title: CLL_Peripheral_Blood_GED142 HG-U133A II

status: Public on Oct 14 2011

city: Munich

first: Tobias

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

institute: University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)

hyb_protocol: Sample hybridisation was performed for 16 hours according to standard Affymetrix protocols

scan_protocol: Samples were scanned using an Affymetrix GeneChip scanner

data_processing: Normalization was performed using the Robust Multichip Average (RMA) method. Quality control consisted of visual inspection of the array image for artifacts, assessment of RNA degradation plots, and inspection of rank-vs.-residual plots after normalization and probe set  summarization.

source_name: peripheral_blood_mononuclear cells

label_protocol: Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols

extract_protocol: Mononuclear cells from peripheral blood (PB) were enriched by Ficoll gradient centrifugation. Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany). cDNA preparation and  in vitro transcription were performed according to standard Affymetrix protocols.

treatment_protocol: Peripheral blood mononuclear cells from patients with chronic lymphocytic leukaemia (CLL)

tag: FISH (del 13q14)

tag: FISH (del 13q14 single)

tag: FISH (del 17p13)

tag: FISH (trisomy 12)

tag: FISH (no del 13q14, no del 11q22-23, no del 17p13, no trisomy 12)

value: peripheral blood mononuclear cell

tag: disease state

value: CLL


title: CLL_Peripheral_Blood_GED144 HG-U133A II

type: RNA

country: Germany

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: cell type


title: CLL_Peripheral_Blood_GED141 HG-U133A II


title: CLL_Peripheral_Blood_GED152 HG-U133A II


title: Acute Myeloid Leukemia, sample 17

status: Public on Jan 05 2012

city: Milan

first: Myriam

last: Alcalay

address: Via Adamello 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology

hyb_protocol: 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.

data_processing: The data were analyzed with MASv5 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: AML blasts from bone marrow (at diagnosis), mutated NPM

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

growth_protocol: RNA was extracted directly from fresh AML blasts.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen).

value: AML blasts from bone marrow

tag: set

value: training

tag: npm status

value: mutated

tag: fab classification

tag: flt3 status

value: WT


title: CLL_Peripheral_Blood_GED131 HG-U133A II


title: CLL_Peripheral_Blood_GED073 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED150 HG-U133A II


title: CLL_Peripheral_Blood_GED127 HG-U133A II


title: CLL_Peripheral_Blood_GED128 HG-U133A II


title: CLL_Peripheral_Blood_GED078 HG-U133A II


title: CLL_Peripheral_Blood_GED086 HG-U133A II


title: CLL_Peripheral_Blood_GED083 HG-U133A II


title: CLL_Peripheral_Blood_GED122 HG-U133A II


title: CLL_Peripheral_Blood_GED116 HG-U133A II


title: CLL_Peripheral_Blood_GED069 HG-U133A II


title: CLL_Peripheral_Blood_GED037 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED041 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED085 HG-U133A II


title: CLL_Peripheral_Blood_GED145 HG-U133A II


title: CLL_Peripheral_Blood_GED108 HG-U133A II


title: CLL_Peripheral_Blood_GED101 HG-U133A II


title: CLL_Peripheral_Blood_GED058 HG-U133A II


title: CLL_Peripheral_Blood_GED066 HG-U133A II


title: CLL_Peripheral_Blood_GED054 HG-U133A II


title: CLL_Peripheral_Blood_GED042 HG_U133plus2 II


title: CLL_Peripheral_Blood_GED064 HG-U133A II


title: CLL_Peripheral_Blood_GED063 HG-U133A II


title: CLL_Peripheral_Blood_GED053 HG-U133A II


title: liver recipients maintaining stable graft function in the absence of immunosuppressive therapy LTOL07

status: Public on Jan 01 2012

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: PBMC from L-Tol group

hyb_protocol: Standard Affymetrix protocol

scan_protocol: The labelled arrays were scanned with a Gene chip scanner 3000.

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v2.4) 'affy' in R.2.9.1

source_name: Peripheral blood mononuclear cells

label_protocol: Standard Affymetrix protocol

extract_protocol: RNA was extracted from peripheral blood using the TRIzol method (Invitrogen, Cergy Pontoise, France). Genomic DNA was removed by DNase treatment (Roche, Indianapolis, IN, USA). RNA quality and quantity was determined using an Agilent 2100 BioAnalyzer (Palo Alto, CA, USA). RNA was reverse transcribed into cDNA using polydT oligonucleotide and Maloney leukemia virus reverse transcription (Invitrogen).

treatment_protocol: Ficoll PBMC isolation from peripheral blood

tag: immunotolerance group

value: L-Tol

tag: outcome

value: Liver recipients maintaining stable graft function in the absence of immunosuppressive therapy

value: Peripheral blood mononuclear cells


title: CLL_Peripheral_Blood_GED050 HG-U133A II


title: CLL_Peripheral_Blood_GED156 HGU133plus2

data_processing: Normalization was performed using the Robust Multichip Average (RMA) method. Quality control consisted of visual inspection of the array image for artifacts, assessment of RNA degradation plots, and inspection of rank-vs.-residual plots after normalization and probe set summarization. The 44 HG-U133 A, B chips and the 107 HG-U133 Plus 2.0 chips were normalized separately by the Robust Multichip Average (RMA) method as described by Irizarry et al 2003. Only the 44754 probe sets present on A, B chips and the 2.0 chips were included in the analysis. Some probe sets on the A, B chips tend to have lower mean signal levels and higher standard deviations than the corresponding probe sets on the Plus 2.0 chips. To eliminate this batch effect resulting from the different chip designs, we performed a second normalization using an empirical Bayesian method. This data was used in the statistical analysis. Finally we separated the normalized data for publication in GEO again. This separated normalized data is provided in the VALUE column.

tag: life status (censoring day)

tag: overall survival (days)

tag: treatment status (censoring day)

tag: time to treatment (days)

value: Chronic lymphocytic leukemia


title: CLL_Peripheral_Blood_GED154 HGU133plus2


title: CLL_Peripheral_Blood_GED148 HGU133plus2


title: CLL_Peripheral_Blood_GED153 HGU133plus2


title: CLL_Peripheral_Blood_GED155 HGU133plus2


title: CLL_Peripheral_Blood_GED149 HGU133plus2


title: CLL_Peripheral_Blood_GED049 HG-U133A II

tag: FISH (del 13q14)


title: CLL_Peripheral_Blood_GED140 HGU133plus2


title: CLL_Peripheral_Blood_GED046 HG-U133A II

tag: FISH (del 13q14 single)


title: CLL_Peripheral_Blood_GED143 HGU133plus2


title: CLL_Peripheral_Blood_GED147 HGU133plus2


title: CLL_Peripheral_Blood_GED151 HGU133plus2


title: CLL_Peripheral_Blood_GED044 HG-U133A II

tag: FISH (del 17p13)


title: CLL_Peripheral_Blood_GED139 HGU133plus2


title: CLL_Peripheral_Blood_GED146 HGU133plus2


title: CLL_Peripheral_Blood_GED137 HGU133plus2


title: CLL_Peripheral_Blood_GED040 HG-U133A II

tag: FISH (trisomy 12)


title: CLL_Peripheral_Blood_GED136 HGU133plus2


title: CLL_Peripheral_Blood_GED138 HGU133plus2


title: CLL_Peripheral_Blood_GED134 HGU133plus2


title: CLL_Peripheral_Blood_GED045 HG-U133A II

tag: FISH (no del 13q14, no del 11q22-23, no del 17p13, no trisomy 12)


title: CLL_Peripheral_Blood_GED038 HG-U133A II

tag: disease state


title: CLL_Peripheral_Blood_GED133 HGU133plus2

tag: cell type


title: CLL_Peripheral_Blood_GED129 HGU133plus2


title: CLL_Peripheral_Blood_GED130 HGU133plus2


title: CLL_Peripheral_Blood_GED135 HGU133plus2


title: CLL_Peripheral_Blood_GED036 HG-U133A II


title: CLL_Peripheral_Blood_GED126 HGU133plus2


title: CLL_Peripheral_Blood_GED035 HG-U133A II


title: CLL_Peripheral_Blood_GED125 HGU133plus2


title: CLL_Peripheral_Blood_GED033 HG-U133A II


title: CLL_Peripheral_Blood_GED132 HGU133plus2


title: CLL_Peripheral_Blood_GED120 HGU133plus2


title: CLL_Peripheral_Blood_GED121 HGU133plus2


title: liver recipients maintaining stable graft function in the absence of immunosuppressive therapy LTOL08

