title: [E-MTAB-5] run38_s3

data_processing:
Sequence data processing:  FASTQ files of sequencing reads were retrieved from the sequencing machine and converted into FASTA files. FASTA sequences were filtered to remove any sequences which were shorter than 15 bp after trimming the sequence from the position of the first N. All remaining FASTA sequences were matched back to the S. pombe genome using BLAT, with tilesize set to 8 and oneoff set to 1, in parallel on the Sanger compute farm. All fasta reads were also matched back to a spliced genome using BLAT (same settings as above), where all known intron sequences were removed. The result files of matches to the spliced and unspliced genome were compiled into a complete and non-redundant set that was used for subsequent analysis.
Sequencing expression scores:  Expression scores for every basepair in the genome were assigned based on how many Illumina reads covered each basepair position. The log2 of the score for each nucleotide position was then taken and used for plotting images in R/Bioconductor. The numbers of sequence reads drop towards the 5'-end of long genes. To not bias expression scores against long genes, scores were determined first by taking the sum of the Illumina expression scores for only 300 bp at the 3'-end of each coding region, or the entire length if the coding region was <300 bp, and then dividing by 300 or the length of the coding region if <300 bp.
processed data files:
normM11_solexa_logscore_Rchrm1.txt
normM11_solexa_logscore_Rchrm2.txt
normM11_solexa_logscore_Rchrm3.txt
normM12_solexa_logscore_Rchrm1.txt
normM12_solexa_logscore_Rchrm2.txt
normM12_solexa_logscore_Rchrm3.txt
normM13_solexa_logscore_Rchrm1.txt
normM13_solexa_logscore_Rchrm2.txt
normM13_solexa_logscore_Rchrm3.txt


title: [E-MTAB-5] run34_s5

status: Public on Feb 05 2011

type: SRA

city: Hinxton

first: ArrayExpress

last: EBI

state: Cambridgeshire

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: European Bioinformatics Institute

library_source: transcriptomic

data_processing:
Sequence data processing:  FASTQ files of sequencing reads were retrieved from the sequencing machine and converted into FASTA files. FASTA sequences were filtered to remove any sequences which were shorter than 15 bp after trimming the sequence from the position of the first N. All remaining FASTA sequences were matched back to the S. pombe genome using BLAT, with tilesize set to 8 and oneoff set to 1, in parallel on the Sanger compute farm. All fasta reads were also matched back to a spliced genome using BLAT (same settings as above), where all known intron sequences were removed. The result files of matches to the spliced and unspliced genome were compiled into a complete and non-redundant set that was used for subsequent analysis.
Sequencing expression scores:  Expression scores for every basepair in the genome were assigned based on how many Illumina reads covered each basepair position. The log2 of the score for each nucleotide position was then taken and used for plotting images in R/Bioconductor. The numbers of sequence reads drop towards the 5'-end of long genes. To not bias expression scores against long genes, scores were determined first by taking the sum of the Illumina expression scores for only 300 bp at the 3'-end of each coding region, or the entire length if the coding region was <300 bp, and then dividing by 300 or the length of the coding region if <300 bp.

molecule: total RNA

organism: Schizosaccharomyces pombe

extract_protocol: nucleic_acid_extraction | All cDNA samples used for Illumina sequencing were prepared by first treating ~1 mg of total RNA for 30 min with amplification grade RNase-free DNase (Invitrogen), according to the manufacturers protocols. PolyA enriched RNA was then prepared using an oligo(dT) selection kit (Oligotex Direct mRNA MiniKit, Qiagen). The resulting poly(A)-enriched RNA was then converted to double-stranded cDNA using a cDNA synthesis kit (Superscript choice system for cDNA synthesis, Invitrogen) , primed by an oligo(dT) primer, according to the manufacturers protocols. Random-primed RNA from rapidly proliferating cells was treated with an enzyme that specifically degrades non-capped RNA molecules (mRNA-only, Eukaryotic mRNA isolation kit, Epicentre Biotechnologies) according to the manufacturers protocols. The resulting cDNA was then converted to double-stranded cDNA as above, except that the reaction was primed with random hexamers. RNA samples from the pooled meiotic timepoints were subjected to IVT amplification after undergoing a poly(A) enrichment step as described above. RNA from the oxidative stress condition and prp2 mutant was treated in the same way as the rapidly proliferating samples with oligo(dT)-primed cDNA synthesis after mRNA enrichment.

tag: material type

tag: Sex

tag: strainorline

tag: genotype

tag: growthcondition

value: normal

tag: time

tag: temperature

tag: media

value: YE

tag: culture density


title: [E-MTAB-5] run38_s1

data_processing:
Sequence data processing:  FASTQ files of sequencing reads were retrieved from the sequencing machine and converted into FASTA files. FASTA sequences were filtered to remove any sequences which were shorter than 15 bp after trimming the sequence from the position of the first N. All remaining FASTA sequences were matched back to the S. pombe genome using BLAT, with tilesize set to 8 and oneoff set to 1, in parallel on the Sanger compute farm. All fasta reads were also matched back to a spliced genome using BLAT (same settings as above), where all known intron sequences were removed. The result files of matches to the spliced and unspliced genome were compiled into a complete and non-redundant set that was used for subsequent analysis.
Sequencing expression scores:  Expression scores for every basepair in the genome were assigned based on how many Illumina reads covered each basepair position. The log2 of the score for each nucleotide position was then taken and used for plotting images in R/Bioconductor. The numbers of sequence reads drop towards the 5'-end of long genes. To not bias expression scores against long genes, scores were determined first by taking the sum of the Illumina expression scores for only 300 bp at the 3'-end of each coding region, or the entire length if the coding region was <300 bp, and then dividing by 300 or the length of the coding region if <300 bp.
processed data files:
normM01_solexa_logscore_Rchrm1.txt
normM01_solexa_logscore_Rchrm2.txt
normM01_solexa_logscore_Rchrm3.txt
normM02_solexa_logscore_Rchrm1.txt
normM02_solexa_logscore_Rchrm2.txt
normM02_solexa_logscore_Rchrm3.txt
normM03_solexa_logscore_Rchrm1.txt
normM03_solexa_logscore_Rchrm2.txt
normM03_solexa_logscore_Rchrm3.txt

value: meiosis

value: EMM minus nitrogen


title: [E-MTAB-5] run38_s4

value: EMM low nitrogen


title: Renal_Cell_Carcinoma_21

status: Public on Feb 28 2011

type: RNA

city: Nashville

first: Kimryn

last: Rathmell

state: TN

address: 2220 Pierce Ave

department: Medicine

country: USA

institute: Vanderbilt

description: Gene expression data from Human RCC sample_21

hyb_protocol: Tumor sample RNA and reference RNA were hybridized on Agilent Whole Human Genome 4x44k arrays by UNC Lineberger Comprehensive Cancer Center Genomics Core

scan_protocol: Agilent gene chips were scanned on an Agilent scanner by UNC Lineberger Comprehensive Cancer Center Genomics Core

data_processing: LOWESS normalized, log2 of processed Red/Green signal (median), filter for 70% good data (Exclude if spot is not found in either channel, spot or spot background is a non-uniform outlier, spot or spot background is a non-uniform outlier for the population, spot is not a positive and significant signal in either channel, or Ch1 and 2 lowess normalized net (median) <10). UNC Microarry Database software was used. Missing data was imputed with KNN (k=10) in SAM.

organism: Homo sapiens

source_name: Renal Clear Cell Carcinoma

label_protocol: Tumor sample RNA and reference RNA was labelled by UNC Lineberger Comprehensive Cancer Center Genomics Core

extract_protocol:
Frozen RCCs were obtained through University of North Carolina - Chapel Hill's Tissue Procurement Facility.  H&E was performed on tumor tissue samples to confirm clear cell or normal histopathology.
RNA was extracted with Qiagen RNeasy kit.
RNA quality was determined using an Agilent LabChip Bioanalyzer.

