Search results for the GEO ID: GSE2842  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM60535 | GPL570 |
|
Adult-B-ALL-24h
|
Adult B-ALL patient, peripheral blood
|
biological source:
homo sapiens, childhood ALL patient (male, aged 72 years), peripheral blood taken 24h after GC-monotherapy initiation
|
homo sapiens, childhood ALL patient (male, aged 72 years), peripheral blood taken 24h after GC-monotherapy initiation
|
| Sample_geo_accession | GSM60535
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BFM2000 treatment protocol
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_extract_protocol_ch1 | For Affymetrix GeneChip analysis 1.5ug 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, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60535/suppl/GSM60535.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60536 | GPL570 |
|
Adult-B-ALL-6h
|
Adult B-ALL patient, peripheral blood
|
biological source:
homo sapiens, childhood ALL patient (male, aged 72 years), peripheral blood taken 6h after GC-monotherapy initiation, leukocyte isolation CD10 targeted enrichment for malignant blasts
|
homo sapiens, childhood ALL patient (male, aged 72 years), peripheral blood taken 6h after GC-monotherapy initiation, leukocyte isolation CD10 targeted enrichment for malignant blasts
|
| Sample_geo_accession | GSM60536
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BFM2000 treatment protocol
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60536/suppl/GSM60536.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60537 | GPL570 |
|
Adult-B-ALL-0h
|
Adult B-ALL patient, peripheral blood
|
biological source:
homo sapiens, ALL patient (male, aged 72 years), peripheral blood taken prior to treatment, leukocyte isolation CD10 targeted enrichment for malignant blasts.
|
biological source:
homo sapiens, ALL patient (male, aged 72 years), peripheral blood taken prior to treatment, leukocyte isolation CD10 targeted enrichment for malignant blasts.
|
| Sample_geo_accession | GSM60537
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BFM2000 treatment protocol
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60537/suppl/GSM60537.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60538 | GPL570 |
|
IV-B-ALL-40-6h-EtOH
|
B-ALL patient 40, peripheral blood
|
biological source:
homo sapiens, ALL ex vivo material from adult B-ALL patient, peripheral blood taken prior to treatment, leukocyte isolation CD10 targeted enrichment for malignant blasts, cultivated in the presence of ethanol 0,1% for 6h
|
biological source:
homo sapiens, ALL ex vivo material from adult B-ALL patient, peripheral blood taken prior to treatment, leukocyte isolation CD10 targeted enrichment for malignant blasts, cultivated in the presence of ethanol 0,1% for 6h
|
| Sample_geo_accession | GSM60538
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60538/suppl/GSM60538.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60539 | GPL570 |
|
IV-B-ALL-40-6h-GC
|
B-ALL patient 40, peripheral blood
|
biological source:
homo sapiens, ALL ex vivo material from adult B-ALL patient, peripheral blood taken prior to treatment, leukocyte isolation CD10 targeted enrichment for malignant blasts, cultivated in the presence of dexamethasone 10e-7M for 6h
|
biological source:
homo sapiens, ALL ex vivo material from adult B-ALL patient, peripheral blood taken prior to treatment, leukocyte isolation CD10 targeted enrichment for malignant blasts, cultivated in the presence of dexamethasone 10e-7M for 6h
|
| Sample_geo_accession | GSM60539
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60539/suppl/GSM60539.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60540 | GPL570 |
|
IV-B-ALL-40-24h-EtOH
|
B-ALL patient 40, peripheral blood
|
biological source:
homo sapiens, ALL ex vivo material from adult B-ALL patient, peripheral blood taken prior to treatment, leukocyte isolation CD10 targeted enrichment for malignant blasts, cultivated in the presence of ethanol 0,1% for 24h
|
biological source:
homo sapiens, ALL ex vivo material from adult B-ALL patient, peripheral blood taken prior to treatment, leukocyte isolation CD10 targeted enrichment for malignant blasts, cultivated in the presence of ethanol 0,1% for 24h
|
| Sample_geo_accession | GSM60540
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60540/suppl/GSM60540.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60541 | GPL570 |
|
IV-B-ALL-40-24h-GC
|
B-ALL patient 40, peripheral blood
|
biological source:
homo sapiens, ALL ex vivo material from adult B-ALL patient, peripheral blood taken prior to treatment, leukocyte isolation CD10 targeted enrichment for malignant blasts, cultivated in the presence of dexamethasone 10e-7M for 24h
|
biological source:
homo sapiens, ALL ex vivo material from adult B-ALL patient, peripheral blood taken prior to treatment, leukocyte isolation CD10 targeted enrichment for malignant blasts, cultivated in the presence of dexamethasone 10e-7M for 24h
|
| Sample_geo_accession | GSM60541
