title: AML Patient A158_T Diagnostic

source_name: AML Patient A158 Diagnostic

value: Patient A158


title: AML Patient A161_N Remission

status: Public on Apr 10 2017

type: genomic

city: Philadelphia, PA

first: Richard

last: Aplenc

state: PA

address: 3501 Civic Center Blvd

department: Division of Oncology

country: USA

institute: Children's Hospital of Philadelphia

description: hybridized to Genome-Wide Human SNP 6.0 Array

hyb_protocol: Samples were hybridized for 16-18 hr and washed and stained on the GeneChip fluidics station 450 using the appropriate fluidics protocol.

scan_protocol: The arrays were inserted into the Affymetrix autoloader carousel and scanned using the GeneChip Scanner 3000 7G.

data_processing: Genotyping Console 3.02 was used for data processing and GeneChip quality control. Data quality control and data analysis was performed using Partek GS 6.4.  SNP calls were made using Birdseed V-2.  Copy number calls of SNP 6.0  data were determined using R package ASCAT (van Loo et al, PNAS 2010).

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: AML Patient A161 Remission

label_protocol: Samples were end labeled using terminal deoxynucleotidyl transferase according to the Affymetrix protocol.

extract_protocol: Genomic DNA was isolated with phenol extraction according to the standard protocol (Sambrook, J., Fritsch, E. F. & Maniatis, T. Molecular cloning; a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989).

