Search results for the GEO ID: GSE34733  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM854186 | GPL570 |
|
MLL_00111
|
CEBPA non-methylated/non-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
control
|
| Sample_geo_accession | GSM854186
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854186/suppl/GSM854186_MLL_00111_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854187 | GPL570 |
|
MLL_00106
|
CEBPA non-methylated/non-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
control
|
| Sample_geo_accession | GSM854187
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854187/suppl/GSM854187_MLL_00106_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854188 | GPL570 |
|
MLL_00114
|
CEBPA non-methylated/non-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
control
|
| Sample_geo_accession | GSM854188
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854188/suppl/GSM854188_MLL_00114_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854189 | GPL570 |
|
MLL_00109
|
CEBPA non-methylated/non-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
control
|
| Sample_geo_accession | GSM854189
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854189/suppl/GSM854189_MLL_00109_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854190 | GPL570 |
|
MLL_00116
|
CEBPA non-methylated/non-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
control
|
| Sample_geo_accession | GSM854190
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854190/suppl/GSM854190_MLL_00116_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854191 | GPL570 |
|
MLL_00118
|
CEBPA non-methylated/non-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
control
|
| Sample_geo_accession | GSM854191
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854191/suppl/GSM854191_MLL_00118_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854192 | GPL570 |
|
MLL_00107
|
CEBPA non-methylated/non-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
control
|
| Sample_geo_accession | GSM854192
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854192/suppl/GSM854192_MLL_00107_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854193 | GPL570 |
|
MLL_00117
|
CEBPA non-methylated/non-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
control
|
| Sample_geo_accession | GSM854193
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854193/suppl/GSM854193_MLL_00117_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854194 | GPL570 |
|
MLL_00110
|
CEBPA non-methylated/non-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
control
|
| Sample_geo_accession | GSM854194
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854194/suppl/GSM854194_MLL_00110_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854195 | GPL570 |
|
MLL_00112
|
CEBPA non-methylated/non-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
control
|
| Sample_geo_accession | GSM854195
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854195/suppl/GSM854195_MLL_00112_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854196 | GPL570 |
|
MLL_00231
|
CEBPA methylated (unmutated)
|
diagnosis: Acute myeloid leukemia (AML)
|
methylated
|
| Sample_geo_accession | GSM854196
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854196/suppl/GSM854196_MLL_00231_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854197 | GPL570 |
|
MLL_00232
|
CEBPA methylated (unmutated)
|
diagnosis: Acute myeloid leukemia (AML)
|
methylated
|
| Sample_geo_accession | GSM854197
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854197/suppl/GSM854197_MLL_00232_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854198 | GPL570 |
|
MLL_00236
|
CEBPA methylated (unmutated)
|
diagnosis: Acute myeloid leukemia (AML)
|
methylated
|
| Sample_geo_accession | GSM854198
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854198/suppl/GSM854198_MLL_00236_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854199 | GPL570 |
|
MLL_00240
|
CEBPA methylated (unmutated)
|
diagnosis: Acute myeloid leukemia (AML)
|
methylated
|
| Sample_geo_accession | GSM854199
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854199/suppl/GSM854199_MLL_00240_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854200 | GPL570 |
|
MLL_00241
|
CEBPA methylated (unmutated)
|
diagnosis: Acute myeloid leukemia (AML)
|
methylated
|
| Sample_geo_accession | GSM854200
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854200/suppl/GSM854200_MLL_00241_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854201 | GPL570 |
|
MLL_00242
|
CEBPA methylated (unmutated)
|
diagnosis: Acute myeloid leukemia (AML)
|
methylated
|
| Sample_geo_accession | GSM854201
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854201/suppl/GSM854201_MLL_00242_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854202 | GPL570 |
|
MLL_00246
|
CEBPA methylated (unmutated)
|
diagnosis: Acute myeloid leukemia (AML)
|
methylated
|
| Sample_geo_accession | GSM854202
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854202/suppl/GSM854202_MLL_00246_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854203 | GPL570 |
|
MLL_00247
|
CEBPA methylated (unmutated)
|
diagnosis: Acute myeloid leukemia (AML)
|
methylated
|
| Sample_geo_accession | GSM854203
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854203/suppl/GSM854203_MLL_00247_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854204 | GPL570 |
|
MLL_00249
|
CEBPA methylated (unmutated)
|
diagnosis: Acute myeloid leukemia (AML)
|
methylated
|
| Sample_geo_accession | GSM854204
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854204/suppl/GSM854204_MLL_00249_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854205 | GPL570 |
|
MLL_00230
|