tag: identifier

tag: tissue

value: kidney

tag: histology

value: Clear Cell

tag: disease state

value: Clear Cell Carcinoma

tag: biosourcetype

value: Frozen Sample

source_name: Perou lab reference RNA

value: Cancer cell lines

tag: cell line

value: various cancer cell lines (reference)


title: Renal_Cell_Carcinoma_A11

description: Gene expression data from Human RCC sample_A11


title: Renal_Cell_Carcinoma_A30

description: Gene expression data from Human RCC sample_A30


title: Renal_Cell_Carcinoma_27

description: Gene expression data from Human RCC sample_27


title: [E-MTAB-5] run34_s2

data_processing:
Sequence data processing:  FASTQ files of sequencing reads were retrieved from the sequencing machine and converted into FASTA files. FASTA sequences were filtered to remove any sequences which were shorter than 15 bp after trimming the sequence from the position of the first N. All remaining FASTA sequences were matched back to the S. pombe genome using BLAT, with tilesize set to 8 and oneoff set to 1, in parallel on the Sanger compute farm. All fasta reads were also matched back to a spliced genome using BLAT (same settings as above), where all known intron sequences were removed. The result files of matches to the spliced and unspliced genome were compiled into a complete and non-redundant set that was used for subsequent analysis.
Sequencing expression scores:  Expression scores for every basepair in the genome were assigned based on how many Illumina reads covered each basepair position. The log2 of the score for each nucleotide position was then taken and used for plotting images in R/Bioconductor. The numbers of sequence reads drop towards the 5'-end of long genes. To not bias expression scores against long genes, scores were determined first by taking the sum of the Illumina expression scores for only 300 bp at the 3'-end of each coding region, or the entire length if the coding region was <300 bp, and then dividing by 300 or the length of the coding region if <300 bp.
processed data files:
normM41_solexa_logscore_Rchrm1.txt
normM41_solexa_logscore_Rchrm2.txt
normM41_solexa_logscore_Rchrm3.txt
normM42_solexa_logscore_Rchrm1.txt
normM42_solexa_logscore_Rchrm2.txt
normM42_solexa_logscore_Rchrm3.txt
normM43_solexa_logscore_Rchrm1.txt
normM43_solexa_logscore_Rchrm2.txt
normM43_solexa_logscore_Rchrm3.txt


title: [E-MTAB-5] run34_s4


title: Renal_Cell_Carcinoma_A31

description: Gene expression data from Human RCC sample_A31


title: [E-MTAB-5] run33_s6

data_processing:
Sequence data processing:  FASTQ files of sequencing reads were retrieved from the sequencing machine and converted into FASTA files. FASTA sequences were filtered to remove any sequences which were shorter than 15 bp after trimming the sequence from the position of the first N. All remaining FASTA sequences were matched back to the S. pombe genome using BLAT, with tilesize set to 8 and oneoff set to 1, in parallel on the Sanger compute farm. All fasta reads were also matched back to a spliced genome using BLAT (same settings as above), where all known intron sequences were removed. The result files of matches to the spliced and unspliced genome were compiled into a complete and non-redundant set that was used for subsequent analysis.
Sequencing expression scores:  Expression scores for every basepair in the genome were assigned based on how many Illumina reads covered each basepair position. The log2 of the score for each nucleotide position was then taken and used for plotting images in R/Bioconductor. The numbers of sequence reads drop towards the 5'-end of long genes. To not bias expression scores against long genes, scores were determined first by taking the sum of the Illumina expression scores for only 300 bp at the 3'-end of each coding region, or the entire length if the coding region was <300 bp, and then dividing by 300 or the length of the coding region if <300 bp.
processed data files:
normM21_solexa_logscore_Rchrm1.txt
normM21_solexa_logscore_Rchrm2.txt
normM21_solexa_logscore_Rchrm3.txt
normM22_solexa_logscore_Rchrm1.txt
normM22_solexa_logscore_Rchrm2.txt
normM22_solexa_logscore_Rchrm3.txt
normM23_solexa_logscore_Rchrm1.txt
normM23_solexa_logscore_Rchrm2.txt
normM23_solexa_logscore_Rchrm3.txt


title: [E-MTAB-5] run33_s5


title: Renal_Cell_Carcinoma_3

description: Gene expression data from Human RCC sample_3


title: [E-MTAB-5] run33_s4


title: Renal_Cell_Carcinoma_6

description: Gene expression data from Human RCC sample_6


title: [E-MTAB-5] run33_s3


title: [E-MTAB-5] run33_s2


title: [E-MTAB-5] run38_s2


title: [E-MTAB-5] run33_s7

data_processing:
Sequence data processing:  FASTQ files of sequencing reads were retrieved from the sequencing machine and converted into FASTA files. FASTA sequences were filtered to remove any sequences which were shorter than 15 bp after trimming the sequence from the position of the first N. All remaining FASTA sequences were matched back to the S. pombe genome using BLAT, with tilesize set to 8 and oneoff set to 1, in parallel on the Sanger compute farm. All fasta reads were also matched back to a spliced genome using BLAT (same settings as above), where all known intron sequences were removed. The result files of matches to the spliced and unspliced genome were compiled into a complete and non-redundant set that was used for subsequent analysis.
Sequencing expression scores:  Expression scores for every basepair in the genome were assigned based on how many Illumina reads covered each basepair position. The log2 of the score for each nucleotide position was then taken and used for plotting images in R/Bioconductor. The numbers of sequence reads drop towards the 5'-end of long genes. To not bias expression scores against long genes, scores were determined first by taking the sum of the Illumina expression scores for only 300 bp at the 3'-end of each coding region, or the entire length if the coding region was <300 bp, and then dividing by 300 or the length of the coding region if <300 bp.
processed data files:
normM31_solexa_logscore_Rchrm1.txt
normM31_solexa_logscore_Rchrm2.txt
normM31_solexa_logscore_Rchrm3.txt
normM32_solexa_logscore_Rchrm1.txt
normM32_solexa_logscore_Rchrm2.txt
normM32_solexa_logscore_Rchrm3.txt
normM33_solexa_logscore_Rchrm1.txt
normM33_solexa_logscore_Rchrm2.txt
normM33_solexa_logscore_Rchrm3.txt


title: [E-MTAB-5] run34_s1


title: Renal_Cell_Carcinoma_25

description: Gene expression data from Human RCC sample_25


title: [E-MTAB-5] run33_s1


title: [E-MTAB-5] run30_s7_Spombe_cDNA

data_processing:
Sequence data processing:  FASTQ files of sequencing reads were retrieved from the sequencing machine and converted into FASTA files. FASTA sequences were filtered to remove any sequences which were shorter than 15 bp after trimming the sequence from the position of the first N. All remaining FASTA sequences were matched back to the S. pombe genome using BLAT, with tilesize set to 8 and oneoff set to 1, in parallel on the Sanger compute farm. All fasta reads were also matched back to a spliced genome using BLAT (same settings as above), where all known intron sequences were removed. The result files of matches to the spliced and unspliced genome were compiled into a complete and non-redundant set that was used for subsequent analysis.
Sequencing expression scores:  Expression scores for every basepair in the genome were assigned based on how many Illumina reads covered each basepair position. The log2 of the score for each nucleotide position was then taken and used for plotting images in R/Bioconductor. The numbers of sequence reads drop towards the 5'-end of long genes. To not bias expression scores against long genes, scores were determined first by taking the sum of the Illumina expression scores for only 300 bp at the 3'-end of each coding region, or the entire length if the coding region was <300 bp, and then dividing by 300 or the length of the coding region if <300 bp.
processed data files:
norm_filtered_wt_current_Set1_solexa_logscore_Rchrm1.txt
norm_filtered_wt_current_Set1_solexa_logscore_Rchrm2.txt
norm_filtered_wt_current_Set1_solexa_logscore_Rchrm3.txt
norm_filtered_wt_current_Set2_solexa_logscore_Rchrm1.txt
norm_filtered_wt_current_Set2_solexa_logscore_Rchrm2.txt
norm_filtered_wt_current_Set2_solexa_logscore_Rchrm3.txt
norm_filtered_wt_current_Set3_solexa_logscore_Rchrm1.txt
norm_filtered_wt_current_Set3_solexa_logscore_Rchrm2.txt
norm_filtered_wt_current_Set3_solexa_logscore_Rchrm3.txt