tag: disease state

value: AML

tag: individual

value: Patient A161

tag: tissue

value: Bone Marrow

tag: patient status

value: Remission


title: AML Patient A160_N Remission

source_name: AML Patient A160 Remission

value: Patient A160


title: AML Patient A159_N Remission

source_name: AML Patient A159 Remission

value: Patient A159


title: AML Patient A156_N Remission

source_name: AML Patient A156 Remission

value: Patient A156


title: AML Patient A160_T Diagnostic

source_name: AML Patient A160 Diagnostic

value: Diagnostic


title: AML Patient A158_N Remission

source_name: AML Patient A158 Remission


title: AML Patient A155_T Diagnostic

source_name: AML Patient A155 Diagnostic

value: Patient A155


title: AML Patient A168_N Remission

source_name: AML Patient A168 Remission

value: Patient A168


title: AML Patient A154_N Remission

source_name: AML Patient A154 Remission

value: Patient A154


title: AML Patient A155_N Remission

source_name: AML Patient A155 Remission


title: AML Patient A156_T Diagnostic

source_name: AML Patient A156 Diagnostic


title: AML Patient A159_T Diagnostic

source_name: AML Patient A159 Diagnostic


title: AML Patient A157_N Remission

source_name: AML Patient A157 Remission

value: Patient A157


title: AML Patient A153_T Diagnostic

source_name: AML Patient A153 Diagnostic

value: Patient A153


title: AML Patient A154_T Diagnostic

source_name: AML Patient A154 Diagnostic


title: AML Patient A152_N Remission

source_name: AML Patient A152 Remission

value: Patient A152


title: AML Patient A152_T Diagnostic

source_name: AML Patient A152 Diagnostic


title: AML Patient A165_T Diagnostic

source_name: AML Patient A165 Diagnostic

value: Patient A165


title: AML Patient A151_T Diagnostic

source_name: AML Patient A151 Diagnostic

value: Patient A151


title: AML Patient A153_N Remission

source_name: AML Patient A153 Remission


title: AML Patient A150_T Diagnostic

source_name: AML Patient A150 Diagnostic

value: Patient A150


title: AML Patient A150_N Remission

source_name: AML Patient A150 Remission

value: AML


title: AML Patient A146_T Diagnostic

source_name: AML Patient A146 Diagnostic

value: Patient A146


title: AML Patient A151_N Remission

source_name: AML Patient A151 Remission

value: Bone Marrow


title: AML Patient A147_N Remission

source_name: AML Patient A147 Remission

value: Patient A147

value: Remission


title: AML Patient A146_N Remission

source_name: AML Patient A146 Remission


title: AML Patient A149_T Diagnostic

source_name: AML Patient A149 Diagnostic

value: Patient A149


title: AML Patient A149_N Remission

source_name: AML Patient A149 Remission


title: AML Patient A147_T Diagnostic

source_name: AML Patient A147 Diagnostic


title: AML Patient A145_T Diagnostic

source_name: AML Patient A145 Diagnostic

value: Patient A145


title: AML Patient A148_N Remission

source_name: AML Patient A148 Remission

value: Patient A148


title: AML Patient A140_N Remission

source_name: AML Patient A140 Remission

value: Patient A140


title: AML Patient A144_N Remission

source_name: AML Patient A144 Remission

value: Patient A144


title: AML Patient A143_N Remission

source_name: AML Patient A143 Remission

value: Patient A143


title: AML Patient A143_T Diagnostic

source_name: AML Patient A143 Diagnostic

value: Diagnostic


title: AML Patient A141_N Remission

source_name: AML Patient A141 Remission

value: Patient A141


title: AML Patient A141_T Diagnostic

source_name: AML Patient A141 Diagnostic


title: AML Patient A139_T Diagnostic

source_name: AML Patient A139 Diagnostic

value: Patient A139


title: AML Patient A145_N Remission

source_name: AML Patient A145 Remission


title: AML Patient A142_N Remission

source_name: AML Patient A142 Remission

value: Patient A142


title: AML Patient A140_T Diagnostic

source_name: AML Patient A140 Diagnostic


title: AML Patient A148_T Diagnostic

source_name: AML Patient A148 Diagnostic


title: AML Patient A139_N Remission

source_name: AML Patient A139 Remission


title: AML Patient A142_T Diagnostic

source_name: AML Patient A142 Diagnostic


title: AML Patient A137_N Remission

source_name: AML Patient A137 Remission

value: Patient A137


title: AML Patient A137_T Diagnostic

source_name: AML Patient A137 Diagnostic


title: AML Patient A138_N Remission

source_name: AML Patient A138 Remission

value: Patient A138


title: AML Patient A144_T Diagnostic

source_name: AML Patient A144 Diagnostic

value: AML


title: AML Patient A136_N Remission

source_name: AML Patient A136 Remission

value: Patient A136


title: AML Patient A136_T Diagnostic

source_name: AML Patient A136 Diagnostic

value: Bone Marrow


title: AML Patient A135_T Diagnostic

source_name: AML Patient A135 Diagnostic

value: Patient A135


title: AML Patient A133_T Diagnostic

source_name: AML Patient A133 Diagnostic

value: Patient A133


title: AML Patient A138_T Diagnostic

source_name: AML Patient A138 Diagnostic


title: AML Patient A133_N Remission

source_name: AML Patient A133 Remission

value: Remission


title: AML Patient A132_T Diagnostic

source_name: AML Patient A132 Diagnostic

value: Patient A132


title: AML Patient A131_T Diagnostic

source_name: AML Patient A131 Diagnostic

value: Patient A131


title: AML Patient A129_N Remission

source_name: AML Patient A129 Remission

value: Patient A129


title: AML Patient A134_T Diagnostic

source_name: AML Patient A134 Diagnostic

value: Patient A134


title: AML Patient A132_N Remission

source_name: AML Patient A132 Remission


title: AML Patient A128_N Remission

source_name: AML Patient A128 Remission

value: Patient A128


title: AML Patient A129_T Diagnostic

source_name: AML Patient A129 Diagnostic

value: Diagnostic


title: AML Patient A131_N Remission

source_name: AML Patient A131 Remission


title: AML Patient A128_T Diagnostic

source_name: AML Patient A128 Diagnostic


title: AML Patient A134_N Remission

source_name: AML Patient A134 Remission


title: AML Patient A135_N Remission

source_name: AML Patient A135 Remission


title: AML Patient A130_N Remission

source_name: AML Patient A130 Remission

value: Patient A130


title: AML Patient A125_N Remission

source_name: AML Patient A125 Remission

value: Patient A125


title: AML Patient A124_T Diagnostic

source_name: AML Patient A124 Diagnostic

value: Patient A124


title: AML Patient A125_T Diagnostic

source_name: AML Patient A125 Diagnostic


title: AML Patient A127_N Remission

source_name: AML Patient A127 Remission

value: Patient A127


title: AML Patient A127_T Diagnostic

source_name: AML Patient A127 Diagnostic


title: AML Patient A126_T Diagnostic

source_name: AML Patient A126 Diagnostic

value: Patient A126


title: AML Patient A126_N Remission

source_name: AML Patient A126 Remission

value: AML


title: AML Patient A124_N Remission

source_name: AML Patient A124 Remission


title: AML Patient A123_N Remission

source_name: AML Patient A123 Remission

value: Patient A123


title: AML Patient A122_N Remission

source_name: AML Patient A122 Remission

value: Patient A122

value: Bone Marrow


title: AML Patient A130_T Diagnostic

source_name: AML Patient A130 Diagnostic


title: AML Patient A121_T Diagnostic

source_name: AML Patient A121 Diagnostic

value: Patient A121


title: AML Patient A120_T Diagnostic

source_name: AML Patient A120 Diagnostic

value: Patient A120


title: AML Patient A123_T Diagnostic

source_name: AML Patient A123 Diagnostic


title: AML Patient A119_T Diagnostic

source_name: AML Patient A119 Diagnostic

value: Patient A119


title: AML Patient A119_N Remission

source_name: AML Patient A119 Remission

value: Remission


title: AML Patient A118_T Diagnostic

source_name: AML Patient A118 Diagnostic

value: Patient A118


title: AML Patient A118_N Remission

source_name: AML Patient A118 Remission


title: AML Patient A122_T Diagnostic

source_name: AML Patient A122 Diagnostic


title: AML Patient A121_N Remission

source_name: AML Patient A121 Remission


title: AML Patient A120_N Remission

source_name: AML Patient A120 Remission


title: AML Patient A117_N Remission

source_name: AML Patient A117 Remission

value: Patient A117


title: AML Patient A114_T Diagnostic

source_name: AML Patient A114 Diagnostic

value: Patient A114


title: AML Patient A116_T Diagnostic

source_name: AML Patient A116 Diagnostic

value: Patient A116

value: Diagnostic


title: AML Patient A115_N Remission

source_name: AML Patient A115 Remission

value: Patient A115


title: AML Patient A117_T Diagnostic

source_name: AML Patient A117 Diagnostic


title: AML Patient A113_T Diagnostic

source_name: AML Patient A113 Diagnostic

value: Patient A113


title: AML Patient A115_T Diagnostic

source_name: AML Patient A115 Diagnostic


title: AML Patient A114_N Remission

source_name: AML Patient A114 Remission


title: AML Patient A112_T Diagnostic

source_name: AML Patient A112 Diagnostic

value: Patient A112


title: AML Patient A111_T Diagnostic

source_name: AML Patient A111 Diagnostic

value: Patient A111


title: AML Patient A113_N Remission

source_name: AML Patient A113 Remission

value: AML


title: AML Patient A116_N Remission

source_name: AML Patient A116 Remission


title: AML Patient A109_T Diagnostic

source_name: AML Patient A109 Diagnostic

value: Patient A109


title: AML Patient A110_N Remission

source_name: AML Patient A110 Remission

value: Patient A110


title: AML Patient A111_N Remission

source_name: AML Patient A111 Remission

value: Bone Marrow


title: AML Patient A112_N Remission

source_name: AML Patient A112 Remission


title: AML Patient A107_T Diagnostic

source_name: AML Patient A107 Diagnostic

value: Patient A107


title: AML Patient A109_N Remission

source_name: AML Patient A109 Remission


title: AML Patient A108_T Diagnostic

source_name: AML Patient A108 Diagnostic

value: Patient A108


title: AML Patient A108_N Remission

source_name: AML Patient A108 Remission


title: AML Patient A110_T Diagnostic

source_name: AML Patient A110 Diagnostic


title: AML Patient A104_T Diagnostic

source_name: AML Patient A104 Diagnostic

value: Patient A104


title: AML Patient A105_N Remission

source_name: AML Patient A105 Remission

value: Patient A105

value: Remission


title: AML Patient A106_N Remission

source_name: AML Patient A106 Remission

value: Patient A106


title: AML Patient A106_T Diagnostic

source_name: AML Patient A106 Diagnostic


title: AML Patient A107_N Remission

source_name: AML Patient A107 Remission


title: AML Patient A103_N Remission

source_name: AML Patient A103 Remission

value: Patient A103


title: AML Patient A103_T Diagnostic

source_name: AML Patient A103 Diagnostic


title: AML Patient A100_T Diagnostic

source_name: AML Patient A100 Diagnostic

value: Patient A100


title: AML Patient A104_N Remission

source_name: AML Patient A104 Remission


title: AML Patient A105_T Diagnostic

source_name: AML Patient A105 Diagnostic

value: Diagnostic


title: AML Patient A099_N Remission

source_name: AML Patient A099 Remission

value: Patient A099


title: AML Patient A102_N Remission

source_name: AML Patient A102 Remission

value: Patient A102


title: AML Patient A101_N Remission

source_name: AML Patient A101 Remission

value: Patient A101


title: AML Patient A098_T Diagnostic

source_name: AML Patient A098 Diagnostic

value: Patient A098


title: AML Patient A100_N Remission

source_name: AML Patient A100 Remission

value: AML


title: AML Patient A102_T Diagnostic

source_name: AML Patient A102 Diagnostic


title: AML Patient A099_T Diagnostic

source_name: AML Patient A099 Diagnostic


title: AML Patient A097_N Remission

source_name: AML Patient A097 Remission

value: Patient A097


title: AML Patient A097_T Diagnostic

source_name: AML Patient A097 Diagnostic


title: AML Patient A096_T Diagnostic

source_name: AML Patient A096 Diagnostic

value: Patient A096


title: AML Patient A095_T Diagnostic

source_name: AML Patient A095 Diagnostic

value: Patient A095

value: Bone Marrow


title: AML Patient A096_N Remission

source_name: AML Patient A096 Remission


title: AML Patient A101_T Diagnostic

source_name: AML Patient A101 Diagnostic


title: AML Patient A098_N Remission

source_name: AML Patient A098 Remission