description: PBMC from L-Tol group


title: CLL_Peripheral_Blood_GED123 HGU133plus2


title: CLL_Peripheral_Blood_GED119 HGU133plus2


title: CLL_Peripheral_Blood_GED118 HGU133plus2


title: CLL_Peripheral_Blood_GED021 HG-U133A II


title: CLL_Peripheral_Blood_GED022 HG-U133A II


title: CLL_Peripheral_Blood_GED014 HG-U133A II


title: CLL_Peripheral_Blood_GED117 HGU133plus2


title: CLL_Peripheral_Blood_GED027 HG-U133A II


title: CLL_Peripheral_Blood_GED114 HGU133plus2


title: CLL_Peripheral_Blood_GED113 HGU133plus2


title: CLL_Peripheral_Blood_GED030 HG-U133A II


title: CLL_Peripheral_Blood_GED013 HG-U133A II


title: CLL_Peripheral_Blood_GED124 HGU133plus2


title: CLL_Peripheral_Blood_GED109 HGU133plus2


title: CLL_Peripheral_Blood_GED017 HG-U133A II


title: CLL_Peripheral_Blood_GED112 HGU133plus2


title: CLL_Peripheral_Blood_GED111 HGU133plus2


title: CLL_Peripheral_Blood_GED107 HGU133plus2


title: CLL_Peripheral_Blood_GED115 HGU133plus2


title: CLL_Peripheral_Blood_GED110 HGU133plus2


title: CLL_Peripheral_Blood_GED106 HGU133plus2


title: CLL_Peripheral_Blood_GED105 HGU133plus2


title: CLL_Peripheral_Blood_GED104 HGU133plus2


title: CLL_Peripheral_Blood_GED007 HG-U133A II


title: CLL_Peripheral_Blood_GED003 HG-U133A II


title: CLL_Peripheral_Blood_GED011 HG-U133A II


title: CLL_Peripheral_Blood_GED001 HG-U133A II


title: CLL_Peripheral_Blood_GED099 HGU133plus2


title: CLL_Peripheral_Blood_GED103 HGU133plus2


title: CLL_Peripheral_Blood_GED100 HGU133plus2


title: CLL_Peripheral_Blood_GED098 HGU133plus2


title: CLL_Peripheral_Blood_GED102 HGU133plus2


title: CLL_Peripheral_Blood_GED096 HGU133plus2


title: CLL_Peripheral_Blood_GED097 HGU133plus2


title: CLL_Peripheral_Blood_GED094 HGU133plus2


title: CLL_Peripheral_Blood_GED090 HGU133plus2


title: CLL_Peripheral_Blood_GED079 HGU133plus2


title: CLL_Peripheral_Blood_GED088 HGU133plus2


title: CLL_Peripheral_Blood_GED087 HGU133plus2


title: CLL_Peripheral_Blood_GED081 HGU133plus2


title: CLL_Peripheral_Blood_GED080 HGU133plus2


title: CLL_Peripheral_Blood_GED093 HGU133plus2


title: CLL_Peripheral_Blood_GED092 HGU133plus2


title: CLL_Peripheral_Blood_GED082 HGU133plus2


title: CLL_Peripheral_Blood_GED084 HGU133plus2


title: CLL_Peripheral_Blood_GED076 HGU133plus2


title: CLL_Peripheral_Blood_GED095 HGU133plus2


title: CLL_Peripheral_Blood_GED089 HGU133plus2


title: CLL_Peripheral_Blood_GED077 HGU133plus2


title: CLL_Peripheral_Blood_GED091 HGU133plus2


title: CLL_Peripheral_Blood_GED075 HGU133plus2


title: CLL_Peripheral_Blood_GED067 HGU133plus2


title: CLL_Peripheral_Blood_GED071 HGU133plus2


title: CLL_Peripheral_Blood_GED070 HGU133plus2


title: CLL_Peripheral_Blood_GED065 HGU133plus2


title: CLL_Peripheral_Blood_GED060 HGU133plus2


title: CLL_Peripheral_Blood_GED074 HGU133plus2


title: CLL_Peripheral_Blood_GED068 HGU133plus2


title: CLL_Peripheral_Blood_GED061 HGU133plus2


title: CLL_Peripheral_Blood_GED055 HGU133plus2


title: CLL_Peripheral_Blood_GED051 HGU133plus2


title: CLL_Peripheral_Blood_GED057 HGU133plus2


title: CLL_Peripheral_Blood_GED039 HGU133plus2


title: CLL_Peripheral_Blood_GED059 HGU133plus2


title: CLL_Peripheral_Blood_GED031 HGU133plus2


title: CLL_Peripheral_Blood_GED052 HGU133plus2


title: CLL_Peripheral_Blood_GED047 HGU133plus2


title: CLL_Peripheral_Blood_GED048 HGU133plus2


title: CLL_Peripheral_Blood_GED056 HGU133plus2


title: CLL_Peripheral_Blood_GED034 HGU133plus2


title: CLL_Peripheral_Blood_GED072 HGU133plus2


title: CLL_Peripheral_Blood_GED062 HGU133plus2


title: CLL_Peripheral_Blood_GED026 HGU133plus2


title: CLL_Peripheral_Blood_GED029 HGU133plus2


title: CLL_Peripheral_Blood_GED028 HGU133plus2


title: CLL_Peripheral_Blood_GED032 HGU133plus2


title: CLL_Peripheral_Blood_GED024 HGU133plus2


title: CLL_Peripheral_Blood_GED025 HGU133plus2


title: CLL_Peripheral_Blood_GED023 HGU133plus2


title: CLL_Peripheral_Blood_GED020 HGU133plus2


title: CLL_Peripheral_Blood_GED019 HGU133plus2


title: CLL_Peripheral_Blood_GED043 HGU133plus2


title: CLL_Peripheral_Blood_GED016 HGU133plus2


title: CLL_Peripheral_Blood_GED018 HGU133plus2


title: CLL_Peripheral_Blood_GED015 HGU133plus2


title: CLL_Peripheral_Blood_GED012 HGU133plus2


title: CLL_Peripheral_Blood_GED008 HGU133plus2


title: CLL_Peripheral_Blood_GED005 HGU133plus2


title: CLL_Peripheral_Blood_GED006 HGU133plus2


title: CLL_Peripheral_Blood_GED010 HGU133plus2


title: CLL_Peripheral_Blood_GED004 HGU133plus2


title: CLL_Peripheral_Blood_GED002 HGU133plus2


title: CLL_Peripheral_Blood_GED009 HGU133plus2


title: p65-D-L

status: Public on Sep 23 2011

city: Stony Brook

first: Laura

middle: E.

last: Hogan

state: New York

department: Department of Pediatrics

country: USA

institute: Stony Brook University

description: pediatric patients with B-precursor ALL

hyb_protocol: Thirteen micrograms of labeled cRNA was fragmented and hybridized to Affymetrix U133Plus2 microarrays according to Affymetrix protocol (Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with GenePattern.

source_name: diagnosis

label_protocol: One microgram of total RNA was used as a template in a double amplification protocol using RiboAmp RNA amplification kits (Arcturus, Mountain View, CA).  In vitro transcription was completed with biotinylated UTP and CTP for labeling using ENZO BioArray HighYield RNA Transcript Labeling kit (ENZO Diagnostics, Farmingdale, NJ)

growth_protocol: Ficoll-enriched, cryopreserved paired diagnosis/relapse bone marrow samples were obtained from patients with relapsed B-precursor acute lymphoblastic leukemia.

extract_protocol: Total RNA was isolated using Qiagen RNEasy Mini Kits (Valencia, CA) and quality was verified by an agilent 2100 Bioanalyzer (Palo Alto, CA)

treatment_protocol: Leukemic bone marrow samples were used for RNA extraction without further treatment

tag: diagnosis

value: acute lymphoblastic leukemia (ALL)

tag: tissue

value: bone marrow

tag: relapse time

value: late (greater than 36 months)


title: p82-D-L

description: pediatric patients with B-precursor ALL


title: p72-D-L

description: pediatric patients with B-precursor ALL


title: p85-D-L

description: pediatric patients with B-precursor ALL


title: p55-D-L

description: pediatric patients with B-precursor ALL


title: p58-D-L

description: pediatric patients with B-precursor ALL


title: p46-D-L

description: pediatric patients with B-precursor ALL


title: p63-D-L

description: pediatric patients with B-precursor ALL


title: p79-D-L

description: pediatric patients with B-precursor ALL


title: p75-R-L

description: pediatric patients with B-precursor ALL

source_name: relapse


title: p75-D-L

description: pediatric patients with B-precursor ALL


title: p66-D-L

description: pediatric patients with B-precursor ALL


title: p52-D-L

description: pediatric patients with B-precursor ALL


title: p61-D-L

description: pediatric patients with B-precursor ALL


title: p54-D-E

description: pediatric patients with B-precursor ALL

value: early (less than 36 months)


title: p53-D-L

description: pediatric patients with B-precursor ALL


title: p44-D-L

description: pediatric patients with B-precursor ALL


title: p39-D-L

description: pediatric patients with B-precursor ALL


title: p45-D-L

description: pediatric patients with B-precursor ALL


title: p38-D-L

description: pediatric patients with B-precursor ALL


title: p79-R-L

description: pediatric patients with B-precursor ALL


title: p42-D-L

description: pediatric patients with B-precursor ALL


title: p63-R-L

description: pediatric patients with B-precursor ALL


title: p41-D-L

description: pediatric patients with B-precursor ALL


title: p85-R-L

description: pediatric patients with B-precursor ALL


title: p82-R-L

description: pediatric patients with B-precursor ALL


title: p72-R-L

description: pediatric patients with B-precursor ALL


title: p66-R-L

description: pediatric patients with B-precursor ALL


title: p65-R-L

description: pediatric patients with B-precursor ALL


title: p58-R-L

description: pediatric patients with B-precursor ALL


title: p61-R-L

description: pediatric patients with B-precursor ALL


title: p53-R-L

description: pediatric patients with B-precursor ALL


title: p41-R-L

description: pediatric patients with B-precursor ALL


title: p78-D-E

description: pediatric patients with B-precursor ALL


title: p45-R-L

description: pediatric patients with B-precursor ALL


title: p55-R-L

description: pediatric patients with B-precursor ALL


title: p71-D-E

description: pediatric patients with B-precursor ALL


title: p76-D-E

description: pediatric patients with B-precursor ALL


title: p39-R-L

description: pediatric patients with B-precursor ALL


title: p81-D-E

description: pediatric patients with B-precursor ALL


title: p68-D-E

description: pediatric patients with B-precursor ALL


title: p77-D-E

description: pediatric patients with B-precursor ALL


title: p80-D-E

description: pediatric patients with B-precursor ALL


title: p51-R-E

description: pediatric patients with B-precursor ALL


title: p44-R-L

description: pediatric patients with B-precursor ALL


title: p52-R-L

description: pediatric patients with B-precursor ALL


title: p38-R-L

description: pediatric patients with B-precursor ALL


title: p84-D-E

description: pediatric patients with B-precursor ALL


title: p69-D-E

description: pediatric patients with B-precursor ALL


title: p74-D-E

description: pediatric patients with B-precursor ALL


title: p64-D-E

description: pediatric patients with B-precursor ALL


title: p73-D-E

description: pediatric patients with B-precursor ALL


title: p46-R-L

description: pediatric patients with B-precursor ALL


title: p67-D-E

description: pediatric patients with B-precursor ALL


title: p42-R-L

description: pediatric patients with B-precursor ALL


title: p70-D-E

description: pediatric patients with B-precursor ALL


title: p62-D-E

description: pediatric patients with B-precursor ALL


title: p83-D-E

description: pediatric patients with B-precursor ALL


title: p59-D-E

description: pediatric patients with B-precursor ALL


title: p60-D-E

description: pediatric patients with B-precursor ALL


title: p86-D-E

description: pediatric patients with B-precursor ALL


title: p57-D-E

description: pediatric patients with B-precursor ALL


title: p51-D-E

description: pediatric patients with B-precursor ALL


title: p49-D-E

description: pediatric patients with B-precursor ALL


title: p56-D-E

description: pediatric patients with B-precursor ALL


title: p47-D-E

description: pediatric patients with B-precursor ALL


title: p43-D-E

description: pediatric patients with B-precursor ALL


title: p50-D-E

description: pediatric patients with B-precursor ALL


title: p80-R-E

description: pediatric patients with B-precursor ALL


title: p81-R-E

description: pediatric patients with B-precursor ALL


title: p74-R-E

description: pediatric patients with B-precursor ALL


title: p48-D-E

description: pediatric patients with B-precursor ALL


title: p77-R-E

description: pediatric patients with B-precursor ALL


title: p84-R-E

description: pediatric patients with B-precursor ALL


title: p70-R-E

description: pediatric patients with B-precursor ALL


title: p73-R-E

description: pediatric patients with B-precursor ALL


title: p40-D-E

description: pediatric patients with B-precursor ALL


title: p59-R-E

description: pediatric patients with B-precursor ALL


title: p83-R-E

description: pediatric patients with B-precursor ALL


title: p69-R-E

description: pediatric patients with B-precursor ALL


title: p68-R-E

description: pediatric patients with B-precursor ALL


title: p64-R-E

description: pediatric patients with B-precursor ALL


title: p60-R-E

description: pediatric patients with B-precursor ALL


title: p62-R-E

description: pediatric patients with B-precursor ALL


title: p71-R-E

description: pediatric patients with B-precursor ALL


title: p67-R-E

description: pediatric patients with B-precursor ALL


title: p86-R-E

description: pediatric patients with B-precursor ALL


title: p76-R-E

description: pediatric patients with B-precursor ALL


title: p57-R-E

description: pediatric patients with B-precursor ALL


title: p78-R-E

description: pediatric patients with B-precursor ALL


title: p54-R-E

description: pediatric patients with B-precursor ALL


title: p56-R-E

description: pediatric patients with B-precursor ALL


title: p47-R-E

description: pediatric patients with B-precursor ALL


title: p40-R-E

description: pediatric patients with B-precursor ALL


title: p48-R-E

description: pediatric patients with B-precursor ALL


title: p43-R-E

description: pediatric patients with B-precursor ALL


title: p49-R-E

description: pediatric patients with B-precursor ALL


title: p50-R-E

description: pediatric patients with B-precursor ALL


title: ILD Study Number 1136

status: Public on Aug 11 2011

city: San Francisco

first: Prescott

middle: Gurney

last: Woodruff

state: CA

address: 505 Parnassus Ave

department: Medicine

institute: UCSF

description: Gene expression data from PBMC total RNA from healthy controls, sarcoid patients, and hypersensitivity pneumonitis patients

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip U133  Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix Model 3000 scanner.