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60541/suppl/GSM60541.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60543 | GPL570 |
|
S-Line-C7H2-6h-GC
|
C7H2 cell line
|
homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 6h
|
biological source:
homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 6h
|
| Sample_geo_accession | GSM60543
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60543/suppl/GSM60543.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60544 | GPL570 |
|
S-Line-C7H2-24h-GC
|
C7H2 cell line
|
homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 24h
|
biological source:
homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 24h
|
| Sample_geo_accession | GSM60544
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60544/suppl/GSM60544.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60545 | GPL570 |
|
S-Line-PreB-6h-EtOH
|
PreB 697 cell line
|
homo sapiens, human B cell precursor leukemia cell line: 697 (DSMZ no: ACC 42), 697 cells are GC-sensitive, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h
|
biological source: homo sapiens, human B cell precursor leukemia cell line: 697 (DSMZ no: ACC 42), 697 cells are GC-sensitive, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h
|
| Sample_geo_accession | GSM60545
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60545/suppl/GSM60545.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60546 | GPL570 |
|
S-Line-PreB-6h-GC
|
PreB 697 cell line
|
homo sapiens, human B cell precursor leukemia cell line: 697 (DSMZ no: ACC 42), 697 cells are GC-sensitive, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 6h
|
biological source: homo sapiens, human B cell precursor leukemia cell line: 697 (DSMZ no: ACC 42), 697 cells are GC-sensitive, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 6h
|
| Sample_geo_accession | GSM60546
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60546/suppl/GSM60546.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60547 | GPL570 |
|
S-Line-PreB-24h-GC
|
PreB 697 cell line
|
homo sapiens, human B cell precursor leukemia cell line: 697 (DSMZ no: ACC 42), 697 cells are GC-sensitive, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 24h
|
biological source: homo sapiens, human B cell precursor leukemia cell line: 697 (DSMZ no: ACC 42), 697 cells are GC-sensitive, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 24h
|
| Sample_geo_accession | GSM60547
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60547/suppl/GSM60547.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60548 | GPL570 |
|
C-Line-CEMC1-ratGR-6h-EtOH
|
rat- Glucocorticoid-receptor transfected CCRF-CEM (ATCC no.: CLL-119) subclone C1
|
GC-sensitivity restored, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h
|
biological source: homo sapiens, rat- Glucocorticoid-receptor transfected CCRF-CEM (ATCC no.: CLL-119) subclone C1, parental cell line C1 = GC resistant, C1-rat-Glucocorticoid-receptor = GC-sensitivity restored, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h
|
| Sample_geo_accession | GSM60548
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60548/suppl/GSM60548.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60549 | GPL570 |
|
C-Line-CEMC1-ratGR-6h-GC
|
rat- Glucocorticoid-receptor transfected CCRF-CEM (ATCC no.: CLL-119) subclone C1
|
GC-sensitivity restored, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 6h
|
biological source: homo sapiens, rat-Glucocorticoid-receptor transfected CCRF-CEM (ATCC no.: CLL-119) subclone C1, parental cell line C1 = GC resistant, C1-rat-GR = GC-sensitivity restored, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 6h
|
| Sample_geo_accession | GSM60549
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60549/suppl/GSM60549.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60550 | GPL570 |
|
C-Line-CEMC1-ratGR-24h-GC
|
rat- Glucocorticoid-receptor transfected CCRF-CEM (ATCC no.: CLL-119) subclone C1
|
GC-sensitivity restored, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 24h
|
biological source: homo sapiens, rat-Glucocorticoid-receptor transfected CCRF-CEM (ATCC no.: CLL-119) subclone C1, parental cell line C1 = GC resistant, C1-rat GR = GC-sensitivity restored, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 24h
|
| Sample_geo_accession | GSM60550
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60550/suppl/GSM60550.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60551 | GPL570 |
|
C-Line-C7R1dim-high-6h-EtOH
|
C7R1 dim-high cell line
|
homo sapiens, CCRF-CEM (ATCC no.: CLL-119) subclone C7R1 (=GC-resistant) transfected with a dimerization deficient Glucocorticoid-receptor-mutant, high expression of mutant resulting in a restored GC-sensitivity, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h
|
biological source: homo sapiens, CCRF-CEM (ATCC no.: CLL-119) subclone C7R1 (=GC-resistant) transfected with a dimerization deficient Glucocorticoid-receptor-mutant, high expression of mutant resulting in a restored GC-sensitivity, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h
|
| Sample_geo_accession | GSM60551