title: AML Patient A094_T Diagnostic

source_name: AML Patient A094 Diagnostic

value: Patient A094


title: AML Patient A095_N Remission

source_name: AML Patient A095 Remission


title: AML Patient A094_N Remission

source_name: AML Patient A094 Remission


title: AML Patient A093_T Diagnostic

source_name: AML Patient A093 Diagnostic

value: Patient A093


title: AML Patient A092_T Diagnostic

source_name: AML Patient A092 Diagnostic

value: Patient A092


title: AML Patient A093_N Remission

source_name: AML Patient A093 Remission

value: Remission


title: AML Patient A090_T Diagnostic

source_name: AML Patient A090 Diagnostic

value: Patient A090


title: AML Patient A091_T Diagnostic

source_name: AML Patient A091 Diagnostic

value: Patient A091


title: AML Patient A088_N Remission

source_name: AML Patient A088 Remission

value: Patient A088


title: AML Patient A087_T Diagnostic

source_name: AML Patient A087 Diagnostic

value: Patient A087

value: Diagnostic


title: AML Patient A088_T Diagnostic

source_name: AML Patient A088 Diagnostic


title: AML Patient A089_N Remission

source_name: AML Patient A089 Remission

value: Patient A089


title: AML Patient A087_N Remission

source_name: AML Patient A087 Remission


title: AML Patient A090_N Remission

source_name: AML Patient A090 Remission


title: AML Patient A091_N Remission

source_name: AML Patient A091 Remission


title: AML Patient A086_N Remission

source_name: AML Patient A086 Remission

value: Patient A086


title: AML Patient A084_T Diagnostic

source_name: AML Patient A084 Diagnostic

value: Patient A084


title: AML Patient A085_T Diagnostic

source_name: AML Patient A085 Diagnostic

value: AML

value: Patient A085


title: AML Patient A085_N Remission

source_name: AML Patient A085 Remission


title: AML Patient A089_T Diagnostic

source_name: AML Patient A089 Diagnostic


title: AML Patient A083_T Diagnostic

source_name: AML Patient A083 Diagnostic

value: Patient A083


title: AML Patient A081_T Diagnostic

source_name: AML Patient A081 Diagnostic

value: Patient A081


title: AML Patient A082_T Diagnostic

source_name: AML Patient A082 Diagnostic

value: Patient A082

value: Bone Marrow


title: AML Patient A083_N Remission

source_name: AML Patient A083 Remission


title: AML Patient A082_N Remission

source_name: AML Patient A082 Remission


title: AML Patient A086_T Diagnostic

source_name: AML Patient A086 Diagnostic


title: AML Patient A084_N Remission

source_name: AML Patient A084 Remission


title: AML Patient A080_N Remission

source_name: AML Patient A080 Remission

value: Patient A080


title: AML Patient A080_T Diagnostic

source_name: AML Patient A080 Diagnostic


title: AML Patient A078_T Diagnostic

source_name: AML Patient A078 Diagnostic

value: Patient A078


title: AML Patient A081_N Remission

source_name: AML Patient A081 Remission

value: Remission


title: AML Patient A092_N Remission

source_name: AML Patient A092 Remission

value: Patient A092


title: AML Patient A079_N Remission

source_name: AML Patient A079 Remission

value: Patient A079


title: AML Patient A076_T Diagnostic

source_name: AML Patient A076 Diagnostic

value: Patient A076


title: AML Patient A077_T Diagnostic

source_name: AML Patient A077 Diagnostic

value: Patient A077


title: AML Patient A077_N Remission

source_name: AML Patient A077 Remission


title: AML Patient A076_N Remission

source_name: AML Patient A076 Remission


title: AML Patient A075_T Diagnostic

source_name: AML Patient A075 Diagnostic

value: Patient A075

value: Diagnostic


title: AML Patient A079_T Diagnostic

source_name: AML Patient A079 Diagnostic


title: AML Patient A078_N Remission

source_name: AML Patient A078 Remission


title: AML Patient A075_N Remission

source_name: AML Patient A075 Remission


title: AML Patient A073_T Diagnostic

source_name: AML Patient A073 Diagnostic

value: Patient A073


title: AML Patient A074_T Diagnostic

source_name: AML Patient A074 Diagnostic

value: Patient A074


title: AML Patient A072_T Diagnostic

source_name: AML Patient A072 Diagnostic

value: AML

value: Patient A072


title: AML Patient A074_N Remission

source_name: AML Patient A074 Remission


title: AML Patient A069_T Diagnostic

source_name: AML Patient A069 Diagnostic

value: Patient A069


title: AML Patient A073_N Remission

source_name: AML Patient A073 Remission


title: AML Patient A071_N Remission

source_name: AML Patient A071 Remission

value: Patient A071


title: AML Patient A072_N Remission

source_name: AML Patient A072 Remission


title: AML Patient A069_N Remission

source_name: AML Patient A069 Remission


title: AML Patient A071_T Diagnostic

source_name: AML Patient A071 Diagnostic


title: AML Patient A070_T Diagnostic

source_name: AML Patient A070 Diagnostic

value: Patient A070


title: AML Patient A070_N Remission

source_name: AML Patient A070 Remission

value: Bone Marrow


title: AML Patient A068_N Remission

source_name: AML Patient A068 Remission

value: Patient A068


title: AML Patient A067_N Remission

source_name: AML Patient A067 Remission

value: Patient A067


title: AML Patient A068_T Diagnostic

source_name: AML Patient A068 Diagnostic


title: AML Patient A066_T Diagnostic

source_name: AML Patient A066 Diagnostic

value: Patient A066


title: AML Patient A065_N Remission

source_name: AML Patient A065 Remission

value: Patient A065

value: Remission


title: AML Patient A067_T Diagnostic

source_name: AML Patient A067 Diagnostic


title: AML Patient A063_T Diagnostic

source_name: AML Patient A063 Diagnostic

value: Patient A063


title: AML Patient A064_N Remission

source_name: AML Patient A064 Remission

value: Patient A064


title: AML Patient A063_N Remission

source_name: AML Patient A063 Remission


title: AML Patient A064_T Diagnostic

source_name: AML Patient A064 Diagnostic


title: AML Patient A066_N Remission

source_name: AML Patient A066 Remission


title: AML Patient A062_T Diagnostic

source_name: AML Patient A062 Diagnostic

value: Patient A062


title: AML Patient A060_T Diagnostic

source_name: AML Patient A060 Diagnostic

value: Patient A060

value: Diagnostic


title: AML Patient A065_T Diagnostic

source_name: AML Patient A065 Diagnostic


title: AML Patient A058_T Diagnostic

source_name: AML Patient A058 Diagnostic

value: Patient A058


title: AML Patient A061_T Diagnostic

source_name: AML Patient A061 Diagnostic

value: AML

value: Patient A061


title: AML Patient A059_N Remission

source_name: AML Patient A059 Remission

value: Patient A059


title: AML Patient A057_T Diagnostic

source_name: AML Patient A057 Diagnostic

value: Patient A057


title: AML Patient A058_N Remission

source_name: AML Patient A058 Remission


title: AML Patient A057_N Remission

source_name: AML Patient A057 Remission


title: AML Patient A056_T Diagnostic

source_name: AML Patient A056 Diagnostic

value: Patient A056


title: AML Patient A062_N Remission

source_name: AML Patient A062 Remission

value: Bone Marrow


title: AML Patient A055_T Diagnostic

source_name: AML Patient A055 Diagnostic

value: Patient A055


title: AML Patient A061_N Remission

source_name: AML Patient A061 Remission


title: AML Patient A059_T Diagnostic

source_name: AML Patient A059 Diagnostic


title: AML Patient A054_N Remission

source_name: AML Patient A054 Remission

value: Patient A054


title: AML Patient A060_N Remission

source_name: AML Patient A060 Remission


title: AML Patient A053_T Diagnostic

source_name: AML Patient A053 Diagnostic

value: Patient A053


title: AML Patient A052_N Remission

source_name: AML Patient A052 Remission

value: Patient A052


title: AML Patient A056_N Remission

source_name: AML Patient A056 Remission

value: Remission


title: AML Patient A055_N Remission

source_name: AML Patient A055 Remission


title: AML Patient A053_N Remission

source_name: AML Patient A053 Remission


title: AML Patient A054_T Diagnostic

source_name: AML Patient A054 Diagnostic


title: AML Patient A052_T Diagnostic

source_name: AML Patient A052 Diagnostic


title: AML Patient A050_N Remission

source_name: AML Patient A050 Remission

value: Patient A050


title: AML Patient A051_T Diagnostic

source_name: AML Patient A051 Diagnostic

value: Patient A051


title: AML Patient A051_N Remission

source_name: AML Patient A051 Remission


title: AML Patient A049_N Remission

source_name: AML Patient A049 Remission

value: Patient A049


title: AML Patient A048_N Remission

source_name: AML Patient A048 Remission

value: Patient A048


title: AML Patient A047_N Remission

source_name: AML Patient A047 Remission

value: Patient A047


title: AML Patient A047_T Diagnostic

source_name: AML Patient A047 Diagnostic

value: Diagnostic


title: AML Patient A049_T Diagnostic

source_name: AML Patient A049 Diagnostic

value: AML


title: AML Patient A045_T Diagnostic

source_name: AML Patient A045 Diagnostic

value: Patient A045


title: AML Patient A048_T Diagnostic

source_name: AML Patient A048 Diagnostic


title: AML Patient A046_T Diagnostic

source_name: AML Patient A046 Diagnostic

value: Patient A046


title: AML Patient A046_N Remission

source_name: AML Patient A046 Remission


title: AML Patient A042_T Diagnostic

source_name: AML Patient A042 Diagnostic

value: Patient A042


title: AML Patient A043_T Diagnostic

source_name: AML Patient A043 Diagnostic

value: Patient A043


title: AML Patient A044_T Diagnostic

source_name: AML Patient A044 Diagnostic

value: Patient A044

value: Bone Marrow


title: AML Patient A042_N Remission

source_name: AML Patient A042 Remission


title: AML Patient A043_N Remission

source_name: AML Patient A043 Remission


title: gamma delta T cells GFP-_rep3

type: RNA

city: Hannover

first: Ciro

last: Novaes Rosa Lino

address: Carl-Neuberg-Str. 1

department: Immunology

country: Germany

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent Technologies), except that 350ng (M4794, M4795, M4796, M4802) or 100ng (M4872-M4873) of each cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing:
Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’. Processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) were normalized by global linear scaling: All gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray (‘Array I’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i).  Measurements of on-chip replicates (quadruplicates) were averaged using the geometric mean of normalized gPS values to retrieve one resulting value per probe and sample. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lie outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.  A lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed to 15. All of those normalized gPS values that fell below this intensity border were substituted by the respective surrogate value of 15.
Normalized processed signal intensity values (non-log), averaged across on-chip replicates / quadruplicate measurements. Measurements of control features were removed.

molecule: total RNA

organism: Mus musculus

source_name: Spleen

label_protocol: 9 ng or 4 ng of total RNA were used to prepare aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp™ II Kit; #AM1753; Life Technologies) as directed by the company (applying one-round of amplification). The labeling of aaUTP-cRNA was performed by use of Alexa Fluor 555 Reactive Dye (#A32756; LifeTechnologies). Prior to the reverse transcription reaction, 1µl of a 1:100000 dilution of Agilent’s ‘One-Color spike-in Kit stock solution’ (#5188-5282, Agilent Technologies) was added to each total RNA sample.

extract_protocol: Total RNA was extracted by use of the RNeasy Micro Kit (Qiagen).

treatment_protocol: Cells were isolated from spleen of Eomes-IRES-GFP (Eomestm1.1Twa). Before the sorting γδ T cells were enriched by the depletion of B220+ CD4+ and CD8β+ cells using the autoMACS Pro Separator (Miltenyi Biotec). Cell populations were sorted through the FACSAria IIu flow cytometer (Becton Dickinson) as Eomes+ (TCRβ‒ TCRγδ+ CD3+ GFP+) or Eomes‒ (TCRβ‒ TCRγδ+ CD3+ GFP‒). The following antibodies were used against CD3 (clone 17A2), TCRβ (clone REA318), TCRγδ (clone GL3), B220 (clone RA3-3A1), CD4 (clone RMCD4) and CD8β (clone RM-CD8). Immediatelly after sorting the RNA of the cells was extracted using the RNeasy® Micro Kit (Qiagen).

