Search results for the GEO ID: GSE42064  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1031831 | GPL570 |
|
MLL_00322
|
MLL_00322
|
case: MLL_00322
disease state: Acute myeloid leukemia (AML)
mutation: ASXL1 mut
|
control
|
| Sample_geo_accession | GSM1031831
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031831/suppl/GSM1031831_MLL_00322_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031832 | GPL570 |
|
MLL_00323
|
MLL_00323
|
case: MLL_00323
disease state: Acute myeloid leukemia (AML)
mutation: ASXL1 mut
|
control
|
| Sample_geo_accession | GSM1031832
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031832/suppl/GSM1031832_MLL_00323_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031833 | GPL570 |
|
MLL_00324
|
MLL_00324
|
case: MLL_00324
disease state: Acute myeloid leukemia (AML)
mutation: ASXL1 mut
|
control
|
| Sample_geo_accession | GSM1031833
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031833/suppl/GSM1031833_MLL_00324_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031834 | GPL570 |
|
MLL_00325
|
MLL_00325
|
case: MLL_00325
disease state: Acute myeloid leukemia (AML)
mutation: ASXL1 mut
|
control
|
| Sample_geo_accession | GSM1031834
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031834/suppl/GSM1031834_MLL_00325_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031835 | GPL570 |
|
MLL_00326
|
MLL_00326
|
case: MLL_00326
disease state: Acute myeloid leukemia (AML)
mutation: ASXL1 mut/ TET2 mut
|
control
|
| Sample_geo_accession | GSM1031835
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031835/suppl/GSM1031835_MLL_00326_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031836 | GPL570 |
|
MLL_00327
|
MLL_00327
|
case: MLL_00327
disease state: Acute myeloid leukemia (AML)
mutation: ASXL1 mut/ TET2 mut
|
control
|
| Sample_geo_accession | GSM1031836
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031836/suppl/GSM1031836_MLL_00327_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031837 | GPL570 |
|
MLL_00328
|
MLL_00328
|
case: MLL_00328
disease state: Acute myeloid leukemia (AML)
mutation: ASXL1 mut/ TET2 mut
|
control
|
| Sample_geo_accession | GSM1031837
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031837/suppl/GSM1031837_MLL_00328_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031838 | GPL570 |
|
MLL_00329
|
MLL_00329
|
case: MLL_00329
disease state: Acute myeloid leukemia (AML)
mutation: ASXL1/GATA2/TET2/DNMT3A wt
|
control
|
| Sample_geo_accession | GSM1031838
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031838/suppl/GSM1031838_MLL_00329_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031839 | GPL570 |
|
MLL_00330
|
MLL_00330
|
case: MLL_00330
disease state: Acute myeloid leukemia (AML)
mutation: ASXL1/GATA2/TET2/DNMT3A wt
|
control
|
| Sample_geo_accession | GSM1031839
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031839/suppl/GSM1031839_MLL_00330_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031840 | GPL570 |
|
MLL_00331
|
MLL_00331
|
case: MLL_00331
disease state: Acute myeloid leukemia (AML)
mutation: ASXL1/GATA2/TET2/DNMT3A wt
|
control
|
| Sample_geo_accession | GSM1031840
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031840/suppl/GSM1031840_MLL_00331_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031841 | GPL570 |
|
MLL_00332
|
MLL_00332
|
case: MLL_00332
disease state: Acute myeloid leukemia (AML)
mutation: ASXL1/GATA2/TET2/DNMT3A wt
|
control
|
| Sample_geo_accession | GSM1031841
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031841/suppl/GSM1031841_MLL_00332_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031842 | GPL570 |
|
MLL_00333
|
MLL_00333
|
case: MLL_00333
disease state: Acute myeloid leukemia (AML)
mutation: ASXL1/GATA2/TET2/DNMT3A wt
|
control
|
| Sample_geo_accession | GSM1031842
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031842/suppl/GSM1031842_MLL_00333_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031843 | GPL570 |
|
MLL_00334
|
MLL_00334
|
case: MLL_00334
disease state: Acute myeloid leukemia (AML)
mutation: GATA2 mut
|
control
|
| Sample_geo_accession | GSM1031843