title: [E-MTAB-5] IL2_22_SPombe


title: [E-MTAB-5] run34_s3


title: [E-MTAB-5] run30_s8_Spombe_cDNA


title: [E-MTAB-5] 67_s_3

data_processing:
Sequence data processing:  FASTQ files of sequencing reads were retrieved from the sequencing machine and converted into FASTA files. FASTA sequences were filtered to remove any sequences which were shorter than 15 bp after trimming the sequence from the position of the first N. All remaining FASTA sequences were matched back to the S. pombe genome using BLAT, with tilesize set to 8 and oneoff set to 1, in parallel on the Sanger compute farm. All fasta reads were also matched back to a spliced genome using BLAT (same settings as above), where all known intron sequences were removed. The result files of matches to the spliced and unspliced genome were compiled into a complete and non-redundant set that was used for subsequent analysis.
Sequencing expression scores:  Expression scores for every basepair in the genome were assigned based on how many Illumina reads covered each basepair position. The log2 of the score for each nucleotide position was then taken and used for plotting images in R/Bioconductor. The numbers of sequence reads drop towards the 5'-end of long genes. To not bias expression scores against long genes, scores were determined first by taking the sum of the Illumina expression scores for only 300 bp at the 3'-end of each coding region, or the entire length if the coding region was <300 bp, and then dividing by 300 or the length of the coding region if <300 bp.
processed data files:
norm_filtered_ox_current_Set3_solexa_logscore_Rchrm1.txt
norm_filtered_ox_current_Set3_solexa_logscore_Rchrm2.txt
norm_filtered_ox_current_Set3_solexa_logscore_Rchrm3.txt

value: oxidative stress (H2O2)

value: YE 0.5mM H2O2


title: [E-MTAB-75] Cell culture 1

data_processing: Sequences in FASTA format were analyzed and header from condition 1 (CGCCATCAGCGTCGAC) and condition 2 (CGCCATCAGTCATATG) were identified. Then tag sequences were found by identifiing the linkers positions. Tags were the 18 bp sequences downstream of each linker. The found tags were aligned in genome using BLAST.

organism: Saccharomyces cerevisiae

source_name: Cell culture 1

growth_protocol: grow | Cells were grown to mid-exponential phase in YPD for a wild type strain (condition 1) and in YPD supplemented with doxycycline (10µg/ml) for 16h for the mutant strain (condition 2).

extract_protocol:
nucleic_acid_extraction | Poly(A)+-enriched RNA from the wild type strain was purified using Dynabeads Oligo (dT)25 (Dynal, Invitrogen). RNA from the CUT fraction was obtained by Cbp20 TAP purification.
TETRATAGS CONSTRUCTION | 3'Long-SAGE tags were obtained by an improved 3' Long-SAGE technique adapted from Wei et al, PNAS, 2004. The 18nt-long 3' tags resulted from MmeI cleavage were ligated into tetratags. These tetratags correspond to 2 ditags and 3 delimiting linkers. First linkers bears a barcode sequence to distinguish the two conditions.

value: MAT_ ura3_0 leu2_0 his3_1 lys2_0


title: [E-MTAB-5] ILease15_16Spombe_cDNA


title: Renal_Cell_Carcinoma_A13

description: Gene expression data from Human RCC sample_A13


title: [E-MTAB-5] 67_s_6


title: [E-MTAB-5] 67_s_5


title: [E-MTAB-5] 67_s_2


title: [E-MTAB-5] 67_s_1


title: NB2697

status: Public on Dec 01 2010

city: Gent

first: Pieter

last: mestdagh

address: De Pintelaan 185

country: Belgium

institute: Center for Medical Genetics

description: primary untreated neuroblastoma tumour

hyb_protocol: Following fragmentation, ~5 ug of cDNA were hybridized for 16 hr at 45°C on GeneChip Human Exon 1.0 ST Arrays (Affymetrix Part No. 900 651). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned in the Affymetrix GeneChip Scanner 3000 with G7 update

data_processing: In order to obtain expression information per gene, exon data was merged by transcript clusters (hg18/core exons). Exon array data was normalized according to the RMA-sketch algorithm using Affymetrix Power Tools (Affymetrix).

label: Biotin

source_name: neuroblastoma tumour, fresh frozen

label_protocol: Biotinylated cDNA was prepared according to the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Rev. 5) from 1000 ng total RNA, including the rRNA reduction step

extract_protocol: Total RNA was isolated using the miRNeasy kit (Qiagen) according to the manufacturer's instructions

tag: tissue type

value: primary untreated neuroblastoma tumour

tag: genomic mycn status

value: amplified

tag: stage


title: NB2509

description: primary untreated neuroblastoma tumour


title: NB2527

description: primary untreated neuroblastoma tumour


title: NB2540

description: primary untreated neuroblastoma tumour


title: NB2507

description: primary untreated neuroblastoma tumour


title: second_trimester_amniotic_fluid_euploid_female4_trisomy18study

status: Public on Dec 03 2010

city: Medford

first: Donna

middle: K

last: Slonim

state: MA

address: 161 College Ave.

department: Computer Science

institute: Tufts University

description: gene expression data from normal second trimester fetus

hyb_protocol: A minimum of 5ug of cDNA from each sample was hybridized to Affymetrix U133 Plus 2.0 microarrays.  Arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).

data_processing: Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method.  Identification of individual differentially-expressed genes was performed via two-sided t-tests using the multtest package in BioConductor, with the Benjamini-Hochberg false-discovery rate adjustment for multiple testing.

label: biotin

source_name: cell free mRNA from second trimester amniotic fluid, euploid control

label_protocol: Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN, San Carlos, CA).

extract_protocol: RNA was extracted from 10 mL amniotic fluid supernatant with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer’s protocol (QIAGEN, Valencia, CA).  RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).

tag: rna source

tag: karyotype


title: NB2505

description: primary untreated neuroblastoma tumour


title: NB2512

description: primary untreated neuroblastoma tumour


title: NB2497

description: primary untreated neuroblastoma tumour


title: NB2525

description: primary untreated neuroblastoma tumour


title: NB2506

description: primary untreated neuroblastoma tumour


title: NB2489

description: primary untreated neuroblastoma tumour


title: NB2535

description: primary untreated neuroblastoma tumour


title: NB2515

description: primary untreated neuroblastoma tumour


title: second_trimester_amniotic_fluid_euploid_female6_trisomy18study

value: cell free mRNA from second trimester amniotic fluid


title: NB2493

description: primary untreated neuroblastoma tumour

value: normal


title: NB2496

description: primary untreated neuroblastoma tumour


title: NB2528

description: primary untreated neuroblastoma tumour


title: second_trimester_amniotic_fluid_euploid_female2_trisomy18study


title: NB2498

description: primary untreated neuroblastoma tumour


title: [E-MTAB-75] Cell culture 2

source_name: Cell culture 2

tag: material type

tag: strainorline

tag: genotype

value: MAT_ ura3_0 leu2_0 his3_1 CBP20-TAP::HIS3 rrp6_::pGID2 Hygrotet07-TRF4


title: second_trimester_amniotic_fluid_euploid_female1_trisomy18study


title: NB2486

description: primary untreated neuroblastoma tumour


title: NB2530

description: primary untreated neuroblastoma tumour


title: NB2495

description: primary untreated neuroblastoma tumour


title: NB2485

description: primary untreated neuroblastoma tumour


title: NB2483

description: primary untreated neuroblastoma tumour


title: NB2484

description: primary untreated neuroblastoma tumour


title: NB2083

description: primary untreated neuroblastoma tumour


title: NB1974

description: primary untreated neuroblastoma tumour


title: NB1972

description: primary untreated neuroblastoma tumour


title: Meningioma_3685_U133P2

status: Public on Nov 30 2010

city: Los Angeles

first: Stanley

middle: F

last: Nelson

state: CA

address: 695 Charles E. Young Drive South, Bldg Gonda, Rm 5554

department: Human Genetics

description: Hybridized to U133P2

hyb_protocol: Labeled and sheared cRNA was manually applied to Affymetrix Human Genome U133 Plus 2.0 Arrays (Santa Clara, CA).

scan_protocol: All microarrays were scanned using the Affymetrix GeneChip 3000 scanner.  All images were manually examined to confirm that none had surface defects and exhibited proper grid alignment.

data_processing: Raw probe intensity values in a .CEL format were generated for analysis using the Affymetrix Gene Chip Operating System (GCOS). Data were normalized using RMA with default settings from the Bioconductor R library.

source_name: Meningioma tumor 3685

label_protocol: 1ug of total RNA was used for single-round biotinylated probe synthesis using the Affymetrix Array Station device made by Caliper Life Sciences (Hopkinton, MA) by manufacturer’s protocols.

extract_protocol: For expression analysis, RNA was extracted from 20-50 mg tumor pieces using QiagenTM (Valencia, CA) RNA easy mini kits per manufacturer’s protocols.  Of 85 total biopsies, 68 samples had a 28s/18s ratio of 1.0 to 2.0 with minimal evidence of degradation or contamination and were selected for gene expression analysis.  The extracted total RNA was assessed for integrity using the 2100 Bioanalyzer by Agilent TechnologiesTM (Santa Clara, CA).

