title: i5i6i19_control_2

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: iaa5-1 iaa6-1 iaa19-1 (ecotype Columbia)
Treatment: Control
Replicate 2


title: axr3-1_control_2

status: Public on Dec 01 2005

type: RNA

city: Albany

first: Yoko

last: Okushima

state: CA

address: 800 Buchanan St.

department: Plant and Microbial Biology

country: USA

institute: Plant Gene Expression Center, U. C. Berkeley

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: axr3-1 (ecotype Columbia)
Treatment: Control
Replicate 2

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Light grown liquid cultured seedlings (7-day old)


title: iaa17-6_control_2

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: iaa17-6  (ecotype Columbia)
Treatment: Control
Replicate 2


title: axr3-1_+IAA_1

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: axr3-1 (ecotype Columbia)
Treatment: IAA treated
Replicate 1


title: arx3-1_control_1

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: axr3-1 (ecotype Columbia)
Treatment: Control
Replicate 1


title: iaa17-6_+IAA_3

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: iaa17-6 (ecotype Columbia)
Treatment: IAA treated
Replicate 3


title: i5i6i19_+IAA_3

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: iaa5-1 iaa6-1 iaa19-1 (ecotype Columbia)
Treatment: IAA treated
Replicate 3


title: axr3-1_+IAA_3

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: axr3-1 (ecotype Columbia)
Treatment: IAA treated
Replicate 3


title: Col_+IAA_I_1

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: Columbia wild-type
Treatment: IAA treated
Replicate 1


title: i5i6i19_control_3

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: iaa5-1 iaa6-1 iaa19-1 (ecotype Columbia)
Treatment: Control
Replicate 3


title: axr3-1_control_3

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: axr3-1 (ecotype Columbia)
Treatment: Control
Replicate 3


title: iaa17-6_+IAA_1

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: iaa17-6  (ecotype Columbia)
Treatment: IAA treated
Replicate 1


title: Col_control_I_3

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: Columbia wild-type
Treatment: Control
Replicate 3


title: i5i6i19_control_1

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: iaa5-1 iaa6-1 iaa19-1 (ecotype Columbia)
Treatment: Control
Replicate 1


title: iaa17-6_control_1

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: iaa17-6  (ecotype Columbia)
Treatment: Control
Replicate 1


title: i5i6i19_+IAA_2

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: iaa5-1 iaa6-1 iaa19-1 (ecotype Columbia)
Treatment: IAA treated
Replicate 2


title: axr3-1_+IAA_2

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: axr3-1 (ecotype Columbia)
Treatment: IAA treated
Replicate 2


title: Col_+IAA_I_2

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: Columbia wild-type
Treatment: IAA treated
Replicate 2


title: iaa17-6_+IAA_2

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: iaa17-6  (ecotype Columbia)
Treatment: IAA treated
Replicate 2


title: Col_+IAA_I_3

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: Columbia wild-type
Treatment: IAA treated
Replicate 3


title: Col_control_I_1

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: Columbia wild-type
Treatment: Control
Replicate 1


title: Col_control_I_2

description:
Surface-sterile seeds were germinated in liquid Murashige and Skoog medium containing 1.5% sucrose and cultured in a 16 h light/ 8 h dark cycle with gentle shaking. After 7 days culture period, seedlings were treated with 5�M IAA (IAA treated) or EtOH (control) for 2 h at 24 �C.

Line: Columbia wild-type
Treatment: Control
Replicate 2


title: VU HNSCCV300663

status: Public on Nov 29 2005

city: Nashville

first: Christine

middle: H.

last: Chung

state: TN

address: 777 PRB

department: Internal Medicine

institute: Vanderbilt University

description: HNSCC from FFPE block

data_processing: quantile normalization of CEL file, PDNN (PerfectMatch) estimation, log2 transformation

label: ENZO BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA)

organism: Homo sapiens

source_name: HNSCC from FFPE block

extract_protocol: Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA)