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60551/suppl/GSM60551.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60552 | GPL570 |
|
C-Line-C7R1dim-high-6h-GC
|
C7R1 dim-high cell line
|
homo sapiens, CCRF-CEM (ATCC no.: CLL-119) subclone C7R1 (=GC-resistant) transfected with a dimerization deficient Glucocorticoid-receptor-mutant, high expression of mutant resulting in a restored GC-sensitivity, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 6h
|
biological source: homo sapiens, CCRF-CEM (ATCC no.: CLL-119) subclone C7R1 (=GC-resistant) transfected with a dimerization deficient Glucocorticoid-receptor-mutant, high expression of mutant resulting in a restored GC-sensitivity, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 6h
|
| Sample_geo_accession | GSM60552
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60552/suppl/GSM60552.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60553 | GPL570 |
|
C-Line-C7R1dim-high-24h-GC
|
C7R1 dim-high cell line
|
homo sapiens, CCRF-CEM (ATCC no.: CLL-119) subclone C7R1 (=GC-resistant) transfected with a dimerization deficient Glucocorticoid-receptor-mutant, high expression of mutant resulting in a restored GC-sensitivity, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 24h
|
biological source: homo sapiens, CCRF-CEM (ATCC no.: CLL-119) subclone C7R1 (=GC-resistant) transfected with a dimerization deficient Glucocorticoid-receptor-mutant, high expression of mutant resulting in a restored GC-sensitivity, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 24h
|
| Sample_geo_accession | GSM60553
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60553/suppl/GSM60553.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60554 | GPL570 |
|
CHX-C7H2-6h-EtOH
|
C7H2 cell line
|
homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity),addition of cycloheximide 10ug/ml 3h prior to addition of ethanol 0,1%, incubation for 6h
|
biological source: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity),addition of cycloheximide 10ug/ml 3h prior to addition of ethanol 0,1%, incubation for 6h
|
| Sample_geo_accession | GSM60554
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60554/suppl/GSM60554.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60555 | GPL570 |
|
CHX-C7H2-6h-GC
|
C7H2 cell line
|
homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), addition of cycloheximide 10ug/ml 3h prior to addition of dexamethansone 10e-7M, incubation for 6h
|
biological source: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), addition of cycloheximide 10ug/ml 3h prior to addition of dexamethansone 10e-7M, incubation for 6h
|
| Sample_geo_accession | GSM60555
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60555/suppl/GSM60555.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60560 | GPL570 |
|
R-Line-CEMC1-6h-EtOH
|
CEMC1 cell line
|
homo sapiens, C1 is a GC-resistant subclone of CCRF-CEM (ATCC no. CLL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h
|
biological source: homo sapiens, C1 is a GC-resistant subclone of CCRF-CEM (ATCC no. CLL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h
|
| Sample_geo_accession | GSM60560
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60560/suppl/GSM60560.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60561 | GPL570 |
|
R-Line-CEMC1-6h-GC
|
CEMC1 cell line
|
homo sapiens, C1 is a GC-resistant subclone of CCRF-CEM (ATCC no. CLL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 6h
|
biological source: homo sapiens, C1 is a GC-resistant subclone of CCRF-CEM (ATCC no. CLL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 6h
|
| Sample_geo_accession | GSM60561
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60561/suppl/GSM60561.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60562 | GPL570 |
|
R-Line-CEMC1-24h-GC
|
CEMC1 cell line
|
homo sapiens, C1 is a GC-resistant subclone of CCRF-CEM (ATCC no. CLL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 24h
|
biological source: homo sapiens, C1 is a GC-resistant subclone of CCRF-CEM (ATCC no. CLL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 24h
|
| Sample_geo_accession | GSM60562
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60562/suppl/GSM60562.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60564 | GPL570 |
|
R-Line-C7R1-6h-EtOH
|
C7R1 cell line
|
homo sapiens, C7R1 is a GC-resistant subclone of CCRF-CEM (ATCC no. CLL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0.1%, for 6h
|
biological source: homo sapiens, C7R1 is a GC-resistant subclone of CCRF-CEM (ATCC no. CLL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0.1%, for 6h
|
| Sample_geo_accession | GSM60564
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60564/suppl/GSM60564.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60566 | GPL570 |
|
R-Line-C7R1-6h-GC
|
C7R1 cell line
|
homo sapiens, C7R1 is a GC-resistant subclone of CCRF-CEM (ATCC no. CLL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 6h
|
biological source: homo sapiens, C7R1 is a GC-resistant subclone of CCRF-CEM (ATCC no. CLL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 6h
|