value: meningioma tumor

tag: who grade

tag: vital status

value: Alive

tag: tts

tag: gender

value: F

tag: age


title: Meningioma_3096_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 3096

tag: tissue

value: Deceased

value: M


title: Meningioma_748_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 748


title: Meningioma_4430_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 4430


title: Meningioma_1024_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 1024


title: Meningioma_3456_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 3456


title: Meningioma_2889_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 2889


title: Meningioma_2469_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 2469


title: Meningioma_3375_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 3375


title: Meningioma_3069_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 3069


title: Meningioma_822_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 822


title: Meningioma_3619_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 3619


title: Meningioma_2950_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 2950


title: Meningioma_2281_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 2281


title: Meningioma_3489_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 3489


title: Meningioma_2827_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 2827


title: Meningioma_3300_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 3300


title: Meningioma_2354_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 2354


title: Meningioma_1919_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 1919


title: Meningioma_1916_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 1916


title: Meningioma_3720_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 3720


title: Meningioma_2364_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 2364


title: Meningioma_2461_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 2461


title: Meningioma_2078_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 2078


title: Meningioma_3655_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 3655


title: Meningioma_2042_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 2042


title: Meningioma_2891_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 2891


title: Meningioma_2407_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 2407


title: Meningioma_1702_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 1702


title: Meningioma_2232_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 2232


title: Meningioma_1811_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 1811


title: Meningioma_1048_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 1048


title: Meningioma_1356_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 1356


title: Meningioma_984_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 984


title: Meningioma_1937_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 1937


title: Meningioma_989_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 989


title: Meningioma_1391_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 1391


title: Meningioma_941_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 941


title: Meningioma_985_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 985


title: Meningioma_856_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 856


title: Meningioma_765_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 765


title: Meningioma_795_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 795


title: Meningioma_816_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 816


title: Meningioma_908_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 908


title: Meningioma_776_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 776


title: Meningioma_760_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 760


title: Meningioma_977_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 977


title: Meningioma_1378_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 1378


title: Meningioma_788_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 788


title: Meningioma_789_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 789


title: Meningioma_731_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 731


title: Meningioma_798_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 798


title: Meningioma_758_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 758


title: Meningioma_769_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 769


title: Meningioma_682_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 682


title: Meningioma_761_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 761


title: Meningioma_710_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 710


title: Meningioma_714_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 714


title: Meningioma_623_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 623


title: Meningioma_679_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 679


title: Meningioma_674_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 674


title: Meningioma_645_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 645


title: Meningioma_600_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 600


title: breast tumor part_IDC_rep1 5387

status: Public on Nov 04 2010

city: Taipei

first: Fon-Jou

last: Hsieh

address: No. 7, Chung-Shan South Rd

department: Department of obstetrics and gynecology

country: Taiwan

institute: National Taiwan University

description: breast tumor part_IDC_rep1

scan_protocol: Agilent Oligo Microarray Kit, hybridization protocol version 5.0 with Agilent scanner and Feature Extraction 6.0.

data_processing: Agilent Two-Color Microarray-Based Gene Expression Analysis, version 4.0. The log2 ratio for each gene was centered by subtracting the median across all samples to discriminate the subclass of the dataset.

source_name: Infiltrating Ductal Carcinoma (IDC), Buffer 1, ER(-), PR(-).

label_protocol: Agilent Low RNA Input Fluorescent Linear Amplification Kit, protocol version 2.0

growth_protocol: The fresh samples used for this study were immediately frozen by liquid nitrogen without any additional growth procedure applied before RNA extraction.

extract_protocol: Trizol reagent combined with RNAeasy mini kit

treatment_protocol: The surgical removed tumors and non-tumor part of breast specimens were excised, collected and snap-frozen in liquid nitrogen immediately before RNA extraction.

tag: er/pr/her status

tag: status

value: female

value: primary tumor

source_name: Commercially available.

tag: sample type

value: Stratagene's human common reference RNA


title: Meningioma_612_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 612


title: Meningioma_654_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 654


title: breast tumor part_IDC_rep1 5373

description: breast tumor part_IDC_rep1

hyb_protocol: Agilent Oligo Microarray Kit, hybridization protocol version 5.0


title: Meningioma_675_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 675


title: Meningioma_606_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 606


title: breast tumor part_IDC_rep1 5393

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5889

description: breast tumor part_IDC_rep1


title: Meningioma_609_U133P2

description: Hybridized to U133P2

source_name: Meningioma tumor 609


title: breast tumor part_IDC_rep1 5375

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5401

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5347

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5357

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5395

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5385

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5359

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5363

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5345

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5339

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5337

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5333

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5321

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5329

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5399

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5325

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5343

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5323

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5341

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5319

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5335

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5301

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5317

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5327

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4413

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4419

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5305

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4415

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4421

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 5307

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4411

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4409

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4417

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4407

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4399

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4397

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4403

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4405

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4387

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4395

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4393

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4385

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4391

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4377

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4373

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4389

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4379

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4375

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4371

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4355

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4365

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4369

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4381

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4361

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4367

description: breast tumor part_IDC_rep1


title: breast nontumor part_N_rep1 5437

description: breast nontumor part_N_rep1

source_name: non-tumor part, Buffer 1

value: non tumor part of breast tissue.


title: breast tumor part_IDC_rep1 4353

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4363

description: breast tumor part_IDC_rep1


title: breast nontumor part_N_rep1 5433

description: breast nontumor part_N_rep1


title: breast tumor part_IDC_rep1 4401

description: breast tumor part_IDC_rep1


title: breast tumor part_IDC_rep1 4359

description: breast tumor part_IDC_rep1


title: breast nontumor part_N_rep1 5435

description: breast nontumor part_N_rep1


title: breast nontumor part_N_rep1 5417

description: breast nontumor part_N_rep1


title: breast nontumor part_N_rep1 5427

description: breast nontumor part_N_rep1


title: breast nontumor part_N_rep1 5409

description: breast nontumor part_N_rep1


title: PC2

status: Public on Aug 01 2010

city: corvallis

first: palitha

last: dharmawardhana

state: OR

address: 321 richarson hall,OSU

institute: OSU

description: Nimblegen pipeline

hyb_protocol: Nimblegen pipeline

scan_protocol: Nimblegen pipeline

data_processing: Nimblegen pipeline, RMA normalization algorithm.

organism: Populus trichocarpa

source_name: Phloem and cortex

label_protocol: Nimblegen pipeline

tag: tissue type

value: Phloem and cortex

tag: tissue source

value: Populus trichocarpa Nisqually-1


title: NZK26

status: Public on Jun 25 2010

city: Dresden

first: Wuttig

last: Daniela

address: Fetscherstr. 74

department: Department of Urology

country: Germany

institute: Dresden, University of Technology

description: late metastatic primary clear-cell renal cell carcinoma, batch 2

hyb_protocol: Following fragmentation, 20 µg of cRNA were hybridized for 16 hr at 45°C on GeneChip HGU133 Plus 2.0 arrays. GeneChips were washed and stained using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS3000 7G (Affymetrix).

data_processing:
data for analysis:
study I: Met1-9, Met11-18, Met20, Met23, Met25 (n=20); study II: all samples (n=48)
Global background correction, quantile normalization and signal calculation were carried out using the RMAExpress 4.1 software. Data of primary ccRCC were batch corrected using the combat modul after all probe sets with less than 5/48 present signals were excluded. Data of all samples were filtered (max-min > 100; max/min > 3; ceiling = 16000, threshold = 20).

source_name: primary clear-cell renal cell carcinoma

label_protocol: Biotinylated cRNA were prepared according to the One-Cycle Target Labeling and Control Reagents Kit protocol (Affymetrix, Santa Clara, USA) from 1.0 - 2.5 µg total RNA.

extract_protocol:
primary ccRCC were obtained by (partial) nephrectomy in the Departments of Urology in the University Hopitals Dresden or Jena.
Cryo-sections (4 µm) of snap-frozen tissues were made and homogenized using QiaShredder (Qiagen, Hilden, Germany)
RNA was isolated with the RNeasy Mini Kit (Qiagen) with additional DNA digestion (RNase-Free DNase Set, Qiagen).

