Search results for the GEO ID: GSE30903  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM766225 | GPL570 |
|
untreated AML 2B blasts
|
untreated AML blasts
|
cell type: AML blasts
fab classification: M1
|
Gene expression data from untreated AML blasts
|
| Sample_geo_accession | GSM766225
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766225/suppl/GSM766225_2B_NT.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766225/suppl/GSM766225_2B_NT_sc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766226 | GPL570 |
|
ATP-treated AML 2B blasts
|
ATP-treated AML blasts
|
cell type: AML blasts
fab classification: M1
|
Gene expression data from ATP-treated AML blasts
|
| Sample_geo_accession | GSM766226
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766226/suppl/GSM766226_2B_ATP.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766226/suppl/GSM766226_2B_ATP_sc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766227 | GPL570 |
|
untreated AML 3 blasts
|
untreated AML blasts
|
cell type: AML blasts
fab classification: M1
|
Gene expression data from untreated AML blasts
|
| Sample_geo_accession | GSM766227
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766227/suppl/GSM766227_3_NT.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766227/suppl/GSM766227_3_NT_sc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766228 | GPL570 |
|
ATP-treated AML 3 blasts
|
ATP-treated AML blasts
|
cell type: AML blasts
fab classification: M1
|
Gene expression data from ATP-treated AML blasts
|
| Sample_geo_accession | GSM766228
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766228/suppl/GSM766228_3_ATP.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766228/suppl/GSM766228_3_ATP_sc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766229 | GPL570 |
|
untreated AML 4B blasts
|
untreated AML blasts
|
cell type: AML blasts
fab classification: M1
|
Gene expression data from untreated AML blasts
|
| Sample_geo_accession | GSM766229
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766229/suppl/GSM766229_4B_NT.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766229/suppl/GSM766229_4B_NT_sc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766230 | GPL570 |
|
ATP-treated AML 4B blasts
|
ATP-treated AML blasts
|
cell type: AML blasts
fab classification: M1
|
Gene expression data from ATP-treated AML blasts
|
| Sample_geo_accession | GSM766230
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766230/suppl/GSM766230_4B_ATP.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766230/suppl/GSM766230_4B_ATP_sc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766231 | GPL570 |
|
untreated AML 6B blasts
|
untreated AML blasts
|
cell type: AML blasts
fab classification: M2
|
Gene expression data from untreated AML blasts
|
| Sample_geo_accession | GSM766231
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766231/suppl/GSM766231_6B_NT.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766231/suppl/GSM766231_6B_NT_sc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766232 | GPL570 |
|
ATP-treated AML 6B blasts
|
ATP-treated AML blasts
|
cell type: AML blasts
fab classification: M2
|
Gene expression data from ATP-treated AML blasts
|
| Sample_geo_accession | GSM766232
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766232/suppl/GSM766232_6B_ATP.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766232/suppl/GSM766232_6B_ATP_sc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766233 | GPL570 |
|
untreated AML 7C blasts
|
untreated AML blasts
|
cell type: AML blasts
fab classification: M2
|
Gene expression data from untreated AML blasts
|
| Sample_geo_accession | GSM766233
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766233/suppl/GSM766233_7C_NT.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766233/suppl/GSM766233_7C_NT_sc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766234 | GPL570 |
|
ATP-treated AML 7C blasts
|
ATP-treated AML blasts
|
cell type: AML blasts
fab classification: M2
|
Gene expression data from ATP-treated AML blasts
|
| Sample_geo_accession | GSM766234
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766234/suppl/GSM766234_7C_ATP.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766234/suppl/GSM766234_7C_ATP_sc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766235 | GPL570 |
|
untreated AML 8 blasts
|
untreated AML blasts
|
cell type: AML blasts
fab classification: M4
|
Gene expression data from untreated AML blasts
|
| Sample_geo_accession | GSM766235
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766235/suppl/GSM766235_8_NT.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766235/suppl/GSM766235_8_NT_sc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766236 | GPL570 |
|
ATP-treated AML 8 blasts
|
ATP-treated AML blasts
|
cell type: AML blasts
fab classification: M4
|
Gene expression data from ATP-treated AML blasts
|
| Sample_geo_accession | GSM766236
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766236/suppl/GSM766236_8_ATP.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766236/suppl/GSM766236_8_ATP_sc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766237 | GPL570 |
|
untreated AML 9 blasts
|
untreated AML blasts
|
cell type: AML blasts
fab classification: M4
|
Gene expression data from untreated AML blasts
|
| Sample_geo_accession | GSM766237
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766237/suppl/GSM766237_9_NT.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766237/suppl/GSM766237_9_NTsc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766238 | GPL570 |
|
ATP-treated AML 9 blasts
|
ATP-treated AML blasts
|
cell type: AML blasts
fab classification: M4
|
Gene expression data from ATP-treated AML blasts
|
| Sample_geo_accession | GSM766238
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766238/suppl/GSM766238_9_ATP.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766238/suppl/GSM766238_9_ATPsc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766239 | GPL570 |
|
untreated AML 10 blasts
|
untreated AML blasts
|
cell type: AML blasts