| Sample_geo_accession | GSM60566
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60566/suppl/GSM60566.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60576 | GPL570 |
|
R-Line-C7R1dim-low-6h-EtOH
|
C7R1 dim-low cell line
|
homo sapiens, CCRF-CEM (ATCC no. CLL-119) subclone C7R1 (=GC-resistant) transfected with a dimerization deficient Glucocorticoid-receptor-mutant, C7R1 dim-low shows low expression of mutant and GC-resistant phenotype, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h
|
biological source: homo sapiens, CCRF-CEM (ATCC no. CLL-119) subclone C7R1 (=GC-resistant) transfected with a dimerization deficient Glucocorticoid-receptor-mutant, C7R1 dim-low shows low expression of mutant and GC-resistant phenotype, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h
|
| Sample_geo_accession | GSM60576
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60576/suppl/GSM60576.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60578 | GPL570 |
|
R-Line-C7R1dim-low-6h-GC
|
C7R1 dim-low cell line
|
homo sapiens, CCRF-CEM (ATCC no. CLL-119) subclone C7R1 (=GC-resistant) transfected with a dimerization deficient Glucocorticoid-receptor-mutant, C7R1 dim-low shows low expression of mutant and GC-resistant phenotype, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 6h
|
biological source: homo sapiens, CCRF-CEM (ATCC no. CLL-119) subclone C7R1 (=GC-resistant) transfected with a dimerization deficient Glucocorticoid-receptor-mutant, C7R1 dim-low shows low expression of mutant and GC-resistant phenotype, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 6h
|
| Sample_geo_accession | GSM60578
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60578/suppl/GSM60578.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60579 | GPL570 |
|
R-Line-C7R1dim-low-24h-GC
|
C7R1 dim-low cell line
|
homo sapiens, CCRF-CEM (ATCC no. CLL-119) subcone C7R1 (=GC-resistant) transfected with a dimerization deficient Glucocorticoid-receptor-mutant, C7R1 dim-low shows low expression of mutant and GC-resistant phenotype, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 24h
|
biological source: homo sapiens, CCRF-CEM (ATCC no. CLL-119) subcone C7R1 (=GC-resistant) transfected with a dimerization deficient Glucocorticoid-receptor-mutant, C7R1 dim-low shows low expression of mutant and GC-resistant phenotype, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 24h
|
| Sample_geo_accession | GSM60579
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60579/suppl/GSM60579.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60581 | GPL570 |
|
R-Line-PreB-6h-EtOH
|
PreB 697 R4G4 cell line
|
GC-sensitive), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h
|
biological source: homo sapiens, GC-resistant subclone (obtained from limiting dilution in the presence of dexamethasone) of 697 cells (DSMZ no: ACC 42) (parental 697 cells = GC-sensitive), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h
|
| Sample_geo_accession | GSM60581
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60581/suppl/GSM60581.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60583 | GPL570 |
|
R-Line-PreB-6h-GC
|
PreB 697 R4G4 cell line
|
GC-sensitive), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 6h
|
biological source: homo sapiens, GC-resistant subclone (obtained from limiting dilution in the presence of dexamethasone) of 697 cells (DSMZ no: ACC 42) (parental 697 cells = GC-sensitive), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 6h
|
| Sample_geo_accession | GSM60583
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60583/suppl/GSM60583.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60584 | GPL570 |
|
R-Line-PreB-24h-EtOH
|
PreB 697 R4G4 cell line
|
GC-sensitive), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 24h
|
biological source: homo sapiens, GC-resistant subclone (obtained from limiting dilution in the presence of dexamethasone) of 697 cells (DSMZ no: ACC 42) (parental 697 cells = GC-sensitive), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 24h
|
| Sample_geo_accession | GSM60584
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60584/suppl/GSM60584.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60586 | GPL570 |
|
R-Line-PreB-24h-GC
|
PreB 697 R4G4 cell line
|
GC-sensitive), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 24h
|
biological source: homo sapiens, GC-resistant subclone (obtained from limiting dilution in the presence of dexamethasone) of 697 cells (DSMZ no: ACC 42) (parental 697 cells = GC-sensitive), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 24h
|
| Sample_geo_accession | GSM60586
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | cultured under standard conditions (37°C, 5% CO2, saturated humidity)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60586/suppl/GSM60586.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60588 | GPL570 |
|
HD1-STS-0h
|
healthy donor HD1, peripheral blood
|
biological source:
homo sapiens, healthy donor (male, aged 32.8 years), peripheral blood taken prior to GC-administration, leukocyte isolation.