tag: HNSCC from FFPE block


title: UNC HNSCC97-0108

description: HNSCC from FFPE block


title: UNC HNSCC03-0079

description: HNSCC from FFPE block


title: UNC HNSCC02-0458

description: HNSCC from FFPE block


title: UNC HNSCC02-0323

description: HNSCC from FFPE block


title: UNC HNSCC01-0393

description: HNSCC from FFPE block


title: UNC HNSCC96-0671

description: HNSCC from FFPE block


title: UNC HNSCC02-0502

description: HNSCC from FFPE block


title: UNC HNSCC02-0421

description: HNSCC from FFPE block


title: VU HNSCCV300520

description: HNSCC from FFPE block


title: VU HNSCCV300637

description: HNSCC from FFPE block


title: UNC HNSCC96-0071

description: HNSCC from FFPE block


title: UNC HNSCC00-0318

description: HNSCC from FFPE block


title: UNC HNSCC02-0136

description: HNSCC from FFPE block


title: UNC HNSCC02-0486

description: HNSCC from FFPE block


title: VU HNSCCV300688

description: HNSCC from FFPE block


title: UNC HNSCC02-0478

description: HNSCC from FFPE block


title: UNC HNSCC01-0394

description: HNSCC from FFPE block


title: VU HNSCCV300710

description: HNSCC from FFPE block


title: UNC HNSCC02-0454

description: HNSCC from FFPE block


title: UNC HNSCC02-0387

description: HNSCC from FFPE block


title: UNC HNSCC01-0291

description: HNSCC from FFPE block


title: UNC HNSCC03-0034

description: HNSCC from FFPE block


title: UNC HNSCC02-0152

description: HNSCC from FFPE block


title: VU HNSCCV300431

description: HNSCC from FFPE block


title: UNC HNSCC01-0446

description: HNSCC from FFPE block


title: VU HNSCCV300148

description: HNSCC from FFPE block


title: UNC HNSCC02-0333

description: HNSCC from FFPE block


title: VU HNSCCV300423

description: HNSCC from FFPE block


title: VU HNSCCV300400

description: HNSCC from FFPE block


title: VU HNSCCV300383

description: HNSCC from FFPE block


title: VU HNSCCV300373

description: HNSCC from FFPE block


title: VU HNSCCV300142

description: HNSCC from FFPE block


title: B-ALL-37-BM-unsorted

status: Public on Nov 14 2005

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

description:
biological source:
homo sapiens, childhood ALL patient (female, aged 15.1 years), bone marrow taken prior to treatment, leukocyte isolation without enrichment for malignant blasts.

hyb_protocol: On rotation (60 rpm) hybridization at 45C for 16 hours

scan_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.

label: R-Phycoerythrin

source_name: B-ALL patient 37, bone marrow

label_protocol: The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.

extract_protocol: For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.

treatment_protocol: (BFM2000 treatment protocol)

tag: biological source:


title: R-Line-PreB-24h-GC

description: biological source: homo sapiens, GC-resistant subclone (obtained from limiting dilution in the presence of dexamethasone) of 697 cells (DSMZ no: ACC 42) (parental 697 cells = GC-sensitive), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 24h

source_name: PreB 697 R4G4 cell line


title: R-Line-PreB-6h-GC

description: biological source: homo sapiens, GC-resistant subclone (obtained from limiting dilution in the presence of dexamethasone) of 697 cells (DSMZ no: ACC 42) (parental 697 cells = GC-sensitive), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 6h


title: VU HNSCCV300533

description: HNSCC from FFPE block


title: B-ALL-32-0h-rep2

description:
biological source:
homo sapiens, childhood ALL patient (female, aged 3.7 years), peripheral blood taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10).
technical replicate to sample B-ALL-32-0h-rep1

source_name: B-ALL patient 32, peripheral blood


title: B-ALL-37-BM-sorted

description:
biological source:
homo sapiens, childhood ALL patient (female, aged 15.1 years), bone marrow taken prior to treatment, leukocyte isolation followed by enrichment for malignant blasts by malignant cell selection (CD10).


title: HD2-RPK-0h

description:
biological source:
homo sapiens, healthy donor (male, aged 54.8 years), peripheral blood taken prior to GC-administration, leukocyte isolation.