data_processing: The CEL files were normalized in the R Bioconductor package affy, version 1.24.2, using the justRMA command, and were later corrected for batch effect using the R COMBAT script, doi 10.1093/biostatistics/kxj037

source_name: Human peripheral blood mononuclear cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: QIAGEN PAXgene Blood RNA Kit IVD, June 2005 protocol

tag: sex

value: F

tag: ethnicity

value: Latino

value: sarcoid vs. BO

tag: dx

value: sarc-vs-bo


title: ILD Study Number 660

value: Black

value: Sarcoidosis


title: ILD Study Number 1078

value: White


title: ILD Study Number S010

value: Healthy

value: health


title: ILD Study Number S017


title: ILD Study Number S035


title: ILD Study Number 425

value: HCV/sarcoid

value: sarc-hcv


title: ILD Study Number 1098

value: M


title: ILD Study Number 774


title: ILD Study Number 908


title: ILD Study Number 545


title: ILD Study Number 1239

value: Asian


title: ILD Study Number 1021


title: ILD Study Number S019


title: ILD Study Number 1259


title: ILD Study Number 93


title: ILD Study Number 897


title: ILD Study Number S013


title: ILD Study Number 1115


title: ILD Study Number S001


title: ILD Study Number 1107


title: ILD Study Number 890


title: ILD Study Number 1000


title: ILD Study Number 917


title: ILD Study Number 1040


title: ILD Study Number 1039


title: ILD Study Number 945

value: Hypersensitivity Pnemonitis

value: hp


title: ILD Study Number 1274


title: ILD Study Number S034


title: ILD Study Number 1319


title: ILD Study Number 1064


title: ILD Study Number S033


title: ILD Study Number 1243


title: ILD Study Number S032


title: ILD Study Number 1164


title: ILD Study Number 998


title: ILD Study Number 1299


title: ILD Study Number S031


title: ILD Study Number 1090


title: ILD Study Number 1236


title: ILD Study Number S030


title: ILD Study Number S038


title: ILD Study Number 1226


title: ILD Study Number 1074


title: ILD Study Number 1113


title: ILD Study Number S011


title: ILD Study Number S036


title: ILD Study Number 901


title: ILD Study Number 1222


title: ILD Study Number 1235


title: ILD Study Number 907


title: ILD Study Number 1035


title: ILD Study Number 558


title: ILD Study Number S037


title: ILD Study Number S014


title: ILD Study Number 1237


title: ILD Study Number 1111


title: ILD Study Number 1196


title: ILD Study Number S012


title: ILD Study Number S024


title: ILD Study Number S020


title: ILD Study Number S027


title: ILD Study Number 1178


title: ILD Study Number 942


title: ILD Study Number 1245


title: ILD Study Number 1281


title: AML with normal karyotype #78

status: Public on Aug 04 2011

city: Rotterdam

first: Erdogan

last: Taskesen

address: dr. molewaterplein 50

country: Netherlands

institute: Erasmus University Medical Center (EMC)

description: CEBPAwt

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default settings and targeted intensity values at 100. Intensity values were log2 transformed and mean centered per probe set.

label: Biotin

source_name: mononuclear cells from bone marrow

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

extract_protocol: The total RNA was purified either with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) or with TRIzol-based protocols.

treatment_protocol: Samples are from untreated patients (de novo AML)

tag: genotype/variation (cebpa single mutant, cebpa double mutant)

value: negative,negative


title: AML with normal karyotype #56

description: CEBPAwt


title: AML with normal karyotype #93

description: CEBPAwt


title: AML with normal karyotype #137

description: CEBPAwt


title: AML with normal karyotype #66

description: CEBPAwt


title: AML with normal karyotype #88

description: CEBPAwt


title: AML with normal karyotype #121

description: CEBPAwt


title: AML with normal karyotype #59

description: CEBPAwt


title: AML with normal karyotype #87

description: CEBPAwt


title: AML with normal karyotype #57

description: CEBPAwt


title: AML with normal karyotype #75

description: CEBPAwt


title: AML with normal karyotype #63

description: CEBPAwt


title: AML with normal karyotype #120

description: CEBPAwt


title: AML with normal karyotype #150

description: CEBPAwt


title: AML 46,XY,inv(10)(p12q21)c #85

description: CEBPAwt


title: AML with normal karyotype #100

description: CEBPAwt


title: AML with normal karyotype #90

description: CEBPAwt


title: AML with normal karyotype #149

description: CEBPAwt


title: AML with normal karyotype #58

description: CEBPAwt


title: AML with normal karyotype #92

description: CEBPAwt


title: AML with normal karyotype #76

description: CEBPAwt


title: AML with normal karyotype #79

description: CEBPAwt


title: AML with normal karyotype #89

description: CEBPAwt


title: AML with normal karyotype #74

description: CEBPAwt


title: AML with normal karyotype #53

description: CEBPAwt


title: AML with normal karyotype #54

description: CEBPAwt


title: AML with normal karyotype #77

description: CEBPAwt


title: AML with normal karyotype #71

description: CEBPAwt


title: AML with normal karyotype #86

description: CEBPAwt


title: AML with normal karyotype #118

description: CEBPAwt


title: AML with normal karyotype #50

description: CEBPAwt


title: AML with normal karyotype #52

description: CEBPAwt


title: AML with normal karyotype #32

description: CEBPAwt


title: AML with normal karyotype #35

description: CEBPAwt


title: AML with normal karyotype #34

description: CEBPAwt


title: AML with normal karyotype #48

description: CEBPAwt


title: AML with normal karyotype #44

description: CEBPAwt


title: AML with normal karyotype #6

description: CEBPAsm

value: positive,negative


title: AML with normal karyotype #27

description: CEBPAwt


title: AML with normal karyotype #30

description: CEBPAwt


title: AML with normal karyotype #7

description: CEBPAdm

value: negative,positive


title: AML with normal karyotype #20

description: CEBPAdm


title: AML with normal karyotype #17

description: CEBPAdm


title: AML with normal karyotype #15

description: CEBPAdm


title: AML with normal karyotype #33

description: CEBPAwt


title: AML with normal karyotype #1

description: CEBPAsm


title: AML 7425

status: Public on Jul 31 2011

city: Houston

first: Roel

last: Verhaak

state: TX

address: 1400 Pressler St

department: Bioinformatics and Comp Bio

institute: MD Anderson Cancer Center

description: AML

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default settings and targeted intensity values at 100. Intensity values were log2 transformed.

value: mononuclear cells from bone marrow

value: Acute myeloid leukemia


title: AML 7427

description: AML


title: AML 7426

description: AML


title: AML 7424

description: AML


title: AML 7404

description: AML


title: AML with normal karyotype #31

description: CEBPAwt


title: AML with normal karyotype #26

description: CEBPAwt


title: AML 7130

description: AML


title: AML 7129

description: AML


title: AML 7132

description: AML


title: SJETV055

status: Public on Apr 20 2011

city: Memphis

first: Charles

middle: G

last: Mullighan

state: TN

address: 262 Danny Thomas Place, MS 342

department: Pathology

institute: St. Jude Children's Research Hospital

description: ETV6-RUNX1 B-precursor ALL

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix One-Cycle protocol from 1 ug of total RNA

growth_protocol: No growth protocol. Cells were obtained from bone marrow or blood from children with acute lymphoblastic leukemia