value: primary clear-cell renal cell carcinoma

value: male

tag: tumor stage (uicc 2002)

tag: lymph node status

tag: initial distant metastases

tag: tumor grade

tag: dfs/follow-up

value: DFS = 82 months

tag: localisation of metastases

value: lung, skin


title: NZK27

value: DFS = 90 months

value: lung


title: NZK25

description: early metastatic primary clear-cell renal cell carcinoma, batch 2

value: DFS = 0 months

value: lymph node


title: NZK24


title: breast tumor part_IDC_rep1 4383

description: breast tumor part_IDC_rep1


title: NZK23

value: skin


title: Cord blood CD4+_Act_12h_rep2

city: Turku

first: Henna

last: Kallionpää

address: P.O. Box 123

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

description: biological replicate 2

hyb_protocol: 15 ug of biotinylated and fragmented cRNA was hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays overnight (16-18 hours) at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with AutoLoader.

data_processing: The PM probe intensities were quantile-normalized using the R/Bioconductor package affy and log2-transformed. To identify consistent changes across the biological replicates, the probe-level expression change averaging procedure (PECA) was applied (Elo et al., Nucleic Acids Res 33:e193, 2005). The benefit of this approach is that is that the reliability of estimation can be improved by considering the distribution of probe-level expression changes instead of a single probeset-level value. Specifically, linear modeling with moderated F- and t-statistics was first applied to the probe-level time series data using the R/Bioconductor package limma and the obtained probe-level estimates were then summarized into probeset-level values using the Tukey biweight average. The probe-level estimates are contained in the sample (57) data tables. Since the PECA-estimation requires always at least two samples to be compared, the probeset-level data is represented as a supplemental file on the Series record and contains the PECA-estimates for the signal log-ratios between each non-Thp sample (54) and the corresponding Th cell precursor-samples (0h timepoint).

source_name: human cord blood CD4+ cell, activated, 12h

label_protocol: Amplification used 100 ng of total RNA using the Affymetrix Two-Cycle cDNA Synthesis Kit (P/N 900432), and cDNA/cRNA synthesis reactions and sample cleanup steps were performed according to Affymetrix´s GeneChip Expression Analysis Technical Manual.

growth_protocol: Umbilical cord blood was collected from healthy neonates born in Turku University Hospital, Hospital District of Southwest Finland. Mononuclear cells were isolated with Ficoll-Paque (Amersham Biosciences) gradient centrifugation, and CD4+ cell population was purified using magnetic beads (Dynal CD4 Positive Isolation Kit, Invitrogen) according to manufacturer's instructions.

extract_protocol: Total RNA was extracted using the RNeasy mini kit (Qiagen) according to manufacturer's instructions. In-column DNase (RNase-Free Dnase Set, Qiagen) treatment was performed for 15 minutes. RNA was eluted in dH2O.

treatment_protocol: Cells were activated on 24-well plates, 4x106 cells/1ml Yssel´s medium, through the T cell receptor (plate bound antiCD3 500 ng/well, and soluble antiCD28 500 ng/ml, Immunotech, France), and to half of the samples IL-4 (10ng/ml, R&D Systems) and anti IL-12 (10µg/ml, R&D Systems) were added to induce Th2 polarization. At 48h timepoint IL-2 (17ng/ml, R&D Systems) was added to the culture medium. Cells were harvested at 0.5, 1, 2, 4, 6, 12, 24, 48 and 72 h. Naive cells without any treatment were collected as 0h controls for every replicate.

value: cord blood

tag: cell type

value: CD4+ T cells


title: Cord blood CD4+_Act_72h_rep3

description: biological replicate 3

source_name: human cord blood CD4+ cell, activated, 72h


title: Cord blood CD4+_Act_12h_rep3

description: biological replicate 3


title: Cord blood CD4+_Act+IL-4_72h_rep3

description: biological replicate 3

source_name: human cord blood CD4+ cell, activated and IL-4 treated, 72h


title: Cord blood CD4+_Act+IL-4_24h_rep3

description: biological replicate 3

source_name: human cord blood CD4+ cell, activated and IL-4 treated, 24h


title: Cord blood CD4+_Act_48h_rep1

description: biological replicate 1

source_name: human cord blood CD4+ cell, activated, 48h


title: Cord blood CD4+_0h_rep2

description: biological replicate 2

source_name: human cord blood CD4+ cell, 0h


title: Cord blood CD4+_Act+IL-4_48h_rep3

description: biological replicate 3

source_name: human cord blood CD4+ cell, activated and IL-4 treated, 48h


title: Cord blood CD4+_Act_24h_rep1

description: biological replicate 1

source_name: human cord blood CD4+ cell, activated, 24h


title: NZK17

description: early metastatic primary clear-cell renal cell carcinoma, batch 1

value: lung, mediastinal


title: NZK22

value: female

value: DFS = 1 month


title: Cord blood CD4+_Act+IL-4_12h_rep3

description: biological replicate 3

source_name: human cord blood CD4+ cell, activated and IL-4 treated, 12h


title: Cord blood CD4+_Act+IL-4_72h_rep2

description: biological replicate 2


title: NZK19_Wied

description: non-metastatic primary clear-cell renal cell carcinoma, batch 1

value: Follow-up = 140 months


title: Cord blood CD4+_Act_48h_rep3

description: biological replicate 3


title: Cord blood CD4+_Act+IL-4_72h_rep1

description: biological replicate 1


title: Cord blood CD4+_Act+IL-4_12h_rep2

description: biological replicate 2


title: Cord blood CD4+_Act+IL-4_24h_rep1

description: biological replicate 1


title: Cord blood CD4+_Act_12h_rep1

description: biological replicate 1


title: Cord blood CD4+_Act_48h_rep2

description: biological replicate 2


title: Cord blood CD4+_Act+IL-4_24h_rep2

description: biological replicate 2


title: NZK18

value: Follow-up = 130 months


title: NZK 13

description: late metastatic primary clear-cell renal cell carcinoma, batch 4

value: DFS = 96 months

value: lymph node, lung


title: Cord blood CD4+_0h_rep1

description: biological replicate 1


title: Cord blood CD4+_0h_rep3

description: biological replicate 3


title: Cord blood CD4+_Act_24h_rep3

description: biological replicate 3


title: Cord blood CD4+_Act_72h_rep2

description: biological replicate 2


title: NZK16

description: late metastatic primary clear-cell renal cell carcinoma, batch 1

value: primary clear-cell renal cell carcinoma

value: male

value: DFS = 60 months

value: adrenal gland, renal, pancreas, parotis


title: Cord blood CD4+_Act+IL-4_12h_rep1

description: biological replicate 1


title: NZK 14

description: non-metastatic primary clear-cell renal cell carcinoma, batch 4

value: Follow-up = 148 months


title: Cord blood CD4+_Act+IL-4_48h_rep2

description: biological replicate 2


title: NZK 10

value: Follow-up = 112 months


title: NZK 9

value: DFS = 45 months

value: lung, bone, adrenal gland


title: NZK 11

value: DFS = 63 months

value: lung


title: NZK 12

value: Follow-up = 143 months


title: Cord blood CD4+_Act_24h_rep2

description: biological replicate 2

value: cord blood

value: CD4+ T cells


title: NZK 8

value: female

value: Follow-up = 99 months


title: Cord blood CD4+_Act+IL-4_48h_rep1

description: biological replicate 1


title: NZK 7

description: early metastatic primary clear-cell renal cell carcinoma, batch 4

value: DFS = 0 months

value: lymph node


title: NZK 5

value: primary clear-cell renal cell carcinoma

value: bone


title: NZK 4

value: DFS = 6 months

value: lung, adrenal gland, renal


title: NZK 6

value: male

value: Follow-up = 155 months


title: NZK 2

description: early metastatic primary clear-cell renal cell carcinoma, batch 3

value: lung, liver


title: Renal_Cell_Carcinoma_E7

status: Public on Feb 17 2010

description: Gene expression data from Human RCC sample

scan_protocol: Agilent gene chips were scanned on an Agilent model C scanner by UNC Lineberger Comprehensive Cancer Center Genomics Core

data_processing: Data was retrieved from the UNC Microarray Database as LOWESS normalized, log2 of processed Red/Green signal (median), filter for 70% good data (Exclude if spot is not found in either channel, spot or spot background is a non-uniform outlier, spot or spot background is a non-uniform outlier for the population, spot is not a positive and significant signal in either channel, or Ch1 and 2 lowess normalized net (median) <10). Missing data was imputed with KNN (k=10) in SAM. Data from three RNA preparation types was merged using Distance Weighted Discriminant. Each array was standard normalized (subtract the mean of the array and divide by the standard deviation).

source_name: Renal Clear Cell Carcinoma

label_protocol: Tumor sample RNA and reference RNA was labelled using the Agilent Two-Color Microarray-Based Gene Expression Analysis v 5.2 protocol by UNC Lineberger Comprehensive Cancer Center Genomics Core.