value: Spleen

tag: age

value: 7.5 weeks

tag: strain

value: Eomes-IRES-GFP

tag: background strain

tag: cell type

value: Eomes‒ γδ T cells

tag: rna input amount

value: 4 ng


title: AML Patient A040_T Diagnostic

source_name: AML Patient A040 Diagnostic

value: Patient A040


title: gamma delta T cells GFP+_rep3

value: Eomes+ γδ T cells


title: AML Patient A045_N Remission

source_name: AML Patient A045 Remission

value: Remission


title: AML Patient A044_N Remission

source_name: AML Patient A044 Remission


title: gamma delta T cells GFP-_rep2

value: 9.5 weeks

value: 9 ng


title: AML Patient A041_N Remission

source_name: AML Patient A041 Remission

value: AML

value: Patient A041


title: AML Patient A039_T Diagnostic

source_name: AML Patient A039 Diagnostic

value: Patient A039

value: Diagnostic


title: AML Patient A040_N Remission

source_name: AML Patient A040 Remission


title: gamma delta T cells GFP+_rep1

value: 9 weeks


title: AML Patient A038_T Diagnostic

source_name: AML Patient A038 Diagnostic

value: Patient A038


title: AML Patient A037_T Diagnostic

source_name: AML Patient A037 Diagnostic

value: Patient A037

value: Bone Marrow


title: AML Patient A038_N Remission

source_name: AML Patient A038 Remission


title: gamma delta T cells GFP+_rep2

value: Spleen


title: AML Patient A041_T Diagnostic

source_name: AML Patient A041 Diagnostic


title: AML Patient A037_N Remission

source_name: AML Patient A037 Remission


title: AML Patient A039_N Remission

source_name: AML Patient A039 Remission


title: gamma delta T cells GFP-_rep1

value: Eomes-IRES-GFP


title: AML Patient A050_T Diagnostic

source_name: AML Patient A050 Diagnostic

value: Patient A050


title: AML Patient A036_T Diagnostic

source_name: AML Patient A036 Diagnostic

value: Patient A036


title: AML Patient A035_T Diagnostic

source_name: AML Patient A035 Diagnostic

value: Patient A035


title: AML Patient A034_T Diagnostic

source_name: AML Patient A034 Diagnostic

value: Patient A034


title: 4OHT_Rosi_3

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Gene 2.0 ST GeneChips (Affymetrix Inc., Santa Clara CA) using the GeneChip Hybridization oven 645. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal.

data_processing: Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters.

label: biotin

label_protocol: cRNA was converted to cDNA and biotinylated by terminal transferase end labeling according to the standard Affymetrix protocol from 250 ng total RNA (Affymetrix GeneChip Expression Analysis Technical Manual).

growth_protocol: Cells were grown in media containing 10%FBS

extract_protocol: Total RNA was extracted by TRIzol (Invitrogen) followed by purification using PureLink RNA columns (Invitrogen)

treatment_protocol: Cells were treated with 1 uM of 4-hydroxy-tamoxifen (Sigma) or ethanol for 3 days in growth phase. Cells were differentiated with medium containing 10% FBS, 0.5 uM isobutylmethylxanthine, 125 nM indomethacin, 1 μM dexamethosone, 20 nM insulin, 1 nM T3, and stimulated with 1 uM rosiglitazone.

tag: genotype

tag: source tissue

value: Inguinal adipose tissue

value: Inguinal adipose precursor cell

tag: treated with

value: 1 uM of 4-hydroxy-tamoxifen for 3 days

tag: stimulated with

value: 1 uM rosiglitazone


title: AML Patient A036_N Remission

source_name: AML Patient A036 Remission

value: AML

value: Remission


title: 4OHT_Rosi_2


title: AML Patient A035_N Remission

source_name: AML Patient A035 Remission


title: AML Patient A032_T Diagnostic

source_name: AML Patient A032 Diagnostic

value: Patient A032

value: Diagnostic


title: EtOH_Rosi_3

value: EtOH for 3 days


title: 4OHT_Rosi_1


title: AML Patient A033_N Remission

source_name: AML Patient A033 Remission

value: Patient A033


title: AML Patient A034_N Remission

source_name: AML Patient A034 Remission

value: Bone Marrow


title: AML Patient A031_N Remission

source_name: AML Patient A031 Remission

value: Patient A031


title: AML Patient A033_T Diagnostic

source_name: AML Patient A033 Diagnostic


title: EtOH_Rosi_1


title: AML Patient A032_N Remission

source_name: AML Patient A032 Remission


title: EtOH_Rosi_2


title: 4OHT_3


title: AML Patient A030_T Diagnostic

source_name: AML Patient A030 Diagnostic

value: Patient A030


title: 4OHT_2


title: AML Patient A030_N Remission

source_name: AML Patient A030 Remission


title: AML Patient A027_T Diagnostic

source_name: AML Patient A027 Diagnostic

value: Patient A027


title: EtOH_2


title: EtOH_3


title: AML Patient A027_N Remission

source_name: AML Patient A027 Remission


title: AML Patient A031_T Diagnostic

source_name: AML Patient A031 Diagnostic


title: AML Patient A024_T Diagnostic

source_name: AML Patient A024 Diagnostic

value: Patient A024


title: AML Patient A029_T Diagnostic

source_name: AML Patient A029 Diagnostic

value: Patient A029


title: AML Patient A029_N Remission

source_name: AML Patient A029 Remission


title: EtOH_1


title: 4OHT_1


title: AML Patient A023_N Remission

source_name: AML Patient A023 Remission

value: Patient A023


title: AML Patient A025_T Diagnostic

source_name: AML Patient A025 Diagnostic

value: Patient A025


title: AML Patient A026_N Remission

source_name: AML Patient A026 Remission

value: Patient A026


title: AML Patient A023_T Diagnostic

source_name: AML Patient A023 Diagnostic


title: AML Patient A025_N Remission

source_name: AML Patient A025 Remission


title: AML Patient A026_T Diagnostic

source_name: AML Patient A026 Diagnostic


title: AML Patient A028_T Diagnostic

source_name: AML Patient A028 Diagnostic

value: Patient A028


title: MN innervating EDL [M33EDL]

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

description: Laser captured motor neurons innervating extensor digitorum longus muscle

hyb_protocol: 5.5µg of sense DNA molecules were heat fragmented and applied to the Mouse transcriptome array 1 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: Scanned on an Affymetrix® GeneChip Scanner 3000 according to manufacturer's protocols

data_processing: Data were RMA normalised using the Affymetrix transcriptome analysis console package

source_name: Laser captured motor neurons

label_protocol: Biotinylation of sense DNA strand was carried out according to Affymetrix protocol

extract_protocol:
20 um cervical spinal cord frozen sections on PEN membrane slides were acetone fixed and dehydrated through graded ethanol concentrations (70%, 90%, 100%). Motor neurons with retrogradely transported WGA-HRP were stained with NovaRed peroxidase (Vector Labs).
From each individual all stained motor neurons (MN) were isolated using a Veritas laser-capture microdissection system (Applied Biosystems)
PicoPure RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions

value: Wild type

value: FVB


title: MN innervating EDL [M14EDL]

value: Laser captured motor neurons innervating extensor digitorum longus muscle


title: AML Patient A024_N Remission

source_name: AML Patient A024 Remission

value: AML

value: Remission


title: AML Patient A022_N Remission

source_name: AML Patient A022 Remission

value: Patient A022


title: MN innervating EDL [M11EDL]


title: MN innervating GC [M31GC]

description: Laser captured motor neurons innervating gastrocnemius muscle


title: AML Patient A022_T Diagnostic

source_name: AML Patient A022 Diagnostic

value: Diagnostic


title: MN innervating GC [M13GC]

value: Laser captured motor neurons innervating gastrocnemius muscle


title: MN innervating GC [M30GC]


title: AML Patient A021_N Remission

source_name: AML Patient A021 Remission

value: Patient A021

value: Bone Marrow


title: MN innervating TA [M3TA]

description: Laser captured motor neurons innervating tibialis anterior muscle


title: AML Patient A019_T Diagnostic

source_name: AML Patient A019 Diagnostic

value: Patient A019


title: MN innervating TA [M1TA]

value: Laser captured motor neurons innervating tibialis anterior muscle


title: AML Patient A021_T Diagnostic

source_name: AML Patient A021 Diagnostic


title: AML Patient A020_T Diagnostic

source_name: AML Patient A020 Diagnostic

value: Patient A020


title: MN innervating TA [M0TA]


title: AML Patient A028_N Remission

source_name: AML Patient A028 Remission


title: AML Patient A019_N Remission

source_name: AML Patient A019 Remission


title: AML Patient A017_T Diagnostic

source_name: AML Patient A017 Diagnostic

value: Patient A017


title: AML Patient A018_N Remission

source_name: AML Patient A018 Remission

value: Patient A018


title: Pread_Prdm16_H3K27ac

type: SRA

library_source: genomic

data_processing:
ChIP-seq reads were aligned to mouse genome (mm9) using Bowtie. All redundant reads were discarded except one. BigWig files for RPM-normalized stack-height profiles were generated using Homer and bedGraphToBigWig command.
Genome_build: mm9
Supplementary_files_format_and_content: RPM-normalized bigwig file

source_name: Brown fat precursor cell

growth_protocol: Cells were grown in media containing 10%FBS until confluent

extract_protocol:
Cells were fixed in 1% formaldehyde for 15 min, then quenched with 125 mM glycine for 5 min. Cell pellet was then sonicated to extract chromatin.
ChIP-Seq libraries were produced and sequenced according to Illumina protocols. Libraries were multiplexed for sequencing.

