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Search results for the GEO ID: GSE2677
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GSM51674
GPL570
B-ALL-24-24h Patient 24, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 2.6 years), peripheral blood taken after 24 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization Measurement data /specifications The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing and presentation. Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry
GSM51675
GPL570
B-ALL-24-6h Patient 24, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 2.6 years), peripheral blood taken after 6 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51676
GPL570
B-ALL-24-0h Patient 24, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 2.6 years), peripheral blood taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51677
GPL570
B-ALL-13-24h Patient 13, peripheral blood biological source: homo sapiens, childhood ALL patient (male, aged 5.9 years), peripheral blood taken after 24 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by non-malignant cell depletion. Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51678
GPL570
B-ALL-13-8h Patient 13, peripheral blood biological source: homo sapiens, childhood ALL patient (male, aged 5.9 years), peripheral blood taken after 8 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by non-malignant cell depletion. Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51679
GPL570
B-ALL-13-0h Patient 13, peripheral blood biological source: homo sapiens, childhood ALL patient (male, aged 5.9 years), peripheral blood taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by non-malignant cell depletion. Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51680
GPL570
B-ALL-17-24h Patient 17, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 14.7 years), peripheral blood taken after 24 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by non-malignant cell depletion. Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51681
GPL570
B-ALL-17-8h Patient 17, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 14.7 years), peripheral blood taken after 8 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by non-malignant cell depletion. Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51682
GPL570
B-ALL-17-0h Patient 17, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 14.7 years), peripheral blood taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by non-malignant cell depletion. Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51683
GPL570
B-ALL-31-24h Patient 31, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 17.2 years), peripheral blood taken after 24 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51684
GPL570
B-ALL-31-6h Patient 31, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 17.2 years), peripheral blood taken after 6 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51685
GPL570
B-ALL-31-0h Patient 31, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 17.2 years), peripheral blood taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51686
GPL570
B-ALL-32-24h Patient 32, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 3.7 years), peripheral blood taken after 24 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51687
GPL570
B-ALL-32-6h Patient 32, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 3.7 years), peripheral blood taken after 6 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51688
GPL570
B-ALL-32-0h Patient 32, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 3.7 years), peripheral blood taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51689
GPL570
B-ALL-33-24h Patient 33, peripheral blood biological source: homo sapiens, childhood ALL patient (male, aged 2.5 years), peripheral blood taken after 24 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51690
GPL570
B-ALL-33-6h Patient 33, peripheral blood biological source: homo sapiens, childhood ALL patient (male, aged 2.5 years), peripheral blood taken after 6 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51691
GPL570
B-ALL-33-0h Patient 33, peripheral blood biological source: homo sapiens, childhood ALL patient (male, aged 2.5 years), peripheral blood taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51692
GPL570
B-ALL-37-24h Patient 37, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 15.1 years), peripheral blood taken after 24 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51693
GPL570
B-ALL-37-6h Patient 37, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 15.1 years), peripheral blood taken after 6 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51694
GPL570
B-ALL-37-0h Patient 37, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 15.1 years), peripheral blood taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51695
GPL570
B-ALL-38-24h Patient 38, peripheral blood biological source: homo sapiens, childhood ALL patient (male, aged 3.2 years), peripheral blood taken after 24 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51696
GPL570
B-ALL-38-6h Patient 38, peripheral blood biological source: homo sapiens, childhood ALL patient (male, aged 3.2 years), peripheral blood taken after 6 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51697
GPL570
B-ALL-38-0h Patient 38, peripheral blood biological source: homo sapiens, childhood ALL patient (male, aged 3.2 years), peripheral blood taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51698
GPL570