|
biological source:
homo sapiens, healthy donor (male, aged 32.8 years), peripheral blood taken prior to GC-administration, leukocyte isolation.
|
| Sample_geo_accession | GSM60588
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60588/suppl/GSM60588.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60589 | GPL570 |
|
HD1-STS-6h
|
healthy donor HD1, peripheral blood
|
biological source:
homo sapiens, healthy donor (male, aged 32.8 years), peripheral blood taken 6h after GC-administration (33% of 60mg/m2 prednisolon) , leukocyte isolation
|
biological source:
homo sapiens, healthy donor (male, aged 32.8 years), peripheral blood taken 6h after GC-administration (33% of 60mg/m2 prednisolon) , leukocyte isolation
|
| Sample_geo_accession | GSM60589
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60589/suppl/GSM60589.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60590 | GPL570 |
|
HD1-STS-24h
|
healthy donor HD1, peripheral blood
|
biological source:
homo sapiens, healthy donor (male, aged 32.8 years), peripheral blood taken 24h after first GC-administration, total GC-administration 33% of 60mg/m2 prednisolon + 1/3 of 66% of 60mg/m2
|
biological source:
homo sapiens, healthy donor (male, aged 32.8 years), peripheral blood taken 24h after first GC-administration, total GC-administration 33% of 60mg/m2 prednisolon + 1/3 of 66% of 60mg/m2
|
| Sample_geo_accession | GSM60590
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60590/suppl/GSM60590.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60591 | GPL570 |
|
HD2-RPK-0h
|
healthy donor HD2, peripheral blood
|
biological source:
homo sapiens, healthy donor (male, aged 54.8 years), peripheral blood taken prior to GC-administration, leukocyte isolation.
|
biological source:
homo sapiens, healthy donor (male, aged 54.8 years), peripheral blood taken prior to GC-administration, leukocyte isolation.
|
| Sample_geo_accession | GSM60591
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60591/suppl/GSM60591.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60592 | GPL570 |
|
HD2-RPK-6h
|
healthy donor HD2, peripheral blood
|
biological source:
homo sapiens, healthy donor (male, aged 54.8 years), peripheral blood taken 6h after GC-administration (33% of 60mg/m2 prednisolon) , leukocyte isolation
|
biological source:
homo sapiens, healthy donor (male, aged 54.8 years), peripheral blood taken 6h after GC-administration (33% of 60mg/m2 prednisolon) , leukocyte isolation
|
| Sample_geo_accession | GSM60592
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60592/suppl/GSM60592.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60593 | GPL570 |
|
HD2-RPK-24h
|
healthy donor HD2, peripheral blood
|
biological source:
homo sapiens, healthy donor (male, aged 54.8 years), peripheral blood taken 24h after first GC-administration, total GC-administration 33% of 60mg/m2 prednisolon + 1/3 of 66% of 60mg/m2
|
biological source:
homo sapiens, healthy donor (male, aged 54.8 years), peripheral blood taken 24h after first GC-administration, total GC-administration 33% of 60mg/m2 prednisolon + 1/3 of 66% of 60mg/m2
|
| Sample_geo_accession | GSM60593
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60593/suppl/GSM60593.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60594 | GPL570 |
|
T-ALL-25-6h-5ug-rep
|
T-ALL patient 25, peripheral blood
|
biological source:
homo sapiens, childhood ALL patient (female, aged 10.3 years), peripheral blood taken after 6 hours of treatment, leukocyte isolation followed by enrichment for malignant blasts by non-malignant cell depletion.