extract_protocol:
Frozen RCCs were obtained through University of North Carolina - Chapel Hill's Tissue Procurement Facility
RNA was extracted with a Qiagen RNeasy kit.
RNA quality was determined using an Agilent LabChip Bioanalyzer. H&E was performed on tumor tissue samples to confirm clear cell or normal histopathology

tag: identifier

value: kidney

tag: histology

value: Clear Cell

tag: disease state

value: Clear Cell Carcinoma

tag: biosourcetype

value: Frozen Sample

source_name: Perou lab reference RNA

value: Cancer cell lines

tag: cell line

value: various cancer cell lines (reference)


title: NZK 1

description: late metastatic primary clear-cell renal cell carcinoma, batch 3

tag: tissue

tag: gender

value: DFS = 106 months

value: lymph node, bone, adrenal gland


title: Renal_Cell_Carcinoma_C3


title: Renal_Cell_Carcinoma_D4


title: Renal_Cell_Carcinoma_E4


title: Renal_Cell_Carcinoma_C9


title: Renal_Cell_Carcinoma_A5a


title: Renal_Cell_Carcinoma_A6


title: Renal_Cell_Carcinoma_E5


title: Renal_Cell_Carcinoma_D3


title: Renal_Cell_Carcinoma_E6


title: Renal_Cell_Carcinoma_C11


title: Renal_Cell_Carcinoma_D6


title: Renal_Cell_Carcinoma_D9


title: Renal_Cell_Carcinoma_D5


title: Renal_Cell_Carcinoma_D10


title: Renal_Cell_Carcinoma_C7


title: Renal_Cell_Carcinoma_D8


title: NZK 3

value: female

value: DFS = 83 months

value: lung, soft tissue


title: Renal_Cell_Carcinoma_C11a


title: Renal_Cell_Carcinoma_A9


title: Renal_Cell_Carcinoma_D11


title: Renal_Cell_Carcinoma_A28


title: Renal_Cell_Carcinoma_A26a


title: Renal_Cell_Carcinoma_11


title: Renal_Cell_Carcinoma_12


title: Renal_Cell_Carcinoma_A10


title: Renal_Cell_Carcinoma_17


title: Renal_Cell_Carcinoma_A26


title: Renal_Cell_Carcinoma_30


title: Renal_Cell_Carcinoma_1


title: Renal_Cell_Carcinoma_15


title: Renal_Cell_Carcinoma_5


title: UNC07-0475A

status: Public on Jan 07 2010

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

description:
A4by44k_5403C
Agilent Catalog 4 by 44k whole genome array of UNC07-0475A

hyb_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were analyzed with Agilent software.

data_processing: Data for both channels were Lowess-normalized using the University of North Carolina (UNC) microarray database, and then the log(2) ratio (test/reference) was taken.

source_name: Human Reference B

extract_protocol: Total RNA isolated by Stratagene.

tag: sample type

value: reference

tag: composition

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs

source_name: Normal Tissue Adjacent to Breast Tumor

extract_protocol: Qiagen RNeasy Kit.

value: normal tissue adjacent to breast tumor

tag: patient id

tag: active or "inactive"

value: negative

tag: age at diagnosis (year)

tag: menopause status

value: Post

tag: histopathology

value: Invasive

tag: breast cancer subtype (pam50)

value: Lum A

tag: er status

value: positive

tag: hormone treated

value: yes

tag: her2 status

tag: tumor size (cm)

tag: overall survival event (dead=1, alive=0)

tag: overall survival (month)


title: Renal_Cell_Carcinoma_8

tag: identifier

value: kidney

tag: histology

value: Clear Cell

tag: disease state

value: Clear Cell Carcinoma

tag: biosourcetype

value: Frozen Sample

tag: cell line


title: UNC06-1291A, rep2

description:
A4by44k_5403A
Agilent Catalog 4 by 44k whole genome array of UNC06-1291A

label_protocol: Described in Hu et al., 2005, BioTechniques, 38:121-124 (PMID: 15679094).

tag: sample type

tag: composition

tag: tissue

tag: patient id

tag: tumor grade


title: Renal_Cell_Carcinoma_4

value: Cancer cell lines

value: various cancer cell lines (reference)


title: UNC06-0121A

description:
A4by44k_5403D
Agilent Catalog 4by44k whole genome array of UNC06-0121A

tag: active or "inactive"

tag: age at diagnosis (year)

tag: menopause status

value: Pre

tag: histopathology

tag: breast cancer subtype (pam50)


title: UNC06-1381A, rep2

description:
A4by44k_5403B
Agilent Catalog 4 by 44k whole genome array of UNC06-1381A

tag: er status

tag: hormone treated

tag: her2 status

tag: tumor size (cm)

tag: overall survival event (dead=1, alive=0)


title: UNC06-1117A

description:
A4by44k_5404
Agilent Catalog 4 by 44k whole genome array of UNC06-1117A

value: unknown

tag: overall survival (month)


title: Renal_Cell_Carcinoma_2

tag: identifier

tag: histology

tag: disease state

tag: biosourcetype

tag: cell line


title: UNC06-1291A, rep1

description:
H1AUNC244k-v3-0102
Agilent Custom array of UNC06-1291A

tag: sample type

value: reference

tag: composition

tag: tissue

tag: patient id

tag: tumor grade


title: UNC99-0428A

description:
251976010069-244K
Agilent Catalog 4 by 44k whole genome array UNC99-0428A, TEST SET

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs

tag: active or "inactive"

tag: age at diagnosis (year)

tag: menopause status

tag: histopathology

tag: breast cancer subtype (pam50)

value: Her 2

value: no

value: positve


title: UNC07-0342A

description:
H1AUNC244k-v3-0107
Agilent Custom array of UNC07-0342A

value: normal tissue adjacent to breast tumor

value: negative

value: Post

value: Invasive

tag: er status

tag: hormone treated

tag: her2 status

tag: tumor size (cm)

tag: overall survival event (dead=1, alive=0)


title: UNC07-0021A

description:
H1AUNC244k-v3-0105
Agilent Custom array of UNC07-0021A

value: positive

value: Lum B

value: yes

tag: overall survival (month)


title: UNC06-1381A, rep1

description:
H1AUNC244k-v3-0103
Agilent Custom array of UNC06-1381A

value: Lum A


title: UNC99-0456A

description:
H1AUNC244k-0377
Agilent Custom array of UNC99-0456A


title: UNC99-0364A

description:
H1AUNC244k-0340
Agilent Custom array of UNC99-0364A

value: Basal-like


title: UNC07-0726A

description:
251976010084-244K
Agilent Catalog 4 by 44k whole genome array UNC07-0726A, TEST SET


title: UNC99-0543A

description:
H1AUNC244k-0378
Agilent Custom array of UNC99-0543A


title: UNC99-0363A

description:
H1AUNC244k-0339
Agilent Custom array of UNC99-0363A


title: UNC06-1067A

description:
H1AUNC244k-v3-0101
Agilent Custom array of UNC06-1067A


title: UNC07-1567A

description:
251976010086-244K
Agilent Catalog 4 by 44k whole genome array UNC07-1567A, TEST SET


title: UNC05-0618A

description:
251976010078-244K
Agilent Catalog 4 by 44k whole genome array UNC05-0618A, TEST SET


title: UNC99-0306A

description:
H1AUNC244k-0397
Agilent Custom array of UNC99-0306A


title: UNC06-1413A

description:
H1AUNC244k-v3-0104
Agilent Custom array of UNC06-1413A


title: UNC06-0678A

description:
H1AUNC244k-v3-0082
Agilent Custom array of UNC06-0678A


title: UNC06-0694A

description:
H1AUNC244k-v3-0083
Agilent Custom array of UNC06-0694A


title: UNC99-0339A

description:
H1AUNC244k-0398
Agilent Custom array of UNC99-0339A


title: UNC07-0804A

description:
251976010085-244K
Agilent Catalog 4 by 44k whole genome array UNC07-0804A, TEST SET


title: VARI_009T

status: Public on Jan 05 2010

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with custom CDF environments created by the MBNI - The version 11 entrez gene ID CDF was used.