B-ALL-40-24h Patient 40, peripheral blood biological source: homo sapiens, childhood ALL patient (male, aged 17.3 years), peripheral blood taken after 24 hours treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51699
GPL570
B-ALL-40-6h Patient 40, peripheral blood biological source: homo sapiens, childhood ALL patient (male, aged 17.3 years), peripheral blood taken after 6 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51700
GPL570
B-ALL-40-0h Patient 40, peripheral blood biological source: homo sapiens, childhood ALL patient (male, aged 17.3 years), peripheral blood taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51701
GPL570
B-ALL-43-24h Patient 43, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 1.6 years), peripheral blood taken after 24 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD19). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51702
GPL570
B-ALL-43-6h Patient 43, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 1.6 years), peripheral blood taken after 6 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD19). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51703
GPL570
B-ALL-43-0h Patient 43, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 1.6 years), peripheral blood taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD19). Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51704
GPL570
T-ALL-20-24h Patient 20, peripheral blood biological source: homo sapiens, childhood ALL patient (male, aged 5 years), peripheral blood taken after 24 hours of treatment (BFM2000 treatment protocol), leukocyte isolation without enrichment for malignant blasts. Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51705
GPL570
T-ALL-20-8h Patient 20, peripheral blood biological source: homo sapiens, childhood ALL patient (male, aged 5 years), peripheral blood taken after 8 hours of treatment (BFM2000 treatment protocol), leukocyte isolation without enrichment for malignant blasts. Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51706
GPL570
T-ALL-20-0h Patient 20, peripheral blood biological source: homo sapiens, childhood ALL patient (male, aged 5 years), peripheral blood taken prior to treatment, leukocyte isolation without enrichment for malignant blasts. Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51707
GPL570
T-ALL-25-24h Patient 25, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 10.3 years), peripheral blood taken after 24 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by non-malignant cell depletion. Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51708
GPL570
T-ALL-25-6h Patient 25, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 10.3 years), peripheral blood taken after 6 hours of treatment (BFM2000 treatment protocol), leukocyte isolation followed by enrichment for malignant blasts by non-malignant cell depletion. Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51709
GPL570
T-ALL-25-0h Patient 25, peripheral blood biological source: homo sapiens, childhood ALL patient (female, aged 10.3 years), peripheral blood taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by non-malignant cell depletion. Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51710
GPL570
T-ALL-2-24h Patient 2, peripheral blood biological source: homo sapiens, childhood ALL patient (male, aged 8.5 years), peripheral blood taken after 24 hours of treatment (BFM2000 treatment protocol), leukocyte isolation without enrichment for malignant blasts. Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51711
GPL570
T-ALL-2-8h Patient 2, peripheral blood biological source: homo sapiens, childhood ALL patient (male, aged 8.5 years), peripheral blood taken after 8 hours of treatment (BFM2000 treatment protocol), leukocyte isolation without enrichment for malignant blasts. Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
GSM51712
GPL570
T-ALL-2-0h Patient 2, peripheral blood biological source: homo sapiens, childhood ALL patient (male, aged 8.5 years), peripheral blood taken prior to treatment, leukocyte isolation without enrichment for malignant blasts. Technical protocols: Target hybridization preparation: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA integrity by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed. For Affymetrix GeneChip analysis 1.5ug total RNA was processed to generate a biotinylated hybridization target using One Cycle cDNA Synthesis and One Cycle Target Labelling kits from Affymetrix (Affymetrix, Santa Clara, CA, USA). All procedures were performed according to the manufacturer’s protocol (Gene Expression Analysis, Technical Manual, Revison 4; Eukaryotic Target Preparation, Revison 3) In brief, total RNA was reverse transcribed into cDNA using an anchored oligo-dT-T7-Primer, converted into double-stranded cDNA and purified with the Affymetrix Sample Clean-up Kit according to the manufacturer’s protocol. Thereafter, cRNA was generated by a T7-in-vitro transcription step including a modified nucleotide for subsequent biotinylation. Following RNA purification, 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with 200ul hybridization buffer containing hybridization controls (as contained in the Affymetrix One Cycle Target Labelling kit) and hybridized to U133 Plus 2.0 chips. Hybridization: Measurement data /specifications: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol. Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2). Data processing: Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
 
 
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