source_name: healthy donor HD2, peripheral blood


title: R-Line-PreB-24h-EtOH

description: biological source: homo sapiens, GC-resistant subclone (obtained from limiting dilution in the presence of dexamethasone) of 697 cells (DSMZ no: ACC 42) (parental 697 cells = GC-sensitive), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 24h


title: HD1-STS-6h

description:
biological source:
homo sapiens, healthy donor (male, aged 32.8 years), peripheral blood taken 6h after GC-administration (33% of 60mg/m2 prednisolon) , leukocyte isolation

source_name: healthy donor HD1, peripheral blood


title: T-ALL-25-6h-1ug-rep

description:
biological source:
homo sapiens, childhood ALL patient (female, aged 10.3 years), peripheral blood taken after 6 hours of treatment, leukocyte isolation followed by enrichment for malignant blasts by non-malignant cell depletion.

source_name: T-ALL patient 25, peripheral blood


title: HD2-RPK-24h

description:
biological source:
homo sapiens, healthy donor (male, aged 54.8 years), peripheral blood taken 24h after first GC-administration, total GC-administration 33% of 60mg/m2 prednisolon + 1/3 of 66% of 60mg/m2


title: R-Line-C7R1-6h-EtOH

description: biological source: homo sapiens, C7R1 is a GC-resistant subclone of CCRF-CEM (ATCC no. CLL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0.1%, for 6h

source_name: C7R1 cell line


title: VU HNSCCV300171

description: HNSCC from FFPE block


title: VU HNSCCV300251

description: HNSCC from FFPE block


title: HD1-STS-24h

description:
biological source:
homo sapiens, healthy donor (male, aged 32.8 years), peripheral blood taken 24h after first GC-administration, total GC-administration 33% of 60mg/m2 prednisolon + 1/3 of 66% of 60mg/m2


title: R-Line-C7R1dim-low-24h-GC

description: biological source: homo sapiens, CCRF-CEM (ATCC no. CLL-119) subcone C7R1 (=GC-resistant) transfected with a dimerization deficient Glucocorticoid-receptor-mutant, C7R1 dim-low shows low expression of mutant and GC-resistant phenotype, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 24h

source_name: C7R1 dim-low cell line


title: R-Line-PreB-6h-EtOH

description: biological source: homo sapiens, GC-resistant subclone (obtained from limiting dilution in the presence of dexamethasone) of 697 cells (DSMZ no: ACC 42) (parental 697 cells = GC-sensitive), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h


title: T-ALL-25-6h-5ug-rep

tag: homo sapiens, childhood ALL patient (female, aged 10.3 years), peripheral blood taken after 6 hours of treatment, leukocyte isolation followed by enrichment for malignant blasts by non-malignant cell depletion.


title: HD1-STS-0h

description:
biological source:
homo sapiens, healthy donor (male, aged 32.8 years), peripheral blood taken prior to GC-administration, leukocyte isolation.


title: R-Line-C7R1dim-low-6h-GC

description: biological source: homo sapiens, CCRF-CEM (ATCC no. CLL-119) subclone C7R1 (=GC-resistant) transfected with a dimerization deficient Glucocorticoid-receptor-mutant, C7R1 dim-low shows low expression of mutant and GC-resistant phenotype, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 6h


title: R-Line-CEMC1-6h-GC

description: biological source: homo sapiens, C1 is a GC-resistant subclone of CCRF-CEM (ATCC no. CLL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 6h

source_name: CEMC1 cell line


title: R-Line-CEMC1-24h-GC

description: biological source: homo sapiens, C1 is a GC-resistant subclone of CCRF-CEM (ATCC no. CLL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 24h


title: B-ALL-32-0h-rep1

description:
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).


title: HD2-RPK-6h

description:
biological source:
homo sapiens, healthy donor (male, aged 54.8 years), peripheral blood taken 6h after GC-administration (33% of 60mg/m2 prednisolon) , leukocyte isolation


title: R-Line-C7R1dim-low-6h-EtOH

description: biological source: homo sapiens, CCRF-CEM (ATCC no. CLL-119) subclone C7R1 (=GC-resistant) transfected with a dimerization deficient Glucocorticoid-receptor-mutant, C7R1 dim-low shows low expression of mutant and GC-resistant phenotype, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h


title: CHX-C7H2-6h-EtOH

description: biological source: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity),addition of cycloheximide 10ug/ml 3h prior to addition of ethanol 0,1%, incubation for 6h