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031843/suppl/GSM1031843_MLL_00334_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031844 | GPL570 |
|
MLL_00335
|
MLL_00335
|
case: MLL_00335
disease state: Acute myeloid leukemia (AML)
mutation: GATA2 mut
|
control
|
| Sample_geo_accession | GSM1031844
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031844/suppl/GSM1031844_MLL_00335_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031845 | GPL570 |
|
MLL_00336
|
MLL_00336
|
case: MLL_00336
disease state: Acute myeloid leukemia (AML)
mutation: GATA2 mut
|
control
|
| Sample_geo_accession | GSM1031845
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031845/suppl/GSM1031845_MLL_00336_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031846 | GPL570 |
|
MLL_00337
|
MLL_00337
|
case: MLL_00337
disease state: Acute myeloid leukemia (AML)
mutation: GATA2 mut
|
control
|
| Sample_geo_accession | GSM1031846
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031846/suppl/GSM1031846_MLL_00337_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031847 | GPL570 |
|
MLL_00338
|
MLL_00338
|
case: MLL_00338
disease state: Acute myeloid leukemia (AML)
mutation: TET2 mut
|
control
|
| Sample_geo_accession | GSM1031847
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031847/suppl/GSM1031847_MLL_00338_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031848 | GPL570 |
|
MLL_00339
|
MLL_00339
|
case: MLL_00339
disease state: Acute myeloid leukemia (AML)
mutation: TET2 mut
|
control
|
| Sample_geo_accession | GSM1031848
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031848/suppl/GSM1031848_MLL_00339_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031849 | GPL570 |
|
MLL_00340
|
MLL_00340
|
case: MLL_00340
disease state: Acute myeloid leukemia (AML)
mutation: TET2 mut
|
control
|
| Sample_geo_accession | GSM1031849
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031849/suppl/GSM1031849_MLL_00340_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031850 | GPL570 |
|
MLL_00341
|
MLL_00341
|
case: MLL_00341
disease state: Acute myeloid leukemia (AML)
mutation: TET2 mut
|
control
|
| Sample_geo_accession | GSM1031850
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031850/suppl/GSM1031850_MLL_00341_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031851 | GPL570 |
|
MLL_00342
|
MLL_00342
|
case: MLL_00342
disease state: Acute myeloid leukemia (AML)
mutation: TET2 mut
|
control
|
| Sample_geo_accession | GSM1031851
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031851/suppl/GSM1031851_MLL_00342_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031852 | GPL570 |
|
MLL_00343
|
MLL_00343
|
case: MLL_00343
disease state: Acute myeloid leukemia (AML)
mutation: TET2 mut
|
control
|
| Sample_geo_accession | GSM1031852
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031852/suppl/GSM1031852_MLL_00343_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031853 | GPL570 |
|
MLL_00344
|
MLL_00344
|
case: MLL_00344
disease state: Acute myeloid leukemia (AML)
mutation: TET2 mut
|
control
|
| Sample_geo_accession | GSM1031853
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031853/suppl/GSM1031853_MLL_00344_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031854 | GPL570 |
|
MLL_00345
|
MLL_00345
|
case: MLL_00345
disease state: Acute myeloid leukemia (AML)
mutation: TET2 mut
|
control
|
| Sample_geo_accession | GSM1031854
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031854/suppl/GSM1031854_MLL_00345_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031855 | GPL570 |
|
MLL_00346
|
MLL_00346
|
case: MLL_00346
disease state: Acute myeloid leukemia (AML)
mutation: TET2 mut
|
control
|
| Sample_geo_accession | GSM1031855
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031855/suppl/GSM1031855_MLL_00346_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031856 | GPL570 |
|
MLL_00347
|
MLL_00347
|
case: MLL_00347
disease state: Acute myeloid leukemia (AML)
mutation: TET2 mut
|
control
|
| Sample_geo_accession | GSM1031856
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031856/suppl/GSM1031856_MLL_00347_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031857 | GPL570 |