extract_protocol: Trizol

value: tumor cells obtained at diagnosis

tag: subtype

tag: day 19

value: neg

tag: day 46


title: SJETV059

description: ETV6-RUNX1 B-precursor ALL


title: AML 7068

description: AML


title: SJHYPO114

description: ETV6-RUNX1 B-precursor ALL


title: SJETV024

description: ETV6-RUNX1 B-precursor ALL


title: AML 7066

description: AML


title: SJETV053

description: ETV6-RUNX1 B-precursor ALL


title: SJETV063

description: ETV6-RUNX1 B-precursor ALL


title: SJETV064

description: ETV6-RUNX1 B-precursor ALL


title: SJETV054

description: ETV6-RUNX1 B-precursor ALL

value: pos


title: SJETV017

description: ETV6-RUNX1 B-precursor ALL


title: AML 7179

description: AML


title: SJETV033

description: ETV6-RUNX1 B-precursor ALL


title: SJETV051

description: ETV6-RUNX1 B-precursor ALL


title: SJETV057

description: ETV6-RUNX1 B-precursor ALL


title: SJETV032

description: ETV6-RUNX1 B-precursor ALL


title: SJETV066

description: ETV6-RUNX1 B-precursor ALL


title: SJETV018

description: ETV6-RUNX1 B-precursor ALL


title: SJETV035

description: ETV6-RUNX1 B-precursor ALL


title: SJETV043

description: ETV6-RUNX1 B-precursor ALL


title: SJETV016

description: ETV6-RUNX1 B-precursor ALL


title: SJETV020

description: ETV6-RUNX1 B-precursor ALL


title: SJETV025

description: ETV6-RUNX1 B-precursor ALL


title: SJETV015

description: ETV6-RUNX1 B-precursor ALL


title: SJETV031

description: ETV6-RUNX1 B-precursor ALL


title: SJETV101

description: ETV6-RUNX1 B-precursor ALL


title: SJETV005

description: ETV6-RUNX1 B-precursor ALL


title: SJETV004

description: ETV6-RUNX1 B-precursor ALL


title: SJETV009

description: ETV6-RUNX1 B-precursor ALL


title: SJETV010

description: ETV6-RUNX1 B-precursor ALL


title: SJETV019

description: ETV6-RUNX1 B-precursor ALL


title: SJETV008

description: ETV6-RUNX1 B-precursor ALL


title: SJETV105

description: ETV6-RUNX1 B-precursor ALL


title: SJETV030

description: ETV6-RUNX1 B-precursor ALL


title: SJETV036

description: ETV6-RUNX1 B-precursor ALL


title: SJETV116

description: ETV6-RUNX1 B-precursor ALL


title: SJETV006

description: ETV6-RUNX1 B-precursor ALL


title: SJETV121

description: ETV6-RUNX1 B-precursor ALL


title: SJETV001

description: ETV6-RUNX1 B-precursor ALL


title: SJETV003

description: ETV6-RUNX1 B-precursor ALL


title: SJETV014

description: ETV6-RUNX1 B-precursor ALL


title: SJETV109

description: ETV6-RUNX1 B-precursor ALL


title: SJETV012

description: ETV6-RUNX1 B-precursor ALL


title: SJETV104

description: ETV6-RUNX1 B-precursor ALL


title: SJETV013

description: ETV6-RUNX1 B-precursor ALL


title: SJETV002

description: ETV6-RUNX1 B-precursor ALL


title: SJETV007

description: ETV6-RUNX1 B-precursor ALL


title: SJETV122

description: ETV6-RUNX1 B-precursor ALL


title: SJETV118

description: ETV6-RUNX1 B-precursor ALL


title: SJETV106

description: ETV6-RUNX1 B-precursor ALL


title: SJETV120

description: ETV6-RUNX1 B-precursor ALL


title: SJETV115

description: ETV6-RUNX1 B-precursor ALL


title: AML 6356

description: AML


title: SJETV011

description: ETV6-RUNX1 B-precursor ALL


title: SJETV108

description: ETV6-RUNX1 B-precursor ALL


title: SJETV119

description: ETV6-RUNX1 B-precursor ALL


title: SJETV117

description: ETV6-RUNX1 B-precursor ALL


title: SJTALL042

description: T-lineage ALL


title: SJETV123

description: ETV6-RUNX1 B-precursor ALL


title: SJTALL214

description: T-lineage ALL


title: SJTALL213

description: T-lineage ALL


title: SJTALL020

description: T-lineage ALL


title: SJTALL017

description: T-lineage ALL


title: SJTALL021

description: T-lineage ALL


title: SJTALL016

description: T-lineage ALL


title: SJTALL015

description: T-lineage ALL


title: SJTALL022

description: T-lineage ALL


title: SJTALL018

description: T-lineage ALL


title: SJTALL058

description: T-lineage ALL


title: SJTALL082

description: T-lineage ALL


title: SJTALL073

description: T-lineage ALL


title: SJTALL079

description: T-lineage ALL


title: SJTALL077

description: T-lineage ALL


title: SJTALL161

description: T-lineage ALL


title: SJTALL080

description: T-lineage ALL


title: SJTALL041

description: T-lineage ALL


title: SJTALL036

description: T-lineage ALL


title: SJTALL076

description: T-lineage ALL


title: SJTALL075

description: T-lineage ALL


title: SJTALL037

description: T-lineage ALL


title: SJTALL019

description: T-lineage ALL


title: SJTALL071

description: T-lineage ALL


title: SJTALL072

description: T-lineage ALL


title: SJTALL070

description: T-lineage ALL


title: SJTALL023

description: T-lineage ALL


title: SJTALL049

description: T-lineage ALL


title: SJTALL078

description: T-lineage ALL


title: SJTALL084

description: T-lineage ALL


title: SJTALL003

description: T-lineage ALL


title: SJTALL001

description: T-lineage ALL


title: SJTALL069

description: MLL-rearranged T-lineage ALL


title: SJTALL063

description: T-lineage ALL


title: SJTALL118

description: T-lineage ALL


title: SJTALL064

description: T-lineage ALL


title: SJTALL068

description: T-lineage ALL


title: SJTALL067

description: T-lineage ALL


title: SJBALL196

description: B-precursor ALL with miscellaneous karyotype


title: SJERG023


title: SJERG028


title: SJTALL127

description: T-lineage ALL


title: SJBALL207


title: SJTALL143

description: T-lineage ALL


title: SJERG030


title: SJERG026


title: SJBALL195


title: SJBALL189


title: SJBALL192


title: SJBALL141


title: SJBALL199


title: SJTALL165

description: T-lineage ALL


title: SJBALL139


title: SJTALL130

description: T-lineage ALL


title: SJERG024


title: SJBALL194


title: SJBALL140


title: SJBALL209


title: SJBALL138


title: SJTALL136

description: T-lineage ALL


title: SJBALL177


title: SJBALL137


title: SJBALL076


title: SJHYPO136

description: B-precursor ALL with hypodiploid karyotype


title: SJERG006


title: SJERG007


title: SJBALL113


title: SJHYPO137


title: SJBALL032


title: SJHYPO115


title: SJERG004


title: SJERG005


title: SJBALL018


title: SJHYPO128


title: SJERG008


title: SJHYPO142


title: SJHYPO141


title: SJERG003


title: SJERG001


title: SJHYPO146


title: SJERG021


title: SJINF008

description: MLL-rearranged B-precursor ALL


title: SJBALL036


title: SJBALL013


title: SJBALL074


title: SJBALL110


title: SJERG002


title: SJINF003

description: MLL-rearranged B-precursor ALL


title: SJBALL122


title: SJINF001

description: MLL-rearranged B-precursor ALL


title: SJBALL011


title: SJINF006

description: MLL-rearranged B-precursor ALL


title: SJBALL066


title: SJINF076

description: MLL-rearranged B-precursor ALL


title: SJHYPO109


title: SJMLL035

description: MLL-rearranged B-precursor ALL


title: SJBALL152


title: SJMLL034

description: MLL-rearranged B-precursor ALL


title: SJMLL036

description: MLL-rearranged B-precursor ALL


title: SJHYPO108


title: SJMLL038

description: MLL-rearranged B-precursor ALL


title: SJINF065

description: MLL-rearranged B-precursor ALL


title: SJBALL161


title: SJMLL027

description: MLL-rearranged B-precursor ALL


title: SJHYPO111

description: MLL-rearranged B-precursor ALL


title: SJHYPO107


title: SJINF064

description: MLL-rearranged B-precursor ALL


title: SJBALL204


title: SJINF062

description: MLL-rearranged B-precursor ALL


title: SJHYPO101


title: SJHYPO112


title: SJBALL206


title: SJERG025


title: SJHYPO132


title: SJHYPO110


title: SJHYPO131


title: SJBALL153


title: SJHYPO122


title: SJBALL202


title: SJBALL200


title: SJHYPO113


title: SJERG029


title: SJBALL201


title: SJHYPER080

description: High hyperdiploid B-precursor ALL


title: SJHYPER054

description: High hyperdiploid B-precursor ALL


title: SJHYPER084

description: High hyperdiploid B-precursor ALL


title: SJBALL198


title: SJHYPER055

description: High hyperdiploid B-precursor ALL


title: SJHYPER078

description: High hyperdiploid B-precursor ALL


title: SJHYPER057

description: High hyperdiploid B-precursor ALL


title: SJHYPER064

description: High hyperdiploid B-precursor ALL


title: SJHYPER070

description: High hyperdiploid B-precursor ALL


title: SJHYPER056

description: High hyperdiploid B-precursor ALL


title: SJBALL193


title: SJHYPER082

description: High hyperdiploid B-precursor ALL


title: SJHYPER051

description: High hyperdiploid B-precursor ALL


title: SJBALL006


title: SJBALL197


title: SJHYPER052

description: High hyperdiploid B-precursor ALL


title: SJHYPER053

description: High hyperdiploid B-precursor ALL


title: SJBALL190


title: SJHYPER076

description: High hyperdiploid B-precursor ALL


title: SJHYPER069

description: High hyperdiploid B-precursor ALL


title: SJHYPER075

description: High hyperdiploid B-precursor ALL


title: SJBALL191


title: SJERG027

description: High hyperdiploid B-precursor ALL


title: SJHYPER047

description: High hyperdiploid B-precursor ALL


title: SJHYPER030

description: High hyperdiploid B-precursor ALL


title: SJHYPER027

description: High hyperdiploid B-precursor ALL


title: SJHYPER024

description: High hyperdiploid B-precursor ALL


title: SJHYPER021

description: High hyperdiploid B-precursor ALL


title: SJHYPER134

description: High hyperdiploid B-precursor ALL


title: SJHYPER029

description: High hyperdiploid B-precursor ALL


title: SJHYPER015

description: High hyperdiploid B-precursor ALL


title: SJHYPER016

description: High hyperdiploid B-precursor ALL


title: SJHYPER018

description: High hyperdiploid B-precursor ALL


title: SJHYPER017

description: High hyperdiploid B-precursor ALL


title: SJHYPER006

description: High hyperdiploid B-precursor ALL


title: SJHYPER008

description: High hyperdiploid B-precursor ALL


title: SJHYPER014

description: High hyperdiploid B-precursor ALL


title: SJHYPER019

description: High hyperdiploid B-precursor ALL


title: SJHYPER012

description: High hyperdiploid B-precursor ALL


title: SJHYPER005

description: High hyperdiploid B-precursor ALL


title: SJHYPER163

description: High hyperdiploid B-precursor ALL


title: SJHYPER013

description: High hyperdiploid B-precursor ALL


title: SJHYPER158

description: High hyperdiploid B-precursor ALL


title: SJBALL203


title: SJHYPER003

description: High hyperdiploid B-precursor ALL


title: SJHYPER002

description: High hyperdiploid B-precursor ALL


title: SJHYPER007

description: High hyperdiploid B-precursor ALL


title: SJHYPER155

description: High hyperdiploid B-precursor ALL


title: SJHYPER156

description: High hyperdiploid B-precursor ALL


title: SJHYPER009

description: High hyperdiploid B-precursor ALL


title: SJHYPER162

description: High hyperdiploid B-precursor ALL


title: SJHYPER160

description: High hyperdiploid B-precursor ALL


title: SJHYPER004

description: High hyperdiploid B-precursor ALL


title: SJHYPER011

description: High hyperdiploid B-precursor ALL


title: SJHYPER157

description: High hyperdiploid B-precursor ALL


title: SJMLL026

description: MLL-rearranged B-precursor ALL


title: SJE2A019

description: TCF3-PBX1 B-precursor ALL


title: SJHYPER159

description: High hyperdiploid B-precursor ALL


title: SJHYPER154

description: High hyperdiploid B-precursor ALL


title: SJE2A014

description: TCF3-PBX1 B-precursor ALL


title: SJE2A017

description: TCF3-PBX1 B-precursor ALL


title: SJHYPER161

description: High hyperdiploid B-precursor ALL


title: SJE2A013

description: TCF3-PBX1 B-precursor ALL


title: SJE2A011

description: TCF3-PBX1 B-precursor ALL


title: SJE2A006

description: TCF3-PBX1 B-precursor ALL


title: SJE2A005

description: TCF3-PBX1 B-precursor ALL


title: SJE2A003

description: TCF3-PBX1 B-precursor ALL


title: SJE2A016

description: TCF3-PBX1 B-precursor ALL


title: SJE2A020

description: TCF3-PBX1 B-precursor ALL


title: SJE2A012

description: TCF3-PBX1 B-precursor ALL


title: SJE2A037

description: TCF3-PBX1 B-precursor ALL


title: SJE2A004

description: TCF3-PBX1 B-precursor ALL


title: SJE2A002

description: TCF3-PBX1 B-precursor ALL


title: SJE2A010

description: TCF3-PBX1 B-precursor ALL


title: SJE2A007

description: TCF3-PBX1 B-precursor ALL


title: SJE2A043

description: TCF3-PBX1 B-precursor ALL


title: SJE2A015

description: TCF3-PBX1 B-precursor ALL


title: SJE2A042

description: TCF3-PBX1 B-precursor ALL


title: SJPHALL021

description: BCR-ABL1 B-precursor ALL


title: SJPHALL019

description: BCR-ABL1 B-precursor ALL


title: SJE2A038

description: TCF3-PBX1 B-precursor ALL


title: SJPHALL002

description: BCR-ABL1 B-precursor ALL


title: SJPHALL001

description: BCR-ABL1 B-precursor ALL


title: SJE2A001

description: TCF3-PBX1 B-precursor ALL


title: SJPHALL020

description: BCR-ABL1 B-precursor ALL


title: SJPHALL008

description: BCR-ABL1 B-precursor ALL


title: SJPHALL005

description: BCR-ABL1 B-precursor ALL


title: SJPHALL011

description: BCR-ABL1 B-precursor ALL


title: SJPHALL006

description: BCR-ABL1 B-precursor ALL


title: SJHYPO121

description: BCR-ABL1 B-precursor ALL


title: SJPHALL010

description: BCR-ABL1 B-precursor ALL


title: SJPHALL017

description: BCR-ABL1 B-precursor ALL


title: SJPHALL003

description: BCR-ABL1 B-precursor ALL


title: SJPHALL007

description: BCR-ABL1 B-precursor ALL


title: SJPHALL004

description: BCR-ABL1 B-precursor ALL


title: SJPHALL024

description: BCR-ABL1 B-precursor ALL


title: pediatric T-ALL patient #70 reanalysis

status: Public on Apr 11 2011

city: Utrecht

first: Jules

last: Meijerink

address: Uppsalalaan 8

institute: Princess Máxima Center for Pediatric Oncology

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267358

hyb_protocol: Hybridization of Humane Genome U133 plus2.0 oligonucleotide microarrays (Affymetrix, Santa-Clara, USA) and washing steps were performed according to the manufacturers’ protocol.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip scanner 3000

data_processing:
Probeset intensities were extracted in R versions 2.8.0 and 2.10.0.
Probeset intensities were normalized using RMA.

source_name: pediatric T-ALL patient #70

label_protocol: Copy-DNA and ccRNA syntheses from total RNA, hybridization of Humane Genome U133 plus2.0 oligonucleotide microarrays (Affymetrix, Santa-Clara, USA) and washing steps were performed according to the manufacturers’ protocol.