source_name: Homo Sapiens

label_protocol: 10 ug of Qiagen-purified total RNA

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

tag: subtype

value: clear cell


title: UNC99-0182A

description:
H1AUNC244k-0394
Agilent Custom array of UNC99-0182A

tag: sample type


title: VARI_005T

description:
ARFGEF1
SETD2
VHL


title: UNC06-0545A

description:
251976010080-244K
Agilent Catalog 4 by 44k whole genome array UNC06-0545A, TEST SET

tag: composition

value: Pre


title: VARI_004T

description: VHL


title: UNC99-0216A

description:
H1AUNC244k-0396
Agilent Custom array of UNC99-0216A

tag: tissue


title: UNC06-0117A

description:
251976010079-244K
Agilent Catalog 4 by 44k whole genome array UNC06-0117A, TEST SET

tag: patient id

value: Normal-like


title: UNC07-0158A

description:
H1AUNC244k-v3-0106
Agilent Custom array of UNC07-0158A

value: reference

tag: tumor grade


title: VARI_002T

description: Gene expression ratios were obtained from human Clear Cell kidney tumor and normal kidney tissues.


title: VARI_003T

description:
PFTK2
VHL


title: VARI_001T


title: VARI_007T

description:
DGKK
N4BP2
PTBP1
RNF20
TEK
USP53
WNK3


title: VARI_008T

description:
BUB1B
VHL


title: VARI_006T

description:
FRS2
IER2
MAGI1
PTPN11


title: UNC99-0158A

description:
H1AUNC244k-0393
Agilent Custom array of UNC99-0158A

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs

tag: active or "inactive"

value: unknown


title: UNC99-0281A

description:
H1AUNC244k-0323
Agilent Custom array of UNC99-0281A

tag: age at diagnosis (year)

value: no


title: UNC05-0088A

description:
251976010073-244K
Agilent Catalog 4 by 44k whole genome array UNC05-0088A, TEST SET

tag: menopause status

value: Her 2


title: UNC99-0141A

description:
H1AUNC244k-0395
Agilent Custom array of UNC99-0141A

value: normal tissue adjacent to breast tumor

tag: histopathology


title: VARI_209T

description: VHL

hyb_protocol: GeneChips were washed and stained in the Affymetrix hybridization oven 640.


title: UNC05-0521A

description:
251976010077-244K
Agilent Catalog 4 by 44k whole genome array UNC05-0521A, TEST SET

tag: breast cancer subtype (pam50)

value: positve


title: UNC05-0093A

description:
251976010074-244K
Agilent Catalog 4 by 44k whole genome array UNC05-0093A, TEST SET

tag: er status

value: negative


title: VARI_297T


title: VARI_292T


title: VARI_235T


title: VARI_195T

description: VHL


title: VARI_232T


title: VARI_322T

description: UTX


title: VARI_155T

description: UTX


title: VARI_148T


title: VARI_143T


title: VARI_112T


title: VARI_110T

description:
FBXO21
GRIPAP1
LRGUK
PALB2
PPP1R3G
PUS10
VHL


title: VARI_136T


title: UNC05-0364A

description:
251976010076-244K
Agilent Catalog 4 by 44k whole genome array UNC05-0364A, TEST SET

value: Post

value: Invasive

tag: hormone treated


title: UNC03-0477A

description:
H1AUNC244k-0343
Agilent Custom array of UNC03-0477A

value: Lum B

value: positive

tag: her2 status


title: VARI_107T

description:
CUL3
JARID1C
NFYC
PHF14
TAF2
VHL


title: UNC04-0547A

description:
H1AUNC244k-0324
Agilent Custom array of UNC04-0547A

tag: tumor size (cm)


title: UNC04-0095A

description:
251976010071-244K
Agilent Catalog 4 by 44k whole genome array of UNC04-0095A, TEST SET

value: Lum A

value: yes

tag: overall survival event (dead=1, alive=0)


title: VARI_105T

description:
ASH1L
CARD10
CSMD3
HUWE1
PPP2R1A
RAPGEF4
RHCG
SETD2
TOP1
VHL
WISP1

value: clear cell


title: VARI_103T

description:
BUB1
COG6
GRIN2A
POLK
POLN
PTPRZ1
USP54
VHL


title: VARI_099T

description:
ARID1A
GNG11
ITGAM
KIF16B
TNPO1
VHL
ZNF189
ZNF423


title: VARI_066T

description:
CASP3
CCNH
HSCB
MLL2
VHL


title: VARI_064T

description:
LAMC1
MLL
RAB8B
VHL


title: VARI_081T

description:
PPM1F
VHL


title: VARI_097T

description:
ADH6
FANCC
TNFRSF19
VHL
XRCC6


title: VARI_059T

description:
ATM
GNAQ
NLRP8
PPFIBP1
UBR4
VHL


title: VARI_073T

description:
DNAJC16
FCRL4
MTM1
PDZRN4
PRKAG1
PTPRC
UTX
VHL
WBP4


title: VARI_067T

description:
CARD11
CSMD3
DDX21
LRP6
XPO5


title: VARI_080T


title: VARI_060T


title: VARI_063T

description:
AKAP4
CCND2
DDX23
HECW2
MED14
MEX3B
RIF1
TRIP11
UAP1
VHL
WRN


title: VARI_053T

description:
CAD
SETD2
SMARCA4
SNX2
VHL


title: UNC00-0164A

description:
H1AUNC244k-0379
Agilent Custom array of UNC00-0164A

tag: overall survival (month)


title: VARI_044T

description:
ADAMTS13
ALDH3B2
COL14A1
DLC1
DNAH8
IGF2BP1
PPM1B
SPSB2
UBP1

tag: subtype


title: VARI_041T

description:
ASB16
UBP1


title: UNC98-2048A

description:
H1AUNC244k-0322
Agilent Custom array of UNC98-2048A

tag: sample type


title: UNC04-0115A

description:
H1AUNC244k-0332
Agilent Custom array of UNC04-0115A

tag: composition

value: Pre

value: Basal-like


title: UNC02-0575A

description:
H1AUNC244k-0342
Agilent Custom array of UNC02-0575A

value: reference

tag: tissue


title: VARI_141T

description: Gene expression ratios were obtained from human Clear Cell kidney tumor and normal kidney tissues.


title: UNC04-0550A

description:
H1AUNC244k-0341
Agilent Custom array of UNC04-0550A

value: Stratagene Human Universal Reference containing 1/10 added MCF7 and ME16C RNAs

tag: patient id


title: VARI_089T


title: VARI_398T


title: VARI_035T

description: VHL


title: VARI_414T

description: UTX


title: VARI_361T


title: VARI_144T


title: VARI_156T


title: VARI_274T

description:
ITPR2
SETD2
VHL


title: VARI_137T


title: VARI_175T

description:
SETD2
VHL


title: VARI_365T

description:
ADAMTS18
CSMD3
SETD2
VHL


title: VARI_245T


title: VARI_256T

description:
SETD2
VHL


title: VARI_200T


title: VARI_139T


title: VARI_352T


title: VARI_130T


title: VARI_176T


title: VARI_194T


title: VARI_109T

description:
ADAMTS20
C3orf63
DDX24
HSPA1L
RICTOR
TRIP4
VHL


title: UNC98-0107A

description:
H1AUNC244k-0327
Agilent Custom array of UNC98-0107A

value: unknown

tag: tumor grade


title: VARI_216T

description:
SETD2
VHL


title: VARI_268T


title: VARI_225T


title: VARI_117T


title: VARI_120T


title: VARI_116T


title: VARI_115T

description:
VHL
VPS13B


title: VARI_106T


title: VARI_108T


title: VARI_113T


title: VARI_126T

description:
JARID1C
VHL


title: VARI_100T


title: VARI_098T

description:
ADAM18
ATRX
BRE
EIF3E
GLI3
MYH9
NIN
NIPBL
NUP88
ORAI2
PIP5K3
RECQL5
SMYD4
TLK2
TNKS2
USP36
VHL
ZRANB1


title: VARI_102T


title: VARI_094T

description:
DDB2
DEK
IPO4
MAFG
NUP98
RABGAP1
SMG6
VHL


title: VARI_101T


title: VARI_092T

description:
CAD
ERCC3
FGD5
NOTCH2
USP24


title: VARI_086T

description:
CTSZ
GPLD1
IGBP1
PLCB2
SETD2
STCH
VHL


title: VARI_087T

description:
BDKRB2
CTNNA1
HUS1
ITPR2
POLI
PPARG
PROM1
TFDP2
VHL
XPO7


title: VARI_090T

description:
CLSPN
VHL


title: VARI_084T

description:
ALDH7A1
CCNG1
FOXA2
MDH1
PML
SMC6
UBR4
VHL


title: VARI_078T

description:
NFKBIB
NME2
UBR5


title: VARI_075T

description:
AKAP3
CCR3
DHX8
MLL4
MMP16
TRIM32
VHL


title: VARI_091T

description:
ASB8
POU2AF1
TNKS2
VHL


title: VARI_074T

description:
PINX1
VHL


title: VARI_088T

description:
ADSS
LOC402569
PTPN13
TOPBP1
VHL


title: VARI_085T


title: VARI_083T

description:
BIRC7
ITGA10


title: VARI_070T

description:
APC
BCOR
MCF2L
MLL2
NOV
NSD1
PDHX
PIP5KL1
TRPS1
UBA5
VHL


title: VARI_071T

description:
ARL6IP2
FMO4
NR1D2
TRIM29


title: VARI_076T


title: VARI_093T

description:
ARHGEF11
ESRRG
FAM5C
GDF11
KLK3
MMP3
MYBL2
NCAPD2
NLRP5
PC
PGM1
PPP2R2C
PTPN22
PTPRF
PTPRJ
SPHK1
TMEM74
TRAD
VAV1
VHL