fab classification: M5
|
Gene expression data from untreated AML blasts
|
| Sample_geo_accession | GSM766239
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766239/suppl/GSM766239_10_NT.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766239/suppl/GSM766239_10_NT_sc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766240 | GPL570 |
|
ATP-treated AML 10 blasts
|
ATP-treated AML blasts
|
cell type: AML blasts
fab classification: M5
|
Gene expression data from ATP-treated AML blasts
|
| Sample_geo_accession | GSM766240
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766240/suppl/GSM766240_10_ATP.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766240/suppl/GSM766240_10_ATP_sc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766241 | GPL570 |
|
untreated AML 11 blasts
|
untreated AML blasts
|
cell type: AML blasts
fab classification: M5
|
Gene expression data from untreated AML blasts
|
| Sample_geo_accession | GSM766241
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766241/suppl/GSM766241_11_NT.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766241/suppl/GSM766241_11_NT_sc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766242 | GPL570 |
|
ATP-treated AML 11 blasts
|
ATP-treated AML blasts
|
cell type: AML blasts
fab classification: M5
|
Gene expression data from ATP-treated AML blasts
|
| Sample_geo_accession | GSM766242
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766242/suppl/GSM766242_11_ATP.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766242/suppl/GSM766242_11_ATP_sc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766243 | GPL570 |
|
untreated AML 12 blasts
|
untreated AML blasts
|
cell type: AML blasts
fab classification: M5
|
Gene expression data from untreated AML blasts
|
| Sample_geo_accession | GSM766243
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766243/suppl/GSM766243_12_NT.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766243/suppl/GSM766243_12_NT_sc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766244 | GPL570 |
|
ATP-treated AML 12 blasts
|
ATP-treated AML blasts
|
cell type: AML blasts
fab classification: M5
|
Gene expression data from ATP-treated AML blasts
|
| Sample_geo_accession | GSM766244
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766244/suppl/GSM766244_12_ATP.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766244/suppl/GSM766244_12_ATP_sc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766245 | GPL570 |
|
untreated AML 13 blasts
|
untreated AML blasts
|
cell type: AML blasts
fab classification: M2
|
Gene expression data from untreated AML blasts
|
| Sample_geo_accession | GSM766245
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766245/suppl/GSM766245_13_NT.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766245/suppl/GSM766245_13_NT_sc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766246 | GPL570 |
|
ATP-treated AML 13 blasts
|
ATP-treated AML blasts
|
cell type: AML blasts
fab classification: M2
|
Gene expression data from ATP-treated AML blasts
|
| Sample_geo_accession | GSM766246
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766246/suppl/GSM766246_13_ATP.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766246/suppl/GSM766246_13_ATP_sc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766247 | GPL570 |
|
untreated AML 14 blasts
|
untreated AML blasts
|
cell type: AML blasts
fab classification: M4
|
Gene expression data from untreated AML blasts
|
| Sample_geo_accession | GSM766247
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766247/suppl/GSM766247_14_NT.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766247/suppl/GSM766247_14_NTsc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
|
GSM766248 | GPL570 |
|
ATP-treated AML 14 blasts
|
ATP-treated AML blasts
|
cell type: AML blasts
fab classification: M4
|
Gene expression data from ATP-treated AML blasts
|
| Sample_geo_accession | GSM766248
| | Sample_status | Public on Feb 25 2012
| | Sample_submission_date | Jul 25 2011
| | Sample_last_update_date | Feb 25 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | ATP was purchased from Sigma-Aldrich (Milan, Italy). Blast cells obtained from 12 AML patients were cultured for 24 h with or without 1 mM ATP.
| | Sample_growth_protocol_ch1 | Primary leukemic cells were obtained from the peripheral blood (PB) of 12 AML patients at diagnosis, before treatment. Mononuclear cells (MNC) were separated from AML samples, immediately after peripheral blood harvesting by Ficoll-Hypaque centrifugation (Amersham Bioscience, Piscataway, NJ, USA). Blast cells obtained from AML patients were cultured in IMDM + 10%FBS.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 106 ATP-treated and untreated cells was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard One Cycle Affymetrix protocol from 1 ug total RNA (Gene Chip Expression Analysis Technical Manual, 701024 Rev3, Affymetrix). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133 Plus2 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the instrument’s standard FS450_0001 protocol with antibody-mediated signal amplification and GeneChip Hybridization, Wash and Staining Kit.
| | Sample_scan_protocol | GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.
| | Sample_data_processing | The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples. The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rossella,,Manfredini
| | Sample_contact_email | manfredini.rossella@unimo.it
| | Sample_contact_phone | +390592058065
| | Sample_contact_fax | +390592058115
| | Sample_contact_department | Life Sciences
| | Sample_contact_institute | Centre for Regenerative Medicine
| | Sample_contact_address | Via Gottardi 100
| | Sample_contact_city | Modena
| | Sample_contact_zip/postal_code | 41100
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766248/suppl/GSM766248_14_ATP.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM766nnn/GSM766248/suppl/GSM766248_14_ATPsc150.CHP.gz
| | Sample_series_id | GSE30903
| | Sample_data_row_count | 54675
| | |
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