treatment_protocol: Cells were infected with MSCV-Puromycin (control) or MSCV-PRDM16 retrovirus.

tag: genotype/variation

value: Myf5Cre; Prdm16flox Exon9

value: Brown adipose tissue

value: Immortalized adipocyte precursors

tag: infected with

value: MSCV-PRDM16 retrovirus

tag: antibody

value: H3K27ac (Abcam ab4729)


title: Pread_Puro_H3K27ac

value: MSCV-Puromycin (control)


title: AML Patient A015_N Remission

source_name: AML Patient A015 Remission

value: AML

value: Patient A015

value: Remission


title: AML Patient A016_T Diagnostic

source_name: AML Patient A016 Diagnostic

value: Patient A016

value: Diagnostic


title: AML Patient A020_N Remission

source_name: AML Patient A020 Remission

value: Bone Marrow


title: AML Patient A016_N Remission

source_name: AML Patient A016 Remission


title: AML Patient A018_T Diagnostic

source_name: AML Patient A018 Diagnostic


title: AML Patient A017_N Remission

source_name: AML Patient A017 Remission


title: AML Patient A014_T Diagnostic

source_name: AML Patient A014 Diagnostic

value: Patient A014


title: AML Patient A013_N Remission

source_name: AML Patient A013 Remission

value: Patient A013


title: AML Patient A014_N Remission

source_name: AML Patient A014 Remission


title: AML Patient A015_T Diagnostic

source_name: AML Patient A015 Diagnostic


title: AML Patient A012_T Diagnostic

source_name: AML Patient A012 Diagnostic

value: Patient A012


title: AML Patient A011_T Diagnostic

source_name: AML Patient A011 Diagnostic

value: Patient A011


title: DPN treatment in adherent culture, biological rep2

city: Stockholm

first: Johan

last: Hartman

state: Sweden

address: Karolinska Vägen

department: Department of Clinical Pathology and Cytology

country: Sweden

institute: Karolinska University Hospital

description:
Gene expression data from MCF7 adherent cells treated with DPN.
RM15_D2_MCF7

hyb_protocol: 5ug of target is hybridizedto HTA 2.0 Array in Affymetrix Hybridization Oven 645 for 16 hr at 45C

scan_protocol: Arrays  were scanned using the Affymetrix Gene Chip Scanner 3000 7G

data_processing: Gene level normalization was done using Robust MultiChip Analysis (RMA) algorithm in Affymetrix Expression Console. Differentially expressed genes between treatment groups were identified by one-way Analysis of Variance (ANOVA) of preprocessed data in Affymetrix Trancriptome Analysis Console, including genes with±1.2 fold change, P-value of <0.05 and known gene annotation.

source_name: DPN treatment in adherent culture

label_protocol: Biotinylated sense-strend DNA is generated from 100ng of total RNA using Affymetrix standard protcol(WT PLUS reagent user manual)

growth_protocol: MCF7 spheres were cultured in the selective medium for 3 generations. MCF7 adherent cultures were maitained in white DMEM supplied with 5%FBS

extract_protocol: Total RNA was extracted by using RNeasy mini kit from QIAGEN according to the manufacturer's instructions.

treatment_protocol: Single cells were dissociated from MCF7 spheres and treated with 10nM phtpp or dpn in triplicates for 48h. Monolayer MCF7 adherent cells were treated with 10nM dpn in triplicates for 48h.

tag: cell line

tag: phenotype

value: adherent monolayer cells

tag: cell state

value: differentiated state

value: 10nM DPN for 48hrs


title: DPN treatment in adherent culture, biological rep3

description:
Gene expression data from MCF7 adherent cells treated with DPN.
RM16_D3_MCF7


title: DPN treatment in adherent culture, biological rep1

description:
Gene expression data from MCF7 adherent cells treated with DPN.
RM14_D1_MCF7


title: Pread_Puro_Prdm16

value: Myf5Cre; Prdm16flox Exon9

value: Brown adipose tissue

value: Immortalized adipocyte precursors

value: PRDM16 (Made in Lab, Harms et al. 2014. Cell Metab.)


title: AML Patient A010_T Diagnostic

source_name: AML Patient A010 Diagnostic

tag: disease state

value: AML

tag: individual

value: Patient A010

tag: tissue


title: Ctrl in adherent culture, biological rep1

description:
Gene expression data from control MCF7 adherent cells.
RM11_C1_MCF7

source_name: Ctrl in adherent culture

value: none (control)


title: Ctrl in adherent culture, biological rep2

description:
Gene expression data from control MCF7 adherent cells.
RM12_C2_MCF7


title: Ctrl in adherent culture, biological rep3

description:
Gene expression data from control MCF7 adherent cells.
RM13_C3_MCF7


title: Ctrl in spheres, biological rep4

description:
Gene expression data from control MCF7 spheres.
RM10_C4_MCF7_S

source_name: Ctrl in spheres

value: spheres

value: cancer stem cell state


title: Ctrl in spheres, biological rep3

description:
Gene expression data from control MCF7 spheres.
RM09_C3_MCF7_S


title: Ctrl in spheres, biological rep2

description:
Gene expression data from control MCF7 spheres.
RM08_C2_MCF7_S


title: AML Patient A009_T Diagnostic

source_name: AML Patient A009 Diagnostic

value: Patient A009

value: Bone Marrow

tag: patient status

value: Diagnostic


title: 9974366123_R01C01_SLE patient (case)

city: OKC

first: Jonathan

middle: Daniel

last: Wren

state: OK

address: 825 NE 13th St

department: Arthritis & Clinical Immunology

institute: Oklahoma Medical Research Foundation

hyb_protocol: Hybridization: 22 hr at 48 degrees C. (full protocol details for all steps can be found in Illumina Infinium HD Methylation Assay manual)

scan_protocol: iScan Scan Setting: Methylation  NXT

data_processing:
Average Beta value. β values are calculated using the formula:  β = Methylated / (Methylated + Unmethylated + 100)
The average beta calculation is given by the formula above (no special software)

label: cy3, cy5

source_name: Naïve CD4+ T cell

label_protocol: Staining Protocol (Tecan Freedom Evo): XStain HD BeadChip

growth_protocol: n/a (isolated cell populations)

extract_protocol: Naïve CD4+ T cells were isolated from whole blood by negative selection using the Naïve CD4+ T cell Isolation Kit II, human (Miltenyi Biotec, San Diego, CA, USA) according to manufacturer’s instructions. This kit uses an antibody cocktail to directly label the surface of undesired cells which are then bound to magnetic beads, allowing unlabeled naïve CD4+ T cells to be separated. The purity of the isolated populations was confirmed using surface protein staining and flow cytometry as CD3+, CD4+ and CD45RA+ using human FITC-conjugated human anti-CD3, human PE-conjugated anti-CD4, and human Pacific Blue-conjugated anti-CD45RA antibodies (BioLegend, San Diego, CA, USA). Cell population purity for all samples included in this study was >95%. Genomic DNA was extracted from isolated naïve CD4+ T cell populations using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, USA). Total RNA was also extracted simultaneously by lysing cells in TRIzol Reagent (ThermoFisher Scientific, Grand Island, NY, USA) and then purified using Direct-zol RNA MiniPrep Kit (Zymo Research, Irvine, CA, USA) according to manufacturer’s instructions.