|
MLL_00348
|
MLL_00348
|
case: MLL_00348
disease state: Acute myeloid leukemia (AML)
mutation: TET2 mut
|
control
|
| Sample_geo_accession | GSM1031857
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031857/suppl/GSM1031857_MLL_00348_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031858 | GPL570 |
|
MLL_00349
|
MLL_00349
|
case: MLL_00349
disease state: Acute myeloid leukemia (AML)
mutation: TET2 mut
|
control
|
| Sample_geo_accession | GSM1031858
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031858/suppl/GSM1031858_MLL_00349_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031859 | GPL570 |
|
MLL_00350
|
MLL_00350
|
case: MLL_00350
disease state: Acute myeloid leukemia (AML)
mutation: ASXL1/GATA2/TET2/DNMT3A wt
|
control
|
| Sample_geo_accession | GSM1031859
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031859/suppl/GSM1031859_MLL_00350_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031860 | GPL570 |
|
MLL_00351
|
MLL_00351
|
case: MLL_00351
disease state: Acute myeloid leukemia (AML)
mutation: ASXL1/GATA2/TET2/DNMT3A wt
|
control
|
| Sample_geo_accession | GSM1031860
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031860/suppl/GSM1031860_MLL_00351_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031861 | GPL570 |
|
MLL_00352
|
MLL_00352
|
case: MLL_00352
disease state: Acute myeloid leukemia (AML)
mutation: ASXL1/GATA2/TET2/DNMT3A wt
|
control
|
| Sample_geo_accession | GSM1031861
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031861/suppl/GSM1031861_MLL_00352_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031862 | GPL570 |
|
MLL_00353
|
MLL_00353
|
case: MLL_00353
disease state: Acute myeloid leukemia (AML)
mutation: ASXL1/GATA2/TET2/DNMT3A wt
|
control
|
| Sample_geo_accession | GSM1031862
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031862/suppl/GSM1031862_MLL_00353_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031863 | GPL570 |
|
MLL_00354
|
MLL_00354
|
case: MLL_00354
disease state: Acute myeloid leukemia (AML)
mutation: ASXL1/GATA2/TET2/DNMT3A wt
|
control
|
| Sample_geo_accession | GSM1031863
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031863/suppl/GSM1031863_MLL_00354_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031864 | GPL570 |
|
MLL_00355
|
MLL_00355
|
case: MLL_00355
disease state: Acute myeloid leukemia (AML)
mutation: ASXL1/GATA2/TET2/DNMT3A wt
|
control
|
| Sample_geo_accession | GSM1031864
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031864/suppl/GSM1031864_MLL_00355_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031865 | GPL570 |
|
MLL_00358
|
MLL_00358
|
case: MLL_00358
disease state: Acute myeloid leukemia (AML)
mutation: GATA2 mut
|
control
|
| Sample_geo_accession | GSM1031865
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031865/suppl/GSM1031865_MLL_00358_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031866 | GPL570 |
|
MLL_00359
|
MLL_00359
|
case: MLL_00359
disease state: Acute myeloid leukemia (AML)
mutation: GATA2 mut
|
control
|
| Sample_geo_accession | GSM1031866
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031866/suppl/GSM1031866_MLL_00359_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031867 | GPL570 |
|
MLL_00360
|
MLL_00360
|
case: MLL_00360
disease state: Acute myeloid leukemia (AML)
mutation: GATA2 mut
|
control
|
| Sample_geo_accession | GSM1031867
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031867/suppl/GSM1031867_MLL_00360_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
| | |
|
GSM1031868 | GPL570 |
|
MLL_00361
|
MLL_00361
|
case: MLL_00361
disease state: Acute myeloid leukemia (AML)
mutation: GATA2 mut
|
control
|
| Sample_geo_accession | GSM1031868
| | Sample_status | Public on Apr 20 2013
| | Sample_submission_date | Nov 06 2012
| | Sample_last_update_date | Apr 21 2013
| | 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/GSM1031nnn/GSM1031868/suppl/GSM1031868_MLL_00361_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE42064
| | Sample_data_row_count | 54675
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