|
biological source:
homo sapiens, childhood ALL patient (female, aged 10.3 years), peripheral blood taken after 6 hours of treatment, leukocyte isolation followed by enrichment for malignant blasts by non-malignant cell depletion.
|
| Sample_geo_accession | GSM60594
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | (BFM2000 treatment protocol)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60594/suppl/GSM60594.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60595 | GPL570 |
|
T-ALL-25-6h-1ug-rep
|
T-ALL patient 25, peripheral blood
|
biological source:
homo sapiens, childhood ALL patient (female, aged 10.3 years), peripheral blood taken after 6 hours of treatment, leukocyte isolation followed by enrichment for malignant blasts by non-malignant cell depletion.
|
biological source:
homo sapiens, childhood ALL patient (female, aged 10.3 years), peripheral blood taken after 6 hours of treatment, leukocyte isolation followed by enrichment for malignant blasts by non-malignant cell depletion.
|
| Sample_geo_accession | GSM60595
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | (BFM2000 treatment protocol)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60595/suppl/GSM60595.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60597 | GPL570 |
|
B-ALL-32-0h-rep1
|
B-ALL patient 32, peripheral blood
|
biological source:
homo sapiens, childhood ALL patient (female, aged 3.7 years), peripheral blood taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10).
|
biological source:
homo sapiens, childhood ALL patient (female, aged 3.7 years), peripheral blood taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10).
|
| Sample_geo_accession | GSM60597
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | (BFM2000 treatment protocol)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60597/suppl/GSM60597.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60599 | GPL570 |
|
B-ALL-32-0h-rep2
|
B-ALL patient 32, peripheral blood
|
biological source:
homo sapiens, childhood ALL patient (female, aged 3.7 years), peripheral blood taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10).
technical replicate to sample B-ALL-32-0h-rep1
|
biological source:
homo sapiens, childhood ALL patient (female, aged 3.7 years), peripheral blood taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10).
technical replicate to sample B-ALL-32-0h-rep1
|
| Sample_geo_accession | GSM60599
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | (BFM2000 treatment protocol)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60599/suppl/GSM60599.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60601 | GPL570 |
|
B-ALL-37-BM-sorted
|
B-ALL patient 37, bone marrow
|
biological source:
homo sapiens, childhood ALL patient (female, aged 15.1 years), bone marrow taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10).
|
biological source:
homo sapiens, childhood ALL patient (female, aged 15.1 years), bone marrow taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10).
|
| Sample_geo_accession | GSM60601
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | (BFM2000 treatment protocol)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60601/suppl/GSM60601.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
|
GSM60603 | GPL570 |
|
B-ALL-37-BM-unsorted
|
B-ALL patient 37, bone marrow
|
biological source:
homo sapiens, childhood ALL patient (female, aged 15.1 years), bone marrow taken prior to treatment, leukocyte isolation without enrichment for malignant blasts.
|
biological source:
homo sapiens, childhood ALL patient (female, aged 15.1 years), bone marrow taken prior to treatment, leukocyte isolation without enrichment for malignant blasts.
|
| Sample_geo_accession | GSM60603
| | Sample_status | Public on Nov 14 2005
| | Sample_submission_date | Jun 09 2005
| | Sample_last_update_date | Nov 14 2005
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | (BFM2000 treatment protocol)
| | 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, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
| | Sample_label_ch1 | R-Phycoerythrin
| | Sample_label_protocol_ch1 | The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
| | Sample_hyb_protocol | On rotation (60 rpm) hybridization at 45C for 16 hours
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
| | Sample_data_processing | Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
| | 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/GSM60nnn/GSM60603/suppl/GSM60603.CEL.gz
| | Sample_series_id | GSE2842
| | Sample_data_row_count | 54675
| | |
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