tag: subject status

value: Systemic lupus erythematosus patient

tag: Sex

value: female

tag: ethnicity

value: European-American

tag: age (yrs)

tag: sledai score

value: peripheral blood

value: Naïve CD4+ T cell


title: AML Patient A008_T Diagnostic

source_name: AML Patient A008 Diagnostic

value: Patient A008


title: AML Patient A011_N Remission

source_name: AML Patient A011 Remission

value: Patient A011

value: Remission


title: AML Patient A013_T Diagnostic

source_name: AML Patient A013 Diagnostic

value: Patient A013


title: AML Patient A007_N Remission

source_name: AML Patient A007 Remission

value: AML

value: Patient A007


title: AML Patient A006_T Diagnostic

source_name: AML Patient A006 Diagnostic

value: Patient A006


title: DPN/PHTPP treatment in spheres, biological rep3

description:
Gene expression data from MCF7 spheres treated with DPN/PHTPP.
RM06_DP3_MCF7_S

source_name: DPN/PHTPP treatment in spheres

value: spheres

tag: treated with

value: 10nM DPN/PHTPP for 48hrs


title: AML Patient A010_N Remission

source_name: AML Patient A010 Remission

value: Patient A010


title: AML Patient A012_N Remission

source_name: AML Patient A012 Remission

value: Patient A012

value: Bone Marrow


title: DPN/PHTPP treatment in spheres, biological rep1

description:
Gene expression data from MCF7 spheres treated with DPN/PHTPP.
RM04_DP1_MCF7_S

value: cancer stem cell state


title: Ctrl in spheres, biological rep1

description:
Gene expression data from control MCF7 spheres.
RM07_C1_MCF7_S

value: none (control)


title: AML Patient A008_N Remission

source_name: AML Patient A008 Remission


title: 9974366114_R05C01_SLE patient (case)

value: Systemic lupus erythematosus patient

value: female

value: European-American

tag: cell type


title: DPN treatment in spheres, biological rep3

description:
Gene expression data from MCF7 spheres treated with DPN.
RM03_D3_MCF7_S

source_name: DPN treatment in spheres

value: 10nM DPN for 48hrs


title: DPN treatment in spheres, biological rep1

description:
Gene expression data from MCF7 spheres treated with DPN.
RM01_D1_MCF7_S


title: 9974366114_R03C01_SLE patient (case)

value: African-American

value: peripheral blood

value: Naïve CD4+ T cell


title: Patient L064 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L064_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

hyb_protocol: 20 hours at 48°C, according to manufacturer's instructions

scan_protocol: arrays were scanned using iScan

data_processing:
Genomic DNA extracted from AML diagnostic and remission bone marrow samples and genotyped using Human Omni 2.5M SNP arrays (2.5-4v1-D or 2.5-4v1-H) (Illumina).
Raw image data were saved to a project using Genome Studio (Illumina) and B-Allele Frequencies and Log-R Ratios were exported for analysis using ASCAT in R.

label: cy3 and cy5

source_name: Patient L064 Remission

label_protocol: 200 ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix, according to the manufacturer's instructions

extract_protocol: Genomic DNA was extracted using the DNeasy Blood & Tissues Kit  from Qiagen according to manufacturer's instructions.  DNA concentration was determined by measuring absorbance at 260nm on a Nanodrop2000

value: Patient L064

value: AML

value: Remission


title: Patient L063 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L063_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L063 Remission

value: Patient L063


title: Patient L063 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L063_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L063 Diagnostic

value: Diagnostic


title: DPN treatment in spheres, biological rep2

description:
Gene expression data from MCF7 spheres treated with DPN.
RM02_D2_MCF7_S

value: spheres


title: 9974366114_R05C02_SLE patient (case)


title: Patient L062 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L062_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L062 Remission

value: Patient L062


title: AML Patient A009_N Remission

description: hybridized to Genome-Wide Human SNP 6.0 Array

source_name: AML Patient A009 Remission

value: Patient A009

value: Bone Marrow


title: 9974366114_R03C02_SLE patient (case)


title: Patient L062 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L062_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L062 Diagnostic


title: 9974366114_R01C01_SLE patient (case)

source_name: Naïve CD4+ T cell


title: Patient L061 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L061_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L061 Diagnostic

value: Patient L061


title: Patient L061 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L061_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L061 Remission


title: 9974366111_R05C02_SLE patient (case)

value: Systemic lupus erythematosus patient


title: Patient L059 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L059_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L059 Diagnostic

value: Patient L059


title: Patient L060 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L060_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L060 Diagnostic

value: Patient L060


title: DPN/PHTPP treatment in spheres, biological rep2

description:
Gene expression data from MCF7 spheres treated with DPN/PHTPP.
RM05_DP2_MCF7_S

value: cancer stem cell state

value: 10nM DPN/PHTPP for 48hrs


title: Pread_Prdm16_Prdm16

source_name: Brown fat precursor cell

tag: genotype/variation

value: Myf5Cre; Prdm16flox Exon9

tag: source tissue

value: Brown adipose tissue

value: Immortalized adipocyte precursors

value: MSCV-PRDM16 retrovirus

value: PRDM16 (Made in Lab, Harms et al. 2014. Cell Metab.)


title: Patient L066 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L066_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L066 Remission

value: Patient L066

value: AML

value: Remission


title: Patient L059 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L059_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L059 Remission


title: Patient L066 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L066_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L066 Diagnostic

value: Diagnostic


title: Patient L057 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L057_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L057 Diagnostic

value: Patient L057


title: AML Patient A006_N Remission

source_name: AML Patient A006 Remission

value: Patient A006

value: Bone Marrow


title: 9974366111_R03C02_SLE patient (case)

value: Systemic lupus erythematosus patient

value: female

value: African-American

value: peripheral blood

value: Naïve CD4+ T cell


title: Patient L064 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L064_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L064 Diagnostic

value: Patient L064


title: Patient L057 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L057_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L057 Remission


title: 9974366114_R01C02_SLE patient (case)


title: Patient L055 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L055_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L055 Diagnostic

value: Patient L055


title: AML Patient A007_T Diagnostic

source_name: AML Patient A007 Diagnostic

value: Patient A007


title: 9974366111_R03C01_SLE patient (case)


title: Patient L055 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L055_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L055 Remission


title: Patient L054 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L054_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L054 Diagnostic

value: Patient L054


title: Patient L054 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L054_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L054 Remission


title: Patient L052 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L052_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L052 Diagnostic

value: Patient L052


title: AML Patient A005_N Remission

description: hybridized to Genome-Wide Human SNP 6.0 Array

source_name: AML Patient A005 Remission

value: Patient A005


title: 9974366111_R01C02_SLE patient (case)

source_name: Naïve CD4+ T cell


title: 9974366111_R01C01_SLE patient (case)

value: Hispanic


title: 9974366108_R05C02_SLE patient (case)


title: 9974366108_R05C01_SLE patient (case)

value: European-American


title: Patient L051 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L051_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L051 Remission

value: Patient L051

value: AML

value: Remission


title: Patient L050 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L050_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L050 Diagnostic

value: Patient L050

value: Bone Marrow

value: Diagnostic


title: Patient L051 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L051_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L051 Diagnostic


title: Patient L049 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L049_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L049 Diagnostic

value: Patient L049


title: Patient L049 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L049_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L049 Remission


title: 9974366108_R03C02_SLE patient (case)

value: Systemic lupus erythematosus patient

value: female

value: African-American

value: peripheral blood


title: Patient L048 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L048_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L048 Diagnostic

value: Patient L048


title: DFSP

city: Beijing

first: Cheng

last: Li

address: No.5 Yiheyuan Road

country: China

institute: Peking University

description: total RNA without samll RNA

hyb_protocol: Total RNA was hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array

scan_protocol: not provided

data_processing: Expression levels were calculated by affy package based on bioconductor.

source_name: Fresh dermatofibrosarcoma tumor

label_protocol: not provided

growth_protocol: Fresh dermatofibrosarcoma tumor was gotten from patients.

extract_protocol: Fresh dermatofibrosarcoma tumor was homogenized and total RNA isolated using Ambion mirVana miRNA isolation kit without enrichment for small RNAs.

value: dermatofibrosarcoma


title: Patient L048 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L048_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L048 Remission


title: 9974366108_R03C01_SLE patient (case)

value: Naïve CD4+ T cell


title: Patient L050 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L050_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L050 Remission


title: Patient L047 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L047_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L047 Diagnostic

value: Patient L047


title: 9974366108_R01C02_SLE patient (case)


title: 9974366111_R05C01_SLE patient (case)

value: Asian-Indian


title: Patient L047 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L047_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L047 Remission


title: Patient L046 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L046_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L046 Diagnostic

value: Patient L046


title: Patient L045 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L045_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L045 Diagnostic

value: Patient L045


title: 9974366108_R01C01_SLE patient (case)

value: European-American


title: AML Patient A002_N Remission

source_name: AML Patient A002 Remission

value: AML

value: Patient A002

value: Remission


title: AML Patient A003_T Diagnostic

source_name: AML Patient A003 Diagnostic

value: Patient A003

value: Bone Marrow

value: Diagnostic


title: Patient L045 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L045_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L045 Remission


title: Patient L044 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L044_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L044 Remission

value: Patient L044


title: 9974366089_R05C02_SLE patient (case)

source_name: Naïve CD4+ T cell

value: Systemic lupus erythematosus patient

value: female

value: African-American


title: 9974366089_R05C01_SLE patient (case)

value: peripheral blood


title: Patient L042 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L042_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L042 Diagnostic

value: Patient L042


title: Patient L041 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L041_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L041 Remission

value: Patient L041


title: Patient L041 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L041_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L041 Diagnostic