extract_protocol: Genomic DNA and total cellular RNA were isolated using Trizol (Invitrogen) according to the manufacturers’ protocol, with minor modifications. An additional phenol-chloroform extraction was performed and the RNA was precipitated with isopropanol along with 1 mL (20 mg/mL) glycogen (Roche, Almere, The Netherlands). After precipitation, RNA pellets were dissolved in 20 mL RNAse-free TE-buffer (10 mM Tris-HCl, 1 mM EDTA, pH=8.0). The RNA concentration was quantified spectrophotometrically. Integrity of total RNA was checked using the Agilent 2100 Bio-analyzer (Agilent, Santa-Clara, USA).

treatment_protocol: Leukemic cells were isolated and enriched from these samples. Within 24 hours after sampling, mononuclear cells were isolated by density gradient centrifugation using Lymphoprep (density 1.077 g/mL; Nycomed Pharma, Oslo, Norway), and centrifuged at 480g for 15 minutes at room temperature. The collected mononuclear cells were washed twice and kept in culture medium consisting of RPMI 1640 medium (Dutch modification without L-glutamine; Gibco BRL, Life Technologies, Breda, The Netherlands), 20% fetal calf serum (FCS; Integro, Zaandam, The Netherlands), 2 mM L-glutamine (Gibco BRL, Life Technologies) 5 µg/mL insulin, 5 µg/mL transferrin, 5 ng/mL sodium selenite (ITS media supplement; Sigma, St Louis, MO), 100 IU/mL penicillin, 100 µg/mL streptomycin, 0.125 µg/mL fungizone (Gibco BRL, Life Technologies), and 0.2 mg/mL gentamycin (Gibco BRL, Life Technologies). Contaminating nonleukemic cells were removed by immunomagnetic beads. as described by Kaspers et al (1994). All resulting samples contained 90% leukemic cells, as determined morphologically by May-Grünwald-Giemsa-stained cytospins (Merck, Darmstadt, Germany). Viably frozen T-ALL cells were used for DNA and RNA extraction, and a minimum of 5 million leukemic cells were lysed in Trizol reagent (Invitrogen, Life Technologies, Breda, The Netherlands) and stored at -80°C.

value: pediatric T-ALL cells

tag: cytogenetics


title: pediatric T-ALL patient #61 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267355

source_name: pediatric T-ALL patient #61


title: pediatric T-ALL patient #47 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267352

source_name: pediatric T-ALL patient #47

value: unknown


title: pediatric T-ALL patient #7 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267324

source_name: pediatric T-ALL patient #7


title: pediatric T-ALL patient #60

source_name: pediatric T-ALL patient #140


title: pediatric T-ALL patient #50

value: MYB


title: pediatric T-ALL patient #46 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267351

source_name: pediatric T-ALL patient #46


title: pediatric T-ALL patient #39 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267347

source_name: pediatric T-ALL patient #39


title: pediatric T-ALL patient #51


title: pediatric T-ALL patient #63 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267356

source_name: pediatric T-ALL patient #63


title: pediatric T-ALL patient #6 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267323

source_name: pediatric T-ALL patient #6


title: pediatric T-ALL patient #49 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267353

source_name: pediatric T-ALL patient #49


title: pediatric T-ALL patient #53 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267354

source_name: pediatric T-ALL patient #53


title: pediatric T-ALL patient #52


title: pediatric T-ALL patient #64 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267357

source_name: pediatric T-ALL patient #64


title: pediatric T-ALL patient #9 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267326

source_name: pediatric T-ALL patient #9


title: pediatric T-ALL patient #57


title: pediatric T-ALL patient #8 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267325

source_name: pediatric T-ALL patient #8


title: pediatric T-ALL patient #40 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267348

source_name: pediatric T-ALL patient #40


title: pediatric T-ALL patient #66


title: pediatric T-ALL patient #5 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267322

source_name: pediatric T-ALL patient #5


title: pediatric T-ALL patient #38 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267346

source_name: pediatric T-ALL patient #38


title: pediatric T-ALL patient #43 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267349

source_name: pediatric T-ALL patient #43


title: pediatric T-ALL patient #56


title: pediatric T-ALL patient #31 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267341

source_name: pediatric T-ALL patient #31


title: pediatric T-ALL patient #34 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267343

source_name: pediatric T-ALL patient #34


title: pediatric T-ALL patient #32 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267342

source_name: pediatric T-ALL patient #32


title: pediatric T-ALL patient #35 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267344

source_name: pediatric T-ALL patient #35


title: pediatric T-ALL patient #36 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267345

source_name: pediatric T-ALL patient #36


title: pediatric T-ALL patient #30 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267340

source_name: pediatric T-ALL patient #30


title: pediatric T-ALL patient #45 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267350

source_name: pediatric T-ALL patient #45


title: pediatric T-ALL patient #29 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267339

source_name: pediatric T-ALL patient #29


title: pediatric T-ALL patient #24 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267336

source_name: pediatric T-ALL patient #24

value: HOXA


title: pediatric T-ALL patient #25 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267337

source_name: pediatric T-ALL patient #25


title: pediatric T-ALL patient #22 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267334

source_name: pediatric T-ALL patient #22


title: pediatric T-ALL patient #23 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267335

source_name: pediatric T-ALL patient #23


title: pediatric T-ALL patient #21 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267333

source_name: pediatric T-ALL patient #21


title: pediatric T-ALL patient #27 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267338

source_name: pediatric T-ALL patient #27


title: pediatric T-ALL patient #134

source_name: pediatric T-ALL patient #140


title: pediatric T-ALL patient #14 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267331

source_name: pediatric T-ALL patient #14


title: pediatric T-ALL patient #13 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267330

source_name: pediatric T-ALL patient #13


title: pediatric T-ALL patient #19 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267332

source_name: pediatric T-ALL patient #19


title: pediatric T-ALL patient #144


title: pediatric T-ALL patient #10 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267327

source_name: pediatric T-ALL patient #10


title: normal bone marrow control BM#153

source_name: normal bone marrow control

value: normal bone marrow

value: BM


title: normal bone marrow control BM#148


title: pediatric T-ALL patient #139


title: normal bone marrow control BM#152


title: normal bone marrow control BM#149


title: pediatric T-ALL patient #12 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267329

source_name: pediatric T-ALL patient #12


title: pediatric T-ALL patient #1 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267321

source_name: pediatric T-ALL patient #1


title: pediatric T-ALL patient #11 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267328

source_name: pediatric T-ALL patient #11


title: normal bone marrow control BM#150


title: pediatric T-ALL patient #106 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267392

source_name: pediatric T-ALL patient #106


title: normal bone marrow control BM#151


title: normal bone marrow control BM#147


title: PBMC_post-surgery_validation_15

status: Public on Mar 01 2011

city: Durham

first: Erich

last: Huang

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences and Policy

institute: Duke University

description:
Blood collection: Blood samples (8mL) collected by venipuncture into BD Vacutainer CPT Cell Preparation tubes. Samples processed within 2 hours of collection.
PBMC isolation: CPT tubes were centrifuged for 30 minutes at 2,500 rpms in a centrifuge with a swinging bucket rotor. The plasma layer was removed, and then the remaining buffy coat was poured into a 15 mL conical tube. Next, 5 mL of chilled phosphate buffered saline (PBS) with 2% fetal bovine serum (FBS) was added to the CPT tube, which was capped and inverted to mix. The contents were poured into the same 15 mL conical tube, which was then centrifuged for 10 minutes at 1200 rpms at room temperature. The supernatant was then aspirated and the pellet was resuspended in 1 mL of freezing media (RPMI with 20% DMSO and 20% FBS). The cells were then transferred to a cryovial (Nunc, Roskilde, Denmark) and placed in a freezer box at -80°C. After 24 hours samples were transferred to liquid nitrogen storage.

hyb_protocol: Following fragmentation, 15ug of labeled cRNA were hybridized on HU133 Plus 2.0 GeneChips for 16 hours at 45°C. GeneChips were washed and stained using the Biomex FX liquid handler.

scan_protocol: GeneChips were scanned using the Axon Genepix Scanner (Genepix 4000B).

data_processing:
Data processing was performed in a pilot revision control system entitled Quality-Auditable Data Repository and Analysis (QUADRA). For fully versioned and annotated source code and data objects, please see http://quadra.genome.duke.edu/mouse-2-human-mammary-tumor-pbmc-project.
Data were RMA normalized according to the source code found at http://quadra.genome.duke.edu/mouse-2-human-mammary-tumor-pbmc-project/human-dataprep.

source_name: PBMCs from patients with diagnosis of invasive breast cancer, confirmed by diagnostic biopsy; sample taken following surgical excision of tumor.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix IVT 1-cycle protocol from 2.5 ug total RNA.

extract_protocol: Total RNA from peripheral blood mononuclear cells was isolated using the Ambion Ribopure™-Blood kit (Ambion, Austin, TX).

tag: phenotype

value: Post-Surgery

value: peripheral blood mononuclear cells

tag: data set

value: validation


title: PBMC_post-surgery_validation_12


title: PBMC_post-surgery_validation_2


title: PBMC_post-surgery_validation_10


title: PBMC_post-surgery_validation_5


title: PBMC_post-surgery_validation_3


title: PBMC_post-surgery_validation_9


title: PBMC_post-surgery_validation_4


title: PBMC_post-surgery_validation_1


title: PBMC_post-surgery_validation_14


title: PBMC_post-surgery_validation_7


title: PBMC_post-surgery_validation_8


title: PBMC_post-surgery_validation_11


title: PBMC_malignant_validation_47

source_name: PBMCs from patients with diagnosis of invasive breast cancer, confirmed by diagnostic biopsy

value: Pre-Surgery (aka Malignant)


title: PBMC_malignant_validation_44


title: PBMC_post-surgery_validation_13


title: PBMC_malignant_validation_46


title: PBMC_benign_validation_26

source_name: PBMCs from patients with benign diagnosis, confirmed by diagnostic biopsy

value: Benign


title: PBMC_malignant_validation_45


title: PBMC_malignant_validation_42


title: PBMC_benign_validation_23


title: PBMC_malignant_validation_43


title: PBMC_benign_validation_22


title: PBMC_benign_validation_24


title: PBMC_benign_validation_20


title: PBMC_benign_validation_27


title: PBMC_benign_validation_21


title: PBMC_benign_validation_25


title: PBMC_benign_validation_19


title: PBMC_benign_validation_13


title: PBMC_benign_validation_18


title: PBMC_benign_validation_7


title: PBMC_benign_validation_9


title: PBMC_benign_validation_14


title: PBMC_benign_validation_12


title: PBMC_benign_validation_11


title: PBMC_benign_validation_6


title: PBMC_benign_validation_5


title: PBMC_benign_validation_16


title: PBMC_benign_validation_8


title: PBMC_malignant_validation_32

value: Malignant


title: PBMC_malignant_validation_40


title: PBMC_benign_validation_17


title: PBMC_malignant_validation_35


title: PBMC_benign_validation_2


title: PBMC_malignant_validation_41


title: PBMC_malignant_validation_38


title: PBMC_benign_validation_3


title: PBMC_benign_validation_15


title: PBMC_malignant_validation_36


title: PBMC_malignant_validation_34


title: PBMC_benign_validation_4


title: PBMC_malignant_validation_33


title: PBMC_benign_validation_1


title: PBMC_benign_validation_10


title: PBMC_malignant_validation_39


title: PBMC_malignant_validation_30


title: PBMC_malignant_validation_31


title: PBMC_malignant_validation_27


title: PBMC_malignant_validation_29


title: PBMC_malignant_validation_28


title: PBMC_malignant_validation_25


title: PBMC_malignant_validation_24


title: PBMC_malignant_validation_21


title: PBMC_malignant_validation_23


title: PBMC_malignant_validation_18


title: PBMC_malignant_validation_26


title: PBMC_malignant_validation_22


title: PBMC_malignant_validation_19


title: PBMC_malignant_validation_14


title: PBMC_malignant_validation_20


title: PBMC_post-surgery_validation_6


title: PBMC_malignant_validation_17


title: PBMC_malignant_validation_9


title: PBMC_malignant_validation_11


title: PBMC_malignant_validation_16


title: PBMC_malignant_validation_12


title: PBMC_malignant_validation_13


title: PBMC_malignant_validation_8


title: PBMC_malignant_validation_7


title: PBMC_malignant_validation_6


title: PBMC_malignant_validation_5


title: PBMC_malignant_validation_37


title: PBMC_malignant_validation_10


title: PBMC_malignant_validation_4


title: PBMC_malignant_validation_1


title: PBMC_malignant_validation_2


title: PBMC_normal_validation_19

source_name: PBMCs from patients with normal mammogram

value: Normal


title: PBMC_normal_validation_20


title: PBMC_normal_validation_17


title: PBMC_normal_validation_21


title: PBMC_normal_validation_13


title: PBMC_normal_validation_18


title: PBMC_normal_validation_16


title: PBMC_normal_validation_10


title: PBMC_normal_validation_9


title: PBMC_normal_validation_2


title: PBMC_normal_validation_12


title: PBMC_normal_validation_7


title: PBMC_normal_validation_8


title: PBMC_normal_validation_1


title: PBMC_normal_validation_6


title: PBMC_ectopic_validation_21

description:
Blood collection: Samples collected by leukapheresis and stored in liquid nitrogen.
PBMC isolation:

source_name: PBMCs from patients with other cancer types (e.g., gastrointestinal and brain cancers)

value: Ectopic

value: peripheral blood leukocytes


title: PBMC_normal_validation_4


title: PBMC_normal_validation_3


title: PBMC_normal_validation_11


title: PBMC_ectopic_validation_17


title: PBMC_normal_validation_5


title: PBMC_ectopic_validation_16


title: PBMC_malignant_validation_3


title: PBMC_ectopic_validation_18


title: PBMC_ectopic_validation_20


title: PBMC_ectopic_validation_19


title: PBMC_normal_validation_14


title: PBMC_ectopic_validation_22


title: PBMC_normal_validation_15


title: PBMC_ectopic_validation_14


title: PBMC_ectopic_validation_11


title: PBMC_ectopic_validation_12


title: PBMC_ectopic_validation_10


title: PBMC_malignant_validation_15


title: PBMC_ectopic_validation_13


title: PBMC_ectopic_validation_8


title: PBMC_benign_training_1


title: PBMC_benign_training_6


title: PBMC_benign_training_9


title: PBMC_ectopic_validation_5


title: PBMC_malignant_training_8

value: training


title: PBMC_ectopic_validation_2


title: PBMC_ectopic_validation_7


title: PBMC_malignant_training_10


title: PBMC_benign_training_3


title: PBMC_ectopic_validation_15


title: PBMC_benign_training_4


title: PBMC_malignant_training_6


title: PBMC_benign_training_10


title: PBMC_ectopic_validation_1


title: PBMC_ectopic_validation_6


title: PBMC_malignant_training_9


title: PBMC_benign_training_8


title: PBMC_benign_training_5


title: PBMC_malignant_training_7


title: PBMC_ectopic_validation_9


title: PBMC_malignant_training_4


title: PBMC_benign_training_2


title: PBMC_malignant_training_1


title: PBMC_ectopic_validation_4


title: PBMC_normal_training_8


title: PBMC_malignant_training_3


title: PBMC_normal_training_9


title: PBMC_normal_training_10


title: PBMC_malignant_training_2


title: PBMC_malignant_training_5


title: PBMC_normal_training_5


title: PBMC_normal_training_7


title: PBMC_normal_training_1


title: PBMC_normal_training_4


title: PBMC_normal_training_3


title: PBMC_benign_training_7


title: PBMC_normal_training_6


title: PBMC_ectopic_validation_3


title: Muscle-FamilyHistoryNegative-5

city: Boston

first: Mary Elizabeth

last: Patti

state: MA

address: 1 Joslin Place

department: Research Division

institute: Joslin Diabetes Center

description:
Jos3668
Gene expression of skeletal muscle from subject without diabetes

hyb_protocol: 15ug of biotinylated cRNA were hybridized for 16hr at 45C to the Affymetrix GeneChip Human Genome U133 Plus 2.0 array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.

data_processing: Data were analyzed using Affymetrix GCOS v.1.3, MAS5.0 algorithm, and globally scaled with the trimmed mean target intensity set to 1500.

source_name: skeletal muscle

label_protocol: Biotinylated cRNA were prepared from total RNA according to the standard Affymetrix protocol.

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer's instructions.

value: skeletal muscle

tag: gender

value: female

tag: age (years)

tag: family history

value: Family history negative

tag: body mass index (kg/m2)

tag: fasting glucose (ogtt)

tag: 2 hour glucose (ogtt)

tag: hemoglobin a1c

tag: fasting glucose (iv0gavg)

tag: fasting insulin (iv0inavg)

tag: si

tag: waist hip ratio

value: missing value


title: no relapse _ sample 191

status: Public on Feb 10 2011

city: Padova

first: Andrea

last: Zangrando

address: Via Giustiniani, 3

department: Woman and Child's Health

institute: University of Padova

description: Gene expression data from pediatric acute leukemia samples at diagnosis

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.

scan_protocol: GeneChips were scanned using the Scan GCS3000Dx.

data_processing: The data were normalized using RMA algorithm in R software [www.r-ptoject.org], BioConductor package [www.bioconductor.org]

source_name: no relapse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: White blood cells were isolated through Ficoll-Hypaque density gradient centrifugation. Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns.

tag: cell type

value: white blood cells

tag: class

value: pediatric acute leukemia

tag: tissue

value: bone marrow


title: PBMC_normal_training_2


title: no relapse _ sample 157


title: no relapse _ sample 146


title: no relapse _ sample 192


title: early relapse _ sample 166

source_name: early relapse


title: no relapse _ sample 141


title: no relapse _ sample 187


title: no relapse _ sample 189


title: no relapse _ sample 147


title: no relapse _ sample 137


title: early relapse _ sample 144


title: no relapse _ sample 145


title: no relapse _ sample 142


title: no relapse _ sample 138


title: late relapse _ sample 136


title: no relapse _ sample 139


title: no relapse _ sample 140


title: no relapse _ sample 143


title: no relapse _ sample 134


title: no relapse _ sample 131


title: no relapse _ sample 132


title: no relapse _ sample 128


title: early relapse _ sample 133


title: no relapse _ sample 130


title: no relapse _ sample 129


title: no relapse _ sample 135


title: no relapse _ sample 125


title: early relapse _ sample 126


title: no relapse _ sample 124


title: no relapse _ sample 122


title: no relapse _ sample 121


title: no relapse _ sample 127


title: early relapse _ sample 123


title: no relapse _ sample 120


title: no relapse _ sample 118


title: no relapse _ sample 116


title: no relapse _ sample 114


title: no relapse _ sample 113


title: late relapse _ sample 119


title: no relapse _ sample 117


title: no relapse _ sample 115


title: no relapse _ sample 112


title: no relapse _ sample 106


title: no relapse _ sample 111


title: early relapse _ sample 108


title: no relapse _ sample 110


title: no relapse _ sample 109


title: no relapse _ sample 107


title: AML sample #15

status: Public on Jan 01 2011

city: New York

first: Hans-Ulrich

last: Klein

state: NY

department: Neurology

institute: Columbia University Medical Center

description: AML samples investigated according to WHO 2008 classification

data_processing: The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.22.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64).

source_name: mononuclear cells after Ficoll purification

extract_protocol: The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.

treatment_protocol: Samples are from untreated AML patients.

tag: sample id

tag: analysis i

value: AML-NOS

tag: analysis ii

value: AML-NOS plus AML-MLD-sole


title: AML sample #12

value: AML-MLD-sole


title: Patient 5236 AML229

status: Public on Oct 21 2010

first: Brian

last: Balgobind

address: Dr. Molewaterplein 60

department: Pediatric Oncology/Hematology

institute: Erasmus MC - Sophia Children's Hospital

description: Sample collected at diagnosis.

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Array Set HG-U133 Plus 2.0. After sample hybridization, GeneChips were stained using phycoerythrin-conjugated streptavidine in an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner.

data_processing: The CEL files for these samples were read into R using the affy package and normalized at probe-level with vsn (Huber et al, Bioinformatics 2002). Measurements were summarized per probe set using median polish.

source_name: bone marrow or peripheral blood sample from child with acute myeloid leukemia

label_protocol: Biotinylated cRNA was produced according tot the Affymetrix protocol with the ENZO IVT labeling kit, using 5 ug total RNA as input (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated out of leukemic cells using Trizol reagent (GIBCO BRL, Life Technologies). Quality of RNA was checked using an Agilent 2100 Bio-analyzer.

value: bone marrow or peripheral blood

tag: patient id

tag: cohort

value: Validation

tag: karyotype

tag: c-kit

value: wild type

tag: n/k-ras

tag: cebpa

tag: mll-ptd


title: AML sample #11


title: AML sample #10


title: AML sample #13


title: Patient 5237 AML230

description: Sample collected at diagnosis.

value: Discovery


title: AML sample #9


title: Patient 5238 AML231

description: Sample collected at diagnosis.

value: unknown cytogenetics


title: Patient 5182 AML226

description: Sample collected at diagnosis.


title: Patient 5185 AML228

description: Sample collected at diagnosis.


title: Patient 5180 AML225

description: Sample collected at diagnosis.

value: CN-AML


title: Patient 5178 AML223

description: Sample collected at diagnosis.


title: AML sample #14


title: Patient 8446 AML236

description: Sample collected at diagnosis.


title: Patient 5501 AML234

description: Sample collected at diagnosis.


title: Patient 5173 AML219

description: Sample collected at diagnosis.

value: remaining cytogenetics


title: Patient 5239 AML232

description: Sample collected at diagnosis.


title: Patient 5175 AML221

description: Sample collected at diagnosis.


title: Patient 5174 AML220

description: Sample collected at diagnosis.


title: Patient 5166 AML215

description: Sample collected at diagnosis.


title: Patient 5168 AML216

description: Sample collected at diagnosis.

value: MLL-rearrangement


title: Patient 5170 AML218

description: Sample collected at diagnosis.


title: Patient 5644 AML235

description: Sample collected at diagnosis.


title: Patient 5240 AML233

description: Sample collected at diagnosis.


title: Patient 5169 AML217

description: Sample collected at diagnosis.

value: CEBPA


title: Patient 5177 AML222

description: Sample collected at diagnosis.

value: N/K-RAS


title: Patient 5R AML237

description: Sample collected at diagnosis.


title: Patient 5179 AML224

description: Sample collected at diagnosis.


title: Patient 5183 AML227

description: Sample collected at diagnosis.


title: Patient 5164 AML213

description: Sample collected at diagnosis.


title: Patient 5153 AML206

description: Sample collected at diagnosis.


title: Patient 5160 AML211

description: Sample collected at diagnosis.


title: Patient 5165 AML214

description: Sample collected at diagnosis.


title: Patient 5157 AML210

description: Sample collected at diagnosis.

value: C-KIT


title: Patient 5152 AML205

description: Sample collected at diagnosis.


title: Patient 5148 AML201

description: Sample collected at diagnosis.


title: Patient 5149 AML202

description: Sample collected at diagnosis.

value: MLL-PTD


title: Patient 5163 AML212

description: Sample collected at diagnosis.


title: Patient 5155 AML208

description: Sample collected at diagnosis.


title: Patient 5151 AML204

description: Sample collected at diagnosis.


title: Patient 5150 AML203

description: Sample collected at diagnosis.


title: Patient 5156 AML209

description: Sample collected at diagnosis.


title: Patient 5154 AML207

description: Sample collected at diagnosis.