CEBPA double-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
double-mutated
|
| Sample_geo_accession | GSM854205
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854205/suppl/GSM854205_MLL_00230_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854206 | GPL570 |
|
MLL_00235
|
CEBPA double-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
double-mutated
|
| Sample_geo_accession | GSM854206
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854206/suppl/GSM854206_MLL_00235_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854207 | GPL570 |
|
MLL_00248
|
CEBPA double-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
double-mutated
|
| Sample_geo_accession | GSM854207
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854207/suppl/GSM854207_MLL_00248_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854208 | GPL570 |
|
MLL_00252
|
CEBPA double-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
double-mutated
|
| Sample_geo_accession | GSM854208
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854208/suppl/GSM854208_MLL_00252_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854209 | GPL570 |
|
MLL_00255
|
CEBPA double-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
double-mutated
|
| Sample_geo_accession | GSM854209
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854209/suppl/GSM854209_MLL_00255_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854210 | GPL570 |
|
MLL_00233
|
CEBPA double-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
double-mutated
|
| Sample_geo_accession | GSM854210
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854210/suppl/GSM854210_MLL_00233_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854211 | GPL570 |
|
MLL_00237
|
CEBPA double-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
double-mutated
|
| Sample_geo_accession | GSM854211
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854211/suppl/GSM854211_MLL_00237_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854212 | GPL570 |
|
MLL_00239
|
CEBPA double-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
double-mutated
|
| Sample_geo_accession | GSM854212
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854212/suppl/GSM854212_MLL_00239_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854213 | GPL570 |
|
MLL_00245
|
CEBPA double-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
double-mutated
|
| Sample_geo_accession | GSM854213
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854213/suppl/GSM854213_MLL_00245_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854214 | GPL570 |
|
MLL_00257
|
CEBPA double-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
double-mutated
|
| Sample_geo_accession | GSM854214
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854214/suppl/GSM854214_MLL_00257_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854215 | GPL570 |
|
MLL_00234
|
CEBPA single-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
single-mutated
|
| Sample_geo_accession | GSM854215
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854215/suppl/GSM854215_MLL_00234_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854216 | GPL570 |
|
MLL_00238
|
CEBPA single-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
single-mutated
|
| Sample_geo_accession | GSM854216
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854216/suppl/GSM854216_MLL_00238_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854217 | GPL570 |
|
MLL_00250
|
CEBPA single-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
single-mutated
|
| Sample_geo_accession | GSM854217
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854217/suppl/GSM854217_MLL_00250_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854218 | GPL570 |
|
MLL_00251
|
CEBPA single-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
single-mutated
|
| Sample_geo_accession | GSM854218
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854218/suppl/GSM854218_MLL_00251_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854219 | GPL570 |
|
MLL_00253
|
CEBPA single-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
single-mutated
|
| Sample_geo_accession | GSM854219
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854219/suppl/GSM854219_MLL_00253_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854220 | GPL570 |
|
MLL_00254
|
CEBPA single-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
single-mutated
|
| Sample_geo_accession | GSM854220
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854220/suppl/GSM854220_MLL_00254_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854221 | GPL570 |
|
MLL_00258
|
CEBPA single-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
single-mutated
|
| Sample_geo_accession | GSM854221
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854221/suppl/GSM854221_MLL_00258_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
GSM854222 | GPL570 |
|
MLL_00260
|
CEBPA single-mutated
|
diagnosis: Acute myeloid leukemia (AML)
|
single-mutated
|
| Sample_geo_accession | GSM854222
| | Sample_status | Public on Dec 01 2012
| | Sample_submission_date | Dec 27 2011
| | Sample_last_update_date | Dec 01 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated samples
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Andreas,,Roller
| | Sample_contact_institute | Munich Leukemia Laboratory
| | Sample_contact_address | Max-Lebsche-Platz 31
| | Sample_contact_city | Munich
| | Sample_contact_zip/postal_code | 81377
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM854nnn/GSM854222/suppl/GSM854222_MLL_00260_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE34733
| | Sample_data_row_count | 54675
| | |
|
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