disease state: epilepsy, non-leukemic
treatment: dexamethasone
treatment_time: 24 hrs
patient: E5
|
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of the epilepsy patient E5 taken 24 hours after GC administration.
E5-24h
|
| Sample_geo_accession | GSM563252
| | Sample_status | Public on Feb 01 2011
| | Sample_submission_date | Jul 06 2010
| | Sample_last_update_date | Feb 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Single administration of the glucocorticoid dexamethasone (20 mg/m2).
| | Sample_growth_protocol_ch1 | None.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH, USA) was used according to the manufacturer’s protocol. Briefly, mononuclear cells isolated from peripheral blood (Lymphoprep) were lysed with TRIreagent, 200ul of chloroform was added, the mixture was centrifuged, and the RNA from the aqueous phase was precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA was further processed with the RNeasy Cleanup Kit (Qiagen), and quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA). Only high quality RNA was further processed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS (version 1.4.0.036) software.
| | Sample_data_processing | The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's GCRMA package version 2.18.1).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM563nnn/GSM563252/suppl/GSM563252.CEL.gz
| | Sample_series_id | GSE22779
| | Sample_data_row_count | 54675
| | |
|
GSM563253 | GPL570 |
|
Healthy donor, untreated sample
|
Mononuclear cells, healthy donor, before administration of GC
|
tissue: peripheral blood
cell type: mononuclear cells
disease state: healthy
treatment: untreated
treatment_time: 0 hrs
|
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of a healthy donor before administration of GC.
RPK-II-0h
|
| Sample_geo_accession | GSM563253
| | Sample_status | Public on Feb 01 2011
| | Sample_submission_date | Jul 06 2010
| | Sample_last_update_date | Feb 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Single administration of the glucocorticoid dexamethasone (20 mg/m2).
| | Sample_growth_protocol_ch1 | None.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH, USA) was used according to the manufacturer’s protocol. Briefly, mononuclear cells isolated from peripheral blood (Lymphoprep) were lysed with TRIreagent, 200ul of chloroform was added, the mixture was centrifuged, and the RNA from the aqueous phase was precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA was further processed with the RNeasy Cleanup Kit (Qiagen), and quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA). Only high quality RNA was further processed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS (version 1.4.0.036) software.
| | Sample_data_processing | The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's GCRMA package version 2.18.1).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM563nnn/GSM563253/suppl/GSM563253.CEL.gz
| | Sample_series_id | GSE22779
| | Sample_data_row_count | 54675
| | |
|
GSM563254 | GPL570 |
|
Healthy donor, 2 hours GC treatment
|
Mononuclear cells, healthy donor, 2 hours after GC administration
|
tissue: peripheral blood
cell type: mononuclear cells
disease state: healthy
treatment: dexamethasone
treatment_time: 2 hrs
|
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of a healthy donor taken 2 hours after GC administration.
RPK-II-2h
|
| Sample_geo_accession | GSM563254
| | Sample_status | Public on Feb 01 2011
| | Sample_submission_date | Jul 06 2010
| | Sample_last_update_date | Feb 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Single administration of the glucocorticoid dexamethasone (20 mg/m2).
| | Sample_growth_protocol_ch1 | None.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH, USA) was used according to the manufacturer’s protocol. Briefly, mononuclear cells isolated from peripheral blood (Lymphoprep) were lysed with TRIreagent, 200ul of chloroform was added, the mixture was centrifuged, and the RNA from the aqueous phase was precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA was further processed with the RNeasy Cleanup Kit (Qiagen), and quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA). Only high quality RNA was further processed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS (version 1.4.0.036) software.
| | Sample_data_processing | The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's GCRMA package version 2.18.1).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM563nnn/GSM563254/suppl/GSM563254.CEL.gz
| | Sample_series_id | GSE22779
| | Sample_data_row_count | 54675
| | |
|
GSM563255 | GPL570 |
|
Healthy donor, 6 hours GC treatment
|
Mononuclear cells, healthy donor, 6 hours after GC administration
|
tissue: peripheral blood
cell type: mononuclear cells
disease state: healthy
treatment: dexamethasone
treatment_time: 6 hrs
|
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of a healthy donor taken 6 hours after GC administration.
RPK-II-6h
|
| Sample_geo_accession | GSM563255
| | Sample_status | Public on Feb 01 2011
| | Sample_submission_date | Jul 06 2010
| | Sample_last_update_date | Feb 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Single administration of the glucocorticoid dexamethasone (20 mg/m2).
| | Sample_growth_protocol_ch1 | None.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH, USA) was used according to the manufacturer’s protocol. Briefly, mononuclear cells isolated from peripheral blood (Lymphoprep) were lysed with TRIreagent, 200ul of chloroform was added, the mixture was centrifuged, and the RNA from the aqueous phase was precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA was further processed with the RNeasy Cleanup Kit (Qiagen), and quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA). Only high quality RNA was further processed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS (version 1.4.0.036) software.
| | Sample_data_processing | The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's GCRMA package version 2.18.1).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM563nnn/GSM563255/suppl/GSM563255.CEL.gz
| | Sample_series_id | GSE22779
| | Sample_data_row_count | 54675
| | |
|
GSM563256 | GPL570 |
|
Healthy donor, 24 hours GC treatment
|
Mononuclear cells, healthy donor, 24 hours after GC administration
|
tissue: peripheral blood
cell type: mononuclear cells
disease state: healthy
treatment: dexamethasone
treatment_time: 24 hrs
|
Gene expression of mononuclear cells isolated from the peripheral blood (using Lymphoprep) of a healthy donor taken 24 hours after GC administration.
RPK-II-24h
|
| Sample_geo_accession | GSM563256
| | Sample_status | Public on Feb 01 2011
| | Sample_submission_date | Jul 06 2010
| | Sample_last_update_date | Feb 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Single administration of the glucocorticoid dexamethasone (20 mg/m2).
| | Sample_growth_protocol_ch1 | None.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH, USA) was used according to the manufacturer’s protocol. Briefly, mononuclear cells isolated from peripheral blood (Lymphoprep) were lysed with TRIreagent, 200ul of chloroform was added, the mixture was centrifuged, and the RNA from the aqueous phase was precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA was further processed with the RNeasy Cleanup Kit (Qiagen), and quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA). Only high quality RNA was further processed.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS (version 1.4.0.036) software.
| | Sample_data_processing | The raw data was preprocessed in R (version 2.10) using the GCRMA algorithm (Bioconductor's GCRMA package version 2.18.1).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM563nnn/GSM563256/suppl/GSM563256.CEL.gz
| | Sample_series_id | GSE22779
| | Sample_data_row_count | 54675
| | |
|
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