title: Patient 5145 AML198

description: Sample collected at diagnosis.


title: Patient 5041 AML185

description: Sample collected at diagnosis.


title: Patient 5062 AML191

description: Sample collected at diagnosis.


title: Patient 5066 AML195

description: Sample collected at diagnosis.


title: Patient 5063 AML192

description: Sample collected at diagnosis.


title: Patient 5144 AML197

description: Sample collected at diagnosis.


title: Patient 5064 AML193

description: Sample collected at diagnosis.


title: Patient 5056 AML188

description: Sample collected at diagnosis.


title: Patient 5048 AML187

description: Sample collected at diagnosis.


title: Patient 5065 AML194

description: Sample collected at diagnosis.


title: Patient 5147 AML200

description: Sample collected at diagnosis.


title: Patient 5047 AML186

description: Sample collected at diagnosis.


title: Patient 5146 AML199

description: Sample collected at diagnosis.


title: Patient 5057 AML189

description: Sample collected at diagnosis.


title: Patient 5143 AML196

description: Sample collected at diagnosis.


title: Patient 5061 AML190

description: Sample collected at diagnosis.


title: Patient 5013 AML176

description: Sample collected at diagnosis.


title: Patient 5032 AML181

description: Sample collected at diagnosis.


title: Patient 5035 AML183

description: Sample collected at diagnosis.


title: Patient 5031 AML180

description: Sample collected at diagnosis.


title: Patient 5005 AML173

description: Sample collected at diagnosis.


title: Patient 5023 AML178

description: Sample collected at diagnosis.


title: Patient 5036 AML184

description: Sample collected at diagnosis.


title: Patient 5004 AML172

description: Sample collected at diagnosis.


title: Patient 5017 AML177

description: Sample collected at diagnosis.


title: Patient 5007 AML174

description: Sample collected at diagnosis.


title: Patient 5033 AML182

description: Sample collected at diagnosis.


title: Patient 5026 AML179

description: Sample collected at diagnosis.


title: Patient 5012 AML175

description: Sample collected at diagnosis.


title: Patient 4936 AML171

description: Sample collected at diagnosis.


title: Patient 4528 AML113

description: Sample collected at diagnosis.


title: Patient 4536 AML120

description: Sample collected at diagnosis.


title: Patient 4533 AML118

description: Sample collected at diagnosis.


title: Patient 4531 AML116

description: Sample collected at diagnosis.


title: Patient 4548 AML121

description: Sample collected at diagnosis.


title: Patient 4530 AML115

description: Sample collected at diagnosis.


title: Patient 4534 AML119

description: Sample collected at diagnosis.


title: Patient 4529 AML114

description: Sample collected at diagnosis.


title: Patient 4511 AML110

description: Sample collected at diagnosis.


title: Patient 4532 AML117

description: Sample collected at diagnosis.


title: Patient 4503 AML107

description: Sample collected at diagnosis.


title: Patient 4501 AML106

description: Sample collected at diagnosis.


title: Patient 4728 AML150

description: Sample collected at diagnosis.


title: Patient 4735 AML156

description: Sample collected at diagnosis.


title: Patient 4508 AML109

description: Sample collected at diagnosis.


title: Patient 4507 AML108

description: Sample collected at diagnosis.


title: Patient 4527 AML112

description: Sample collected at diagnosis.


title: Patient 4525 AML111

description: Sample collected at diagnosis.


title: Patient 4559 AML126

description: Sample collected at diagnosis.


title: Patient 4450 AML101

description: Sample collected at diagnosis.


title: Patient 4447 AML99

description: Sample collected at diagnosis.


title: Patient 4445 AML97

description: Sample collected at diagnosis.


title: Patient 4444 AML96

description: Sample collected at diagnosis.


title: Patient 4451 AML102

description: Sample collected at diagnosis.


title: Patient 4448 AML100

description: Sample collected at diagnosis.


title: Patient 4500 AML105

description: Sample collected at diagnosis.


title: Patient 4446 AML98

description: Sample collected at diagnosis.


title: Patient 4427 AML93

description: Sample collected at diagnosis.


title: Patient 4420 AML89

description: Sample collected at diagnosis.


title: Patient 4415 AML85

description: Sample collected at diagnosis.


title: Patient 4425 AML92

description: Sample collected at diagnosis.


title: Patient 4431 AML94

description: Sample collected at diagnosis.


title: Patient 4432 AML95

description: Sample collected at diagnosis.


title: Patient 4414 AML84

description: Sample collected at diagnosis.


title: Patient 4423 AML91

description: Sample collected at diagnosis.


title: Patient 4416 AML86

description: Sample collected at diagnosis.


title: Patient 4422 AML90

description: Sample collected at diagnosis.


title: Patient 4412 AML83

description: Sample collected at diagnosis.


title: Patient 4499 AML104

description: Sample collected at diagnosis.


title: Patient 4408 AML81

description: Sample collected at diagnosis.


title: Patient 4403 AML79

description: Sample collected at diagnosis.


title: Patient 4405 AML80

description: Sample collected at diagnosis.


title: Patient 4417 AML87

description: Sample collected at diagnosis.


title: Patient 4400 AML77

description: Sample collected at diagnosis.


title: Patient 4409 AML82

description: Sample collected at diagnosis.


title: Patient 4399 AML76

description: Sample collected at diagnosis.


title: Patient 4395 AML74

description: Sample collected at diagnosis.


title: Patient 4394 AML73

description: Sample collected at diagnosis.


title: Patient 4418 AML88

description: Sample collected at diagnosis.


title: Patient 4401 AML78

description: Sample collected at diagnosis.


title: Patient 4383 AML69

description: Sample collected at diagnosis.


title: Patient 4385 AML71

description: Sample collected at diagnosis.


title: Patient 4382 AML68

description: Sample collected at diagnosis.


title: Patient 4392 AML72

description: Sample collected at diagnosis.


title: Patient 4380 AML67

description: Sample collected at diagnosis.


title: Patient 3476 AML39

description: Sample collected at diagnosis.


title: Patient 4384 AML70

description: Sample collected at diagnosis.


title: Patient 4372 AML64

description: Sample collected at diagnosis.


title: Patient 3495 AML42

description: Sample collected at diagnosis.


title: Patient 3496 AML43

description: Sample collected at diagnosis.


title: Patient 3474 AML37

description: Sample collected at diagnosis.


title: Patient 3494 AML41

description: Sample collected at diagnosis.


title: Patient 4370 AML63

description: Sample collected at diagnosis.


title: Patient 4373 AML65

description: Sample collected at diagnosis.


title: Patient 4367 AML62

description: Sample collected at diagnosis.


title: Patient 3445 AML30

description: Sample collected at diagnosis.


title: CLL cells  BM  patient #25

status: Public on Oct 01 2010

city: Bethesda

first: Adrian

last: Wiestner

state: MD

address: 10 Center Dr

department: Hematology Branch

institute: NHLBI/NIH

description: primary CLL cells

hyb_protocol: Fragmented RNA was assessed for relative length on Agilent 2100 bioanalyzer and hybridized to Affymetrix HG-U133 Plus 2.0 chips for 16 hours.

scan_protocol: Affymetrix GeneChip scanner

data_processing: Intensities were pre-processed with MAS5.0, and further processed with variance stablization transformation

source_name: BM derived CLL cells

label_protocol: Biotin labeled with Affymetrix's IVT labeling kits (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was extracted using Qiagen RNA extraction kit

value: CLL

tag: origin

value: Bone marrow

tag: patient

value: patient #25


title: CLL cells  BM  patient #26

description: primary CLL cells

value: patient #26


title: CLL cells  BM  patient #23

description: primary CLL cells

value: patient #23


title: CLL cells  BM  patient #19

description: primary CLL cells

value: patient #19


title: Patient 103 AML1

description: Sample collected at diagnosis.

value: bone marrow or peripheral blood


title: CLL cells  BM  patient #22

description: primary CLL cells

value: patient #22


title: Patient 2771 AML5

description: Sample collected at diagnosis.

value: Discovery

value: wild type


title: CLL cells  BM  patient #21

description: primary CLL cells

value: patient #21


title: Patient 3470 AML36

description: Sample collected at diagnosis.

value: remaining cytogenetics


title: CLL cells  BM  patient #13

description: primary CLL cells

value: patient #13


title: CLL cells  BM  patient #11

description: primary CLL cells

value: patient #11


title: CLL cells  BM  patient #10

description: primary CLL cells

value: patient #10


title: CLL cells  BM  patient #18

description: primary CLL cells

value: patient #18


title: CLL cells  BM  patient #9

description: primary CLL cells

value: patient #9


title: CLL cells  BM  patient #8

description: primary CLL cells

value: CLL

value: patient #8


title: CLL cells  BM  patient #16

description: primary CLL cells

value: Bone marrow

value: patient #16


title: CLL cells  BM  patient #12

description: primary CLL cells

value: patient #12


title: CLL cells  BM  patient #3

description: primary CLL cells

value: patient #3


title: Patient 4452 AML103

description: Sample collected at diagnosis.

value: bone marrow or peripheral blood

value: MLL-rearrangement


title: CLL cells  BM  patient #20

description: primary CLL cells

value: patient #20


title: CLL cells  BM  patient #1

description: primary CLL cells

value: patient #1


title: CLL cells  PB  patient #25

description: primary CLL cells

source_name: PB derived CLL cells

value: Peripheral blood

value: patient #25


title: CLL cells  BM  patient #2

description: primary CLL cells

value: patient #2


title: CLL cells  PB  patient #26

description: primary CLL cells

value: patient #26


title: CLL cells  BM  patient #4

description: primary CLL cells

value: patient #4


title: CLL cells  PB  patient #23

description: primary CLL cells

value: patient #23


title: CLL cells  PB  patient #18

description: primary CLL cells

value: patient #18


title: CLL cells  PB  patient #22

description: primary CLL cells

value: CLL

value: patient #22


title: CLL cells  PB  patient #20

description: primary CLL cells


title: CLL cells  PB  patient #13 replicate1

description: primary CLL cells

value: patient #13


title: CLL cells  PB  patient #21

description: primary CLL cells

value: patient #21


title: CLL cells  PB  patient #13 replicate2

description: primary CLL cells


title: CLL cells  PB  patient #24

description: primary CLL cells

value: patient #24


title: CLL cells  PB  patient #12

description: primary CLL cells

value: patient #12


title: Patient 4396 AML75

description: Sample collected at diagnosis.

value: bone marrow or peripheral blood

value: Validation

value: remaining cytogenetics

value: wild type

value: CEBPA


title: CLL cells  PB  patient #19

description: primary CLL cells

value: Peripheral blood

value: patient #19


title: CLL cells  PB  patient #11

description: primary CLL cells

value: patient #11


title: CLL cells  PB  patient #14

description: primary CLL cells

value: patient #14


title: CLL cells  PB  patient #16

description: primary CLL cells

value: patient #16


title: CLL cells  PB  patient #7

description: primary CLL cells

value: patient #7


title: CLL cells  PB  patient #2

description: primary CLL cells

value: CLL

value: patient #2


title: CLL cells  PB  patient #8

description: primary CLL cells

value: patient #8


title: CLL cells  PB  patient #5

description: primary CLL cells

value: patient #5


title: Patient 4770 AML166

status: Public on Jun 02 2010

description: Sample collected at diagnosis.

value: Discovery

value: MLL-rearrangement

value: C-KIT


title: CLL cells PB  patient #4 replicate1

description: primary CLL cells

value: patient #4


title: Patient 4806 AML168

description: Sample collected at diagnosis.

value: bone marrow or peripheral blood

value: unknown cytogenetics


title: Patient 4905 AML170

description: Sample collected at diagnosis.

value: remaining cytogenetics

value: wild type


title: Patient 4747 AML165

description: Sample collected at diagnosis.