title: 9974366089_R03C02_SLE patient (case)

value: Naïve CD4+ T cell


title: Patient L040 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L040_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L040 Remission

value: Patient L040


title: Patient L044 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L044_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L044 Diagnostic


title: 9974366089_R01C02_SLE patient (case)


title: Patient L039 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L039_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L039 Diagnostic

value: Patient L039


title: Patient L039 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L039_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L039 Remission


title: AML Patient A004_T Diagnostic

description: hybridized to Genome-Wide Human SNP 6.0 Array

source_name: AML Patient A004 Diagnostic

value: Patient A004


title: 9611519009_R05C02_SLE patient (case)

value: Asian


title: Patient L038 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L038_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L038 Diagnostic

value: Patient L038

value: AML


title: Patient L038 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L038_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L038 Remission

value: Remission


title: Patient L040 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L040_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L040 Diagnostic

value: Bone Marrow


title: Patient L037 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L037_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L037 Diagnostic

value: Patient L037

value: Diagnostic


title: Patient L035 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L035_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L035 Diagnostic

value: Patient L035


title: 9611519009_R01C01_SLE patient (case)

value: Systemic lupus erythematosus patient

value: female

value: European-American


title: Patient L035 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L035_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L035 Remission


title: 9611519009_R01C02_SLE patient (case)

value: peripheral blood


title: Patient L033 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L033_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L033 Diagnostic

value: Patient L033


title: 9611519009_R05C01_SLE patient (case)

value: Naïve CD4+ T cell


title: Patient L031 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L031_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L031 Diagnostic

value: Patient L031


title: Patient L032 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L032_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L032 Diagnostic

value: Patient L032


title: AML Patient A002_T Diagnostic

source_name: AML Patient A002 Diagnostic

value: Patient A002


title: 9611519008_R06C02_SLE patient (case)

source_name: Naïve CD4+ T cell


title: AML Patient A003_N Remission

source_name: AML Patient A003 Remission

value: Patient A003


title: Patient L030 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L030_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L030 Diagnostic

value: Patient L030


title: Patient L030 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L030_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L030 Remission

value: AML


title: AML Patient A001_T Diagnostic

source_name: AML Patient A001 Diagnostic

value: Patient A001


title: 9611519008_R03C02_SLE patient (case)


title: Patient L028 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L028_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L028 Diagnostic

value: Patient L028

value: Bone Marrow


title: AML Patient A005_T Diagnostic

source_name: AML Patient A005 Diagnostic

value: Patient A005

value: Diagnostic


title: Patient L031 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L031_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L031 Remission

value: Remission


title: Patient L028 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L028_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L028 Remission


title: Patient L027 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L027_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L027 Diagnostic

value: Patient L027


title: 9611518100_R05C01_SLE patient (case)

value: Systemic lupus erythematosus patient

value: female

value: European-American


title: Patient L027 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L027_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L027 Remission


title: Patient L024 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L024_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L024 Diagnostic

value: Patient L024


title: AML Patient A001_N Remission

description: hybridized to Genome-Wide Human SNP 6.0 Array

source_name: AML Patient A001 Remission


title: normal 27

city: rome

first: andrea

last: sacconi

address: via elio chianesi

country: Italy

institute: regina elena cancer institute

description: Gene expression of gastric tissue

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on human GeneChip® Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: data were background adjusted and quantile normalized. The gene expression values were calculated by using Robust    Multiple-array Average (RMA) procedure. Data processed by MATLAB.

source_name: normal 27

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Fresh frozen tissues samples were obtained immediately after surgical resection and stored in RNA later (Ambion)

extract_protocol: total RNA was extracted using miRNeasy Kit (QIAGEN) following the manufacturer’s instructions.

treatment_protocol: Tissues were disrupted and homogenized using QIAzol Lysis Reagent  (Qiagen, Chatsworth, CA)

value: normal


title: tumor 22

description: Gene expression of gastric tissue

source_name: tumor 22

value: tumor


title: AML Patient A004_N Remission

source_name: AML Patient A004 Remission

value: Patient A004


title: Patient L022 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L022_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L022 Diagnostic

value: Patient L022


title: Patient L024 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L024_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L024 Remission


title: 9611518084_R01C02_SLE patient (case)

source_name: Naïve CD4+ T cell

value: peripheral blood

value: Naïve CD4+ T cell


title: 9611518082_R02C01_SLE patient (case)


title: Patient L022 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L022_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L022 Remission

value: AML


title: 9611518082_R01C01_SLE patient (case)


title: Patient L021 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L021_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L021 Diagnostic

value: Patient L021


title: Patient L021 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L021_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L021 Remission

value: Bone Marrow


title: Patient L017 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L017_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L017 Diagnostic

value: Patient L017


title: Patient L020 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L020_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L020 Diagnostic

value: Patient L020

value: Diagnostic


title: normal 26

description: Gene expression of gastric tissue

source_name: normal 26


title: Patient L017 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L017_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L017 Remission

value: Remission


title: tumor 19

description: Gene expression of gastric tissue

source_name: tumor 19


title: tumor 8

description: Gene expression of gastric tissue

source_name: tumor 8


title: tumor 20

description: Gene expression of gastric tissue

source_name: tumor 20


title: tumor 6

description: Gene expression of gastric tissue

source_name: tumor 6


title: 9611518074_R04C01_SLE patient (case)

value: Systemic lupus erythematosus patient

value: African-American


title: 9611518084_R04C01_SLE patient (case)

value: female

value: Asian


title: Patient L015 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L015_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L015 Diagnostic

value: Patient L015


title: Patient L012 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L012_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L012 Diagnostic

value: Patient L012


title: normal 33

description: Gene expression of gastric tissue

source_name: normal 33

value: normal


title: 9611518074_R02C01_SLE patient (case)

value: European-American


title: Patient L011 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L011_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L011 Remission

value: Patient L011


title: 8942334069_R05C02_SLE patient (case)

value: peripheral blood

value: Naïve CD4+ T cell


title: Patient L010 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L010_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L010 Remission

value: Patient L010

value: AML


title: tumor 4

description: Gene expression of gastric tissue

source_name: tumor 4

value: tumor


title: Patient L009 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L009_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L009 Diagnostic

value: Patient L009

value: Bone Marrow


title: Patient L008 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L008_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L008 Diagnostic

value: Patient L008

value: Diagnostic


title: normal 35

description: Gene expression of gastric tissue

source_name: normal 35


title: 8942334069_R03C02_SLE patient (case)

source_name: Naïve CD4+ T cell

value: Systemic lupus erythematosus patient


title: Patient L010 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L010_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L010 Diagnostic


title: tumor 23

description: Gene expression of gastric tissue

source_name: tumor 23


title: Patient L006 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L006_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L006 Remission

value: Patient L006

value: Remission


title: Patient L003 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L003_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L003 Diagnostic

value: Patient L003


title: 9611518074_R01C01_SLE patient (case)

value: female


title: 8942334069_R01C02_SLE patient (case)


title: Patient L003 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L003_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L003 Remission


title: Patient L011 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L011_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L011 Diagnostic


title: tumor 18

description: Gene expression of gastric tissue

source_name: tumor 18


title: Patient L013 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L013_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L013 Diagnostic

value: Patient L013


title: Patient L001 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L001_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L001 Diagnostic

value: Patient L001


title: tumor 3

description: Gene expression of gastric tissue

source_name: tumor 3


title: tumor 11

description: Gene expression of gastric tissue

source_name: tumor 11


title: Patient L006 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L006_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L006 Diagnostic


title: Patient L001 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L001_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L001 Remission


title: 8942334069_R05C01_SLE patient (case)

value: African-American


title: Patient L005 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L005_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L005 Diagnostic

value: Patient L005


title: tumor 7

description: Gene expression of gastric tissue

source_name: tumor 7


title: Patient L250 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L250_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L250 Remission

value: Patient L250


title: Patient L002 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L002_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L002 Diagnostic

value: Patient L002


title: 8942334051_R05C02_SLE patient (case)

source_name: Naïve CD4+ T cell

value: European-American

value: peripheral blood

value: Naïve CD4+ T cell


title: Patient L246 Remission

description:
COG_LUM_AML_Batch_B_Processed_data.txt
COG_LUM_AML_Batch_B_Raw_Intensities.txt
matrix column prefix: L246_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L246 Remission

value: Patient L246

value: AML

value: Bone Marrow


title: tumor 13

description: Gene expression of gastric tissue

source_name: tumor 13

value: tumor


title: 8942334051_R03C02_SLE patient (case)

value: Systemic lupus erythematosus patient


title: Patient L224 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L224_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L224 Remission

value: Patient L224

value: Remission


title: tumor 15

description: Gene expression of gastric tissue

source_name: tumor 15


title: tumor 14

description: Gene expression of gastric tissue

source_name: tumor 14


title: Patient L244 Remission

description:
COG_LUM_AML_Batch_B_Processed_data.txt
COG_LUM_AML_Batch_B_Raw_Intensities.txt
matrix column prefix: L244_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L244 Remission