source_name: C7H2 cell line


title: CHX-C7H2-6h-GC

description: biological source: homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), addition of cycloheximide 10ug/ml 3h prior to addition of dexamethansone 10e-7M, incubation for 6h


title: R-Line-C7R1-6h-GC

description: biological source: homo sapiens, C7R1 is a GC-resistant subclone of CCRF-CEM (ATCC no. CLL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethasone 10e-7M for 6h


title: S-Line-PreB-6h-GC

description: biological source: homo sapiens, human B cell precursor leukemia cell line: 697 (DSMZ no: ACC 42), 697 cells are GC-sensitive, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 6h

source_name: PreB 697 cell line

value: 697 (DSMZ no:ACC 42), 697 cells are GC-sensitive, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 6h


title: R-Line-CEMC1-6h-EtOH

description: biological source: homo sapiens, C1 is a GC-resistant subclone of CCRF-CEM (ATCC no. CLL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h


title: C-Line-C7R1dim-high-6h-GC

description: biological source: homo sapiens, CCRF-CEM (ATCC no.: CLL-119) subclone C7R1 (=GC-resistant) transfected with a dimerization deficient Glucocorticoid-receptor-mutant, high expression of mutant resulting in a restored GC-sensitivity, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 6h

source_name: C7R1 dim-high cell line

tag: homo sapiens, CCRF-CEM (ATCC no.


title: C-Line-C7R1dim-high-24h-GC

description: biological source: homo sapiens, CCRF-CEM (ATCC no.: CLL-119) subclone C7R1 (=GC-resistant) transfected with a dimerization deficient Glucocorticoid-receptor-mutant, high expression of mutant resulting in a restored GC-sensitivity, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 24h


title: C-Line-CEMC1-ratGR-6h-GC

description: biological source: homo sapiens, rat-Glucocorticoid-receptor transfected CCRF-CEM (ATCC no.: CLL-119) subclone C1, parental cell line C1 = GC resistant, C1-rat-GR = GC-sensitivity restored, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 6h

source_name: rat- Glucocorticoid-receptor transfected CCRF-CEM (ATCC no.: CLL-119) subclone C1


title: C-Line-C7R1dim-high-6h-EtOH

description: biological source: homo sapiens, CCRF-CEM (ATCC no.: CLL-119) subclone C7R1 (=GC-resistant) transfected with a dimerization deficient Glucocorticoid-receptor-mutant, high expression of mutant resulting in a restored GC-sensitivity, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h


title: C-Line-CEMC1-ratGR-24h-GC

description: biological source: homo sapiens, rat-Glucocorticoid-receptor transfected CCRF-CEM (ATCC no.: CLL-119) subclone C1, parental cell line C1 = GC resistant, C1-rat GR = GC-sensitivity restored, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 24h


title: S-Line-C7H2-24h-GC

description:
biological source:
homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 24h


title: S-Line-PreB-24h-GC

description: biological source: homo sapiens, human B cell precursor leukemia cell line: 697 (DSMZ no: ACC 42), 697 cells are GC-sensitive, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 24h

value: 697 (DSMZ no:ACC 42), 697 cells are GC-sensitive, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 24h


title: S-Line-C7H2-6h-EtOH

description:
biological source:
homo sapiens, C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h


title: S-Line-PreB-6h-EtOH

description: biological source: homo sapiens, human B cell precursor leukemia cell line: 697 (DSMZ no: ACC 42), 697 cells are GC-sensitive, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h

value: 697 (DSMZ no:ACC 42), 697 cells are GC-sensitive, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h


title: IV-B-ALL-40-24h-EtOH

description:
biological source:
homo sapiens, ALL ex vivo material from adult B-ALL patient, peripheral blood taken prior to treatment, leukocyte isolation CD10 targeted enrichment for malignant blasts, cultivated in the presence of ethanol 0,1% for 24h

source_name: B-ALL patient 40, peripheral blood


title: IV-B-ALL-40-24h-GC

description:
biological source:
homo sapiens, ALL ex vivo material from adult B-ALL patient, peripheral blood taken prior to treatment, leukocyte isolation CD10 targeted enrichment for malignant blasts, cultivated in the presence of dexamethasone 10e-7M  for 24h