value: Validation

value: CEBPA


title: CLL cells  PB  patient #6

description: primary CLL cells

value: Peripheral blood

value: patient #6


title: CLL cells  PB  patient #10

description: primary CLL cells

value: patient #10


title: Patient 4746 AML164

description: Sample collected at diagnosis.


title: Patient 4742 AML162

description: Sample collected at diagnosis.

value: N/K-RAS


title: CLL cells  PB  patient #9

description: primary CLL cells

value: CLL

value: patient #9


title: Patient 4805 AML167

description: Sample collected at diagnosis.


title: CLL cells  PB  patient #1

description: primary CLL cells

value: patient #1


title: Patient 4741 AML161

description: Sample collected at diagnosis.

value: Discovery


title: Patient 4875 AML169

description: Sample collected at diagnosis.


title: Patient 4738 AML159

description: Sample collected at diagnosis.


title: Patient 4740 AML160

description: Sample collected at diagnosis.

value: MLL-rearrangement


title: CLL cells  PB  patient #3

description: primary CLL cells

value: patient #3


title: Patient 4737 AML158

description: Sample collected at diagnosis.


title: CLL cells  PB patient #4 replicate2

description: primary CLL cells

value: patient #4


title: Patient 4734 AML155

description: Sample collected at diagnosis.

value: bone marrow or peripheral blood


title: Patient 4731 AML153

description: Sample collected at diagnosis.

value: CN-AML


title: Patient 4736 AML157

description: Sample collected at diagnosis.

value: remaining cytogenetics


title: H9_ES_1

status: Public on Jun 10 2010

first: Hu

last: Li

address: 3 Blackfan Circle

institute: Wyss Institute

description: Gene expression data obtained from human ES

hyb_protocol: cDNA was fragmented and 10ug hybridized to an Affymetrix U133 Plus 2.0 array for 16 hours. Arrays were washed and stained using the Affy 450 Fluidics Station according to the manufacturer's protocol

scan_protocol: Arrays were scanned using a GeneChip 3000 scanner according to the manufacturers recommendation

data_processing: RMA (Bioconductor Affy and RMA Packages).

source_name: human ES

label_protocol: Preparation of biotinylated cDNA was performed according to the standard Nugen amplification sample preparation protocol, starting with 100ng of total RNA

growth_protocol: standard HESC growth conditions as described in Pick et al. (2009).

extract_protocol: Trizol isolation followed by Rneasy (Qiagen) column purification were performed according to manufacturer's specifications

value: ES

tag: cell line

value: H9 Human embryonic stem cells


title: Patient 4730 AML152

description: Sample collected at diagnosis.

value: wild type


title: Patient 3475 AML38

description: Sample collected at diagnosis.

value: unknown cytogenetics


title: Patient 4733 AML154

description: Sample collected at diagnosis.


title: Patient 4729 AML151

description: Sample collected at diagnosis.


title: Patient 4716 AML146

description: Sample collected at diagnosis.

value: Validation


title: Patient 4721 AML149

description: Sample collected at diagnosis.

value: MLL-PTD


title: Patient 4720 AML148

description: Sample collected at diagnosis.


title: Patient 4708 AML140

description: Sample collected at diagnosis.


title: Patient 4715 AML145

description: Sample collected at diagnosis.

value: N/K-RAS


title: Patient 4703 AML137

description: Sample collected at diagnosis.


title: Patient 4712 AML142

description: Sample collected at diagnosis.


title: Patient 4710 AML141

description: Sample collected at diagnosis.


title: Patient 4713 AML143

description: Sample collected at diagnosis.


title: Patient 4717 AML147

description: Sample collected at diagnosis.


title: Patient 4714 AML144

description: Sample collected at diagnosis.

value: CEBPA


title: Patient 4601 AML130

description: Sample collected at diagnosis.


title: Patient 4603 AML131

description: Sample collected at diagnosis.


title: Patient 4702 AML136

description: Sample collected at diagnosis.


title: Patient 4576 AML129

description: Sample collected at diagnosis.


title: Patient 4701 AML135

description: Sample collected at diagnosis.


title: Patient 4699 AML133

description: Sample collected at diagnosis.


title: Patient 4700 AML134

description: Sample collected at diagnosis.


title: Patient 4567 AML128

description: Sample collected at diagnosis.

value: C-KIT


title: Patient 4561 AML127

description: Sample collected at diagnosis.


title: Patient 4744 AML163

description: Sample collected at diagnosis.


title: Patient 4704 AML138

description: Sample collected at diagnosis.


title: Patient 4555 AML124

description: Sample collected at diagnosis.


title: Patient 4557 AML125

description: Sample collected at diagnosis.


title: Patient 4554 AML123

description: Sample collected at diagnosis.


title: Patient 4218 AML60

description: Sample collected at diagnosis.


title: Patient 4375 AML66

description: Sample collected at diagnosis.


title: Patient 4102 AML56

description: Sample collected at diagnosis.


title: Patient 4549 AML122

description: Sample collected at diagnosis.


title: Patient 4128 AML58

description: Sample collected at diagnosis.


title: Patient 4079 AML45

description: Sample collected at diagnosis.


title: Patient 4216 AML59

description: Sample collected at diagnosis.


title: Patient 4127 AML57

description: Sample collected at diagnosis.


title: Patient 4094 AML53

description: Sample collected at diagnosis.


title: Patient 4089 AML50

description: Sample collected at diagnosis.


title: Patient 4297 AML61

description: Sample collected at diagnosis.


title: Patient 3450 AML34

description: Sample collected at diagnosis.


title: Patient 4087 AML48

description: Sample collected at diagnosis.


title: Patient 4090 AML51

description: Sample collected at diagnosis.


title: Patient 4098 AML55

description: Sample collected at diagnosis.


title: Patient 4092 AML52

description: Sample collected at diagnosis.


title: Patient 3864 AML44

description: Sample collected at diagnosis.


title: Patient 3492 AML40

description: Sample collected at diagnosis.


title: Patient 4096 AML54

description: Sample collected at diagnosis.


title: Patient 3451 AML35

description: Sample collected at diagnosis.


title: Patient 4085 AML47

description: Sample collected at diagnosis.


title: Patient 4088 AML49

description: Sample collected at diagnosis.


title: Patient 3448 AML33

description: Sample collected at diagnosis.


title: Patient 3447 AML32

description: Sample collected at diagnosis.


title: Patient 3446 AML31

description: Sample collected at diagnosis.


title: Patient 4084 AML46

description: Sample collected at diagnosis.


title: Patient 3444 AML29

description: Sample collected at diagnosis.


title: Patient 4706 AML139

description: Sample collected at diagnosis.


title: Patient 3439 AML26

description: Sample collected at diagnosis.


title: Patient 3442 AML27

description: Sample collected at diagnosis.


title: Patient 3443 AML28

description: Sample collected at diagnosis.


title: Patient 3433 AML21

description: Sample collected at diagnosis.


title: Patient 3435 AML23

description: Sample collected at diagnosis.


title: Patient 3436 AML24

description: Sample collected at diagnosis.


title: Patient 3434 AML22

description: Sample collected at diagnosis.


title: Patient 3438 AML25

description: Sample collected at diagnosis.


title: Patient 3421 AML20

description: Sample collected at diagnosis.


title: Patient 3418 AML18

description: Sample collected at diagnosis.


title: Patient 3420 AML19

description: Sample collected at diagnosis.


title: Patient 3414 AML16

description: Sample collected at diagnosis.


title: Patient 3411 AML14

description: Sample collected at diagnosis.


title: Patient 3410 AML13

description: Sample collected at diagnosis.


title: Patient 3415 AML17

description: Sample collected at diagnosis.


title: Patient 3186 AML6

description: Sample collected at diagnosis.


title: Patient 3396 AML8

description: Sample collected at diagnosis.


title: Patient 3412 AML15

description: Sample collected at diagnosis.


title: Patient 3397 AML9

description: Sample collected at diagnosis.


title: Patient 3399 AML11

description: Sample collected at diagnosis.


title: Patient 3398 AML10

description: Sample collected at diagnosis.


title: Patient 2761 AML4

description: Sample collected at diagnosis.


title: Patient 3400 AML12

description: Sample collected at diagnosis.


title: Patient_8549_relapse

status: Public on Mar 10 2010

city: Wageningen

first: Dick

middle: de

last: de Ridder

address: Droevendaalsesteeg 1

department: Plant Sciences

institute: Wageningen University

hyb_protocol: Affymetrix standard 16 hours at 45 C Hybridization Oven 640

scan_protocol: GeneChip® Scanner 3000; GCOSv1

data_processing: Data were quantile normalized and RMA was used for probeset summarization; when subsets were analysed, these were individually normalized and summarized. Differential expression was assessed using SAM (Significance Analysis of Microarrays). All analyses were performed in Matlab; the code is available upon request.

source_name: leukemic cells, purified using CD19 beads on autoMACS

label_protocol: Afymetrix one cycle labeling kit

extract_protocol: Qiagen RNAesy plus shredder

value: leukemic lymphoblasts

tag: disease status

value: Acute Lymphoblastic Leukemia (ALL)

tag: all type

value: Precursor-B-ALL

tag: all subtype

value: Common ALL

tag: gender

value: male

tag: relapse type

value: isolated bone marrow

tag: months to relapse

tag: conclusions ig/tcr

value: stable

tag: selected

value: yes


title: Patient 4698 AML132

description: Sample collected at diagnosis.

tag: tissue

value: bone marrow or peripheral blood

tag: patient id

tag: cohort

value: Discovery


title: Patient_8173_relapse

source_name: leukemic cells, purified using CD7 beads on autoMACS

tag: cell type

value: T-ALL

value: female

value: combined

value: no


title: Patient 3363 AML7

description: Sample collected at diagnosis.

value: Validation

tag: karyotype

value: MLL-rearrangement

value: wild type

tag: c-kit

tag: n/k-ras

value: N/K-RAS

tag: cebpa


title: Patient 1583 AML2

description: Sample collected at diagnosis.

tag: mll-ptd


title: Patient 1732 AML3

description: Sample collected at diagnosis.


title: Patient_7300_relapse

value: leukemic lymphoblasts

tag: disease status

value: Acute Lymphoblastic Leukemia (ALL)


title: Patient_8148_relapse

tag: all type


title: Patient_8711_relapse

tag: all subtype


title: Patient_6633_relapse

value: Precursor-B-ALL

value: Pro-B-ALL

tag: gender


title: Patient_7263_relapse

value: Common ALL

value: male

tag: relapse type

value: some clonal evolution


title: Patient_8198_relapse

value: isolated bone marrow

tag: months to relapse

value: stable

value: yes


title: Patient_6584_relapse

value: T-ALL

tag: conclusions ig/tcr


title: Patient_6411_relapse

tag: selected


title: Patient_5978_relapse

value: unstable


title: Patient_6417_relapse

value: Pre-B-ALL


title: Patient_6345_relapse

value: female

value: combined

value: no


title: Patient_6051_relapse


title: Patient_5775_relapse


title: Patient_6083_relapse


title: Patient_4785_relapse


title: Patient_6329_relapse


title: Patient_8711_diagnosis


title: Patient_8173_diagnosis


title: Patient_7300_diagnosis


title: Patient_4727_relapse


title: Patient_5370_relapse


title: Patient_8198_diagnosis


title: Patient_6345_diagnosis


title: Patient_8148_diagnosis


title: Patient_5370_diagnosis


title: Patient_5775_diagnosis


title: Patient_5978_diagnosis


title: Patient_6892_diagnosis


title: Patient_4785_diagnosis


title: Patient_6051_diagnosis


title: Patient_6329_diagnosis


title: Patient_8549_diagnosis


title: Patient_6558_diagnosis


title: Patient_5818_diagnosis


title: Patient_6417_diagnosis