value: Patient L244


title: Patient L200 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L200_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L200 Remission

value: Patient L200


title: 8942334069_R03C01_SLE patient (case)

value: female


title: 8942334051_R05C01_SLE patient (case)


title: Patient L236 Remission

description:
COG_LUM_AML_Batch_B_Processed_data.txt
COG_LUM_AML_Batch_B_Raw_Intensities.txt
matrix column prefix: L236_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L236 Remission

value: Patient L236


title: Patient L225 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L225_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L225 Remission

value: Patient L225


title: 8942334051_R03C01_SLE patient (case)


title: Patient L207 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L207_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L207 Remission

value: Patient L207


title: 8942326105_R05C02_SLE patient (case)

value: African-American


title: Patient L190 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L190_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L190 Remission

value: Patient L190


title: Patient L189 Diagnostic

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L189_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L189 Diagnostic

value: Patient L189

value: Diagnostic


title: Patient L211 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L211_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L211 Remission

value: Patient L211


title: Patient L172 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L172_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L172 Remission

value: Patient L172

value: AML


title: 8942334051_R01C02_SLE patient (case)

value: European-American

value: peripheral blood

value: Naïve CD4+ T cell


title: 8942334051_R01C01_SLE patient (case)

value: Systemic lupus erythematosus patient


title: 9611519008_R04C02_SLE patient (case)


title: Patient L186 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L186_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L186 Remission

value: Patient L186

value: Bone Marrow

value: Remission


title: Patient L226 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L226_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L226 Remission

value: Patient L226


title: 8942326105_R05C01_SLE patient (case)

source_name: Naïve CD4+ T cell

value: female


title: Patient L165 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L165_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L165 Remission

value: Patient L165


title: Patient L166 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L166_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L166 Remission

value: Patient L166


title: Patient L164 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L164_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L164 Remission

value: Patient L164


title: Patient L163 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L163_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L163 Remission

value: Patient L163


title: 8942326105_R03C02_SLE patient (case)


title: normal 34

description: Gene expression of gastric tissue

source_name: normal 34

value: normal


title: Patient L158 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L158_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L158 Remission

value: Patient L158


title: Patient L160 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L160_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L160 Remission

value: Patient L160


title: tumor 16

description: Gene expression of gastric tissue

source_name: tumor 16

value: tumor


title: 8942326105_R03C01_SLE patient (case)

value: European-American


title: Patient L151 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L151_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L151 Remission

value: Patient L151

value: AML


title: Patient L148 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L148_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L148 Remission

value: Patient L148


title: Patient L150 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L150_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L150 Remission

value: Patient L150


title: Patient L130 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L130_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L130 Remission

value: Patient L130

value: Bone Marrow


title: 8942334069_R01C01_SLE patient (case)

value: Systemic lupus erythematosus patient

value: peripheral blood

value: Naïve CD4+ T cell


title: 8942326105_R01C01_SLE patient (case)

value: female


title: Patient L127 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L127_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L127 Remission

value: Patient L127

value: Remission


title: Patient L113 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L113_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L113 Remission

value: Patient L113


title: Patient L110 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L110_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L110 Remission

value: Patient L110


title: Patient L099 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L099_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L099 Remission

value: Patient L099


title: Patient L097 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L097_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L097 Remission

value: Patient L097


title: 7471147110_R05C02_SLE patient (case)

source_name: Naïve CD4+ T cell

value: European-American


title: GW18_CTX_120

city: San Francisco

first: Chandrasekhar

middle: S

last: Raju

state: CA

address: 1450 3rd Street

department: Neurosurgery

institute: UCSF

description: section number 94

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized in R.

source_name: Human neocortex

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser 2100.

tag: corelabel

tag: age

tag: rin

value: G


title: Patient L078 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L078_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L078 Remission

value: Patient L078

value: AML


title: 8942326105_R01C02_SLE patient (case)

value: African-American


title: Patient L087 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L087_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L087 Remission

value: Patient L087


title: GW18_CTX_119

description: section number 93

value: E


title: GW18_CTX_117

description: section number 91

value: C


title: Patient L067 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L067_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L067 Remission

value: Patient L067

value: Bone Marrow


title: GW18_CTX_115

description: section number 89


title: GW18_CTX_118

description: section number 92

value: D


title: GW18_CTX_114

description: section number 88

value: K


title: Patient L052 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L052_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L052 Remission

value: Patient L052

value: Remission


title: Patient L060 Remission

description:
COG_LUM_AML_Batch_B_Processed_data.txt
COG_LUM_AML_Batch_B_Raw_Intensities.txt
matrix column prefix: L060_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L060 Remission

value: Patient L060


title: 7471147110_R06C02_SLE patient (case)

value: Systemic lupus erythematosus patient

value: female

value: peripheral blood

value: Naïve CD4+ T cell


title: 7471147110_R04C02_SLE patient (case)

value: Asian


title: 7471147110_R04C01_SLE patient (case)

value: European-American


title: GW18_CTX_108

description: section number 85

value: I


title: GW18_CTX_111

description: section number 86

value: B


title: GW18_CTX_106

description: section number 84


title: GW18_CTX_116

description: section number 90

value: J


title: 7471147110_R06C01_SLE patient (case)


title: GW18_CTX_113

description: section number 87

value: H


title: Patient L042 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L042_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L042 Remission

value: Patient L042

value: AML


title: GW18_CTX_104

description: section number 83

value: F


title: Patient L037 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L037_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L037 Remission

value: Patient L037

value: Bone Marrow


title: 7471147110_R05C01_SLE patient (case)


title: 7471147110_R03C02_SLE patient (case)

value: African-American


title: Patient L033 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L033_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L033 Remission

value: Patient L033

value: Remission


title: 7471147110_R03C01_SLE patient (case)

value: Systemic lupus erythematosus patient

value: female


title: Patient L032 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L032_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L032 Remission

value: Patient L032


title: Patient L020 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L020_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L020 Remission

value: Patient L020


title: 7471147110_R02C02_SLE patient (case)

value: European-American

value: peripheral blood

value: Naïve CD4+ T cell


title: Patient L015 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L015_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L015 Remission

value: Patient L015


title: GW18_CTX_101

description: section number 81

value: J


title: GW18_CTX_102

description: section number 82


title: Patient L012 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L012_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L012 Remission

value: Patient L012


title: GW18_CTX_99

description: section number 80


title: Patient L013 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L013_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L013 Remission

value: Patient L013

value: AML


title: 7471147110_R02C01_SLE patient (case)


title: Patient L009 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L009_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L009 Remission

value: Patient L009


title: Patient L008 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L008_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L008 Remission

value: Patient L008

value: Bone Marrow


title: Patient L005 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L005_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L005 Remission

value: Patient L005


title: Patient L002 Remission

description:
COG_LUM_AML_Batch_C_Processed_data.txt
COG_LUM_AML_Batch_C_Raw_Intensities.txt
matrix column prefix: L002_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L002 Remission

value: Patient L002

value: Remission


title: 7471147110_R01C02_SLE patient (case)

source_name: Naïve CD4+ T cell

value: Systemic lupus erythematosus patient

value: female

value: African-American


title: 7471147110_R01C01_SLE patient (case)

value: European-American


title: Patient L251 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L251_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L251 Diagnostic

value: Patient L251

value: Diagnostic


title: GW18_CTX_92

description: section number 76

source_name: Human neocortex

value: C


title: 6929726159_R06C01_SLE patient (case)

value: peripheral blood

value: Naïve CD4+ T cell


title: Patient L251 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L251_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L251 Remission


title: GW18_CTX_91

description: section number 75

value: A


title: Patient L250 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L250_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L250 Diagnostic

value: Patient L250

value: AML


title: 6929726159_R05C01_SLE patient (case)


title: GW18_CTX_90

description: section number 74


title: Patient L249 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L249_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L249 Diagnostic

value: Patient L249


title: GW18_CTX_88

description: section number 73

value: K


title: Patient L046 Remission

description:
COG_LUM_AML_Batch_B_Processed_data.txt
COG_LUM_AML_Batch_B_Raw_Intensities.txt
matrix column prefix: L046_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-H

source_name: Patient L046 Remission

value: Patient L046

value: Bone Marrow


title: Patient L249 Remission

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L249_N
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L249 Remission

value: Remission


title: Patient L248 Diagnostic

description:
COG_LUM_AML_Batch_A_Processed_data.txt
COG_LUM_AML_Batch_A_Raw_Intensities.txt
matrix column prefix: L248_T
hybridized to Illumina Human Omni 2.5M SNP array
HumanOmni2.5-4v1-D

source_name: Patient L248 Diagnostic

value: Patient L248


title: 6929726159_R04C01_SLE patient (case)

value: Systemic lupus erythematosus patient

value: female