title: C-Line-CEMC1-ratGR-6h-EtOH

description: biological source: homo sapiens, rat- Glucocorticoid-receptor transfected CCRF-CEM (ATCC no.: CLL-119) subclone C1, parental cell line C1 = GC resistant, C1-rat-Glucocorticoid-receptor = GC-sensitivity restored, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0,1% for 6h


title: S-Line-C7H2-6h-GC

description:
biological source:
homo sapiens , C7H2 cell line is a GC-sensitive subclone of CCRF-CEM (ATCC no. CCL-119), cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 6h


title: Adult-B-ALL-6h

description: homo sapiens, childhood ALL patient (male, aged 72 years), peripheral blood taken 6h after GC-monotherapy initiation, leukocyte isolation CD10 targeted enrichment for malignant blasts

source_name: Adult B-ALL patient, peripheral blood

treatment_protocol: BFM2000 treatment protocol


title: IV-B-ALL-40-6h-EtOH

description:
biological source:
homo sapiens, ALL ex vivo material from adult B-ALL patient, peripheral blood taken prior to treatment, leukocyte isolation CD10 targeted enrichment for malignant blasts, cultivated in the presence of ethanol 0,1% for 6h


title: Adult-B-ALL-0h

description:
biological source:
homo sapiens, ALL patient (male, aged 72 years), peripheral blood taken prior to treatment, leukocyte isolation CD10 targeted enrichment for malignant blasts.


title: Adult-B-ALL-24h

description: homo sapiens, childhood ALL patient (male, aged 72 years), peripheral blood taken 24h after GC-monotherapy initiation

extract_protocol:
For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
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.


title: T-ALL-2-24h

description:
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.

source_name: Patient 2, peripheral blood


title: IV-B-ALL-40-6h-GC

description:
biological source:
homo sapiens, ALL ex vivo material from adult B-ALL patient, peripheral blood taken prior to treatment, leukocyte isolation CD10 targeted enrichment for malignant blasts, cultivated in the presence of dexamethasone 10e-7M for 6h


title: T-ALL-2-8h

description:
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.


title: T-ALL-25-24h

description:
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.

source_name: Patient 25, peripheral blood


title: B-ALL-43-24h

description:
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.

source_name: Patient 43, peripheral blood


title: B-ALL-43-0h

description:
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.


title: B-ALL-38-0h

description:
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.

source_name: Patient 38, peripheral blood


title: B-ALL-40-6h

description:
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.

source_name: Patient 40, peripheral blood


title: B-ALL-38-24h

description:
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.


title: T-ALL-20-0h

description:
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.

source_name: Patient 20, peripheral blood


title: B-ALL-37-24h

description:
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.

source_name: Patient 37, peripheral blood


title: T-ALL-20-24h

description:
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.


title: B-ALL-40-24h

description:
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.


title: B-ALL-43-6h

description:
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.


title: B-ALL-38-6h

description:
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.


title: B-ALL-33-6h

description:
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.

source_name: Patient 33, peripheral blood


title: B-ALL-37-0h

description:
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.


title: B-ALL-40-0h

description:
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.


title: T-ALL-20-8h

description:
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.


title: B-ALL-33-0h

description:
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.


title: B-ALL-37-6h

description:
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.


title: B-ALL-31-0h

description:
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.

source_name: Patient 31, peripheral blood


title: B-ALL-33-24h

description:
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.


title: B-ALL-32-6h

description:
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.

source_name: Patient 32, peripheral blood


title: B-ALL-17-8h

description:
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.

source_name: Patient 17, peripheral blood


title: B-ALL-31-24h

description:
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.


title: Mouse-in vitro-4h-EtOH

description: mus musculus, three CD-1 mice (males, aged 4-6 weeks), pooled thymic cell suspensions, cultivated in vitro under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of ethanol 0.1%  for 4h

organism: Mus musculus

source_name: Mouse, thymus


title: B-ALL-32-24h

description:
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.


title: Mouse-in vitro-4h-GC

description: mus musculus, three CD-1 mice (males, aged 4-6 weeks), pooled thymic cell suspensions, cultivated in vitro under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 4h


title: B-ALL-17-24h

description:
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.


title: Mouse-untreated

description: mus musculus, three CD-1 mice (males, aged 4-6 weeks), pooled thymic cell suspensions, without treatment