title: VARI_072T


title: VARI_079T


title: VARI_050T


title: VARI_068T

description:
PMS1
TP53
VHL


title: VARI_062T

description:
AKAP4
KNTC1
TP53BP1


title: VARI_049T

description:
AKAP4
MED1
VHL


title: VARI_055T

description:
SEMA3B
VHL


title: VARI_057T

description:
JMJD1B
NF1
PAX1
TRIM56
VHL


title: VARI_056T

description:
AK3L1
VHL


title: VARI_058T


title: VARI_051T

description: PTPLB


title: VARI_061T


title: VARI_052T

description:
CDKN2A
CERKL
CUL7
FMO4
NCAPG2
NLRP10
SOCS4
SUV420H1
TOP3B
UBR4
VHL


title: VARI_039T

description:
JARID1C
PTEN
RNF123
SPIB


title: VARI_042T


title: VARI_036T


title: VARI_031T


title: VARI_045T

description:
DKK1
ENPP2
SETD2


title: VARI_048T


title: VARI_047T

description:
ADAM32
DDX20
MDC1
MDH1
MLL
PLEKHA5
VHL


title: VARI_032T

description:
ATM
CHST12
DDX27
DUSP22
ITPR2
MGA
NINJ1
NODAL
PTPRK
SGMS1
SMG1
SNRPA1
TPO


title: VARI_034T

description:
VHL
XPO4


title: VARI_033T

description:
CDC5L
DDX19B
DGKQ
DHX16
ESPL1
FBXL15
GNAZ
ITPR3
MLL
PPP1R3G
RNF144A
TRIO
UMPS


title: VARI_037T

description:
BTG2
OCRL
VHL


title: VARI_027T

description:
CDC25A
FRAP1


title: VARI_427T


title: VARI_029T


title: VARI_025T

description:
BMPR1A
RIOK2


title: VARI_026T

description:
DDX23
MGA
VHL


title: VARI_030T

description:
ARNT
C19orf2
CADM2
CDKN2C
DDX27
ICK
MMP10
SEMA4B
TOPBP1
VHL


title: VARI_028T

description:
ARHGAP20
COPS4
MAST4
PTPN18
SERPINA11
VHL


title: VARI_024T

description:
CARD11
LOC441344
PAFAH1B2


title: VARI_023T


title: VARI_016T

description:
KCNV1
MERTK
NUP188


title: VARI_021T

description: VHL


title: VARI_017T


title: VARI_014T


title: VARI_013T

description:
DNAJC18
SBK1
SERPINB10
VHL


title: VARI_019T


title: VARI_015T

description: VHL


title: MILES stage 2 data N2_1140

status: Public on Sep 30 2009

city: Pleasanton

first: Wei-Min

last: Liu

address: 4300 Hacienda Drive

institute: Roche Molecular Systems

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

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

data_processing: Data pre-processing included a summarization and quantile normalization step to generate probe set level signal intensities for each microarray experiment and was performed as previously published by Liu WM et al. PQN and DQN: algorithms for expression microarrays. J.Theor.Biol. 2006;243:273-278.

source_name: Leukemia patient sample

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

growth_protocol: not applicable

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

treatment_protocol: Samples are from untreated patients.

value: bone marrow

tag: leukemia class

value: MDS


title: MILES stage 2 data N2_1148

value: peripheral blood

value: AML with normal karyotype + other abnormalities


title: VARI_011T

description:
DDR2
INSRR


title: MILES stage 2 data N2_1150

value: AML with t(15;17)


title: MILES stage 2 data N2_1141


title: MILES stage 2 data N2_1149

value: ALL with t(12;21)


title: MILES stage 2 data N2_1147

value: CLL


title: MILES stage 2 data N2_1143


title: MILES stage 2 data N2_1146

value: T-ALL


title: VARI_012T

description:
FLT4
MAPK8


title: MILES stage 2 data N2_1139


title: MILES stage 2 data N2_1144

value: Non-leukemia and healthy bone marrow


title: MILES stage 2 data N2_1142

value: AML with t(8;21)


title: MILES stage 2 data N2_1138


title: MILES stage 2 data N2_1145

value: ALL with t(1;19)


title: MILES stage 2 data N2_1151


title: VARI_020T

description:
CNKSR1
VTN

value: clear cell


title: MILES stage 2 data N2_1152


title: MILES stage 2 data N2_1137


title: MILES stage 2 data N2_1136

value: CML


title: MILES stage 2 data N2_1135


title: MILES stage 2 data N2_1130


title: MILES stage 2 data N2_1131


title: MILES stage 2 data N2_1128


title: MILES stage 2 data N2_1127


title: MILES stage 2 data N2_1126

value: c-ALL/Pre-B-ALL with t(9;22)


title: MILES stage 1 data N1_1903


title: MILES stage 2 data N2_1120


title: MILES stage 2 data N2_1121


title: MILES stage 2 data N2_1119


title: MILES stage 2 data N2_1133


title: MILES stage 2 data N2_1114


title: MILES stage 2 data N2_1118

value: c-ALL/Pre-B-ALL without t(9;22)


title: MILES stage 2 data N2_1115

value: Pro-B-ALL with t(11q23)/MLL


title: MILES stage 2 data N2_1129


title: MILES stage 2 data N2_1113


title: MILES stage 2 data N2_1116


title: MILES stage 2 data N2_1117

value: AML complex aberrant karyotype


title: MILES stage 2 data N2_1111

value: bone marrow


title: MILES stage 2 data N2_1122


title: MILES stage 2 data N2_1124


title: MILES stage 2 data N2_1112

value: MDS


title: MILES stage 2 data N2_1110


title: MILES stage 2 data N2_1123


title: MILES stage 1 data N1_1988


title: MILES stage 2 data N2_1125

value: peripheral blood


title: MILES stage 2 data N2_1108


title: MILES stage 2 data N2_1132


title: MILES stage 2 data N2_1107


title: MILES stage 2 data N2_1109


title: MILES stage 2 data N2_1106


title: MILES stage 2 data N2_1104


title: MILES stage 2 data N2_1105


title: MILES stage 2 data N2_1093


title: MILES stage 2 data N2_1095


title: MILES stage 2 data N2_1091


title: MILES stage 2 data N2_1094


title: MILES stage 2 data N2_1103


title: MILES stage 2 data N2_1092


title: MILES stage 2 data N2_1090


title: MILES stage 2 data N2_1101

value: AML with normal karyotype + other abnormalities


title: MILES stage 2 data N2_1089


title: MILES stage 2 data N2_1088


title: MILES stage 2 data N2_1099


title: MILES stage 2 data N2_1098


title: MILES stage 2 data N2_1097


title: MILES stage 2 data N2_1102


title: MILES stage 2 data N2_1100


title: MILES stage 2 data N2_1096


title: MILES stage 2 data N2_1086

value: ALL with hyperdiploid karyotype


title: MILES stage 2 data N2_1085


title: MILES stage 2 data N2_1087


title: MILES stage 2 data N2_1084


title: MILES stage 2 data N2_1081


title: MILES stage 2 data N2_1083

value: ALL with t(12;21)


title: MILES stage 2 data N2_1082


title: MILES stage 2 data N2_1079


title: MILES stage 2 data N2_1078

value: CLL


title: MILES stage 2 data N2_1080


title: MILES stage 2 data N2_1076

value: AML with t(15;17)


title: MILES stage 2 data N2_1077


title: MILES stage 2 data N2_1075

value: Non-leukemia and healthy bone marrow


title: MILES stage 2 data N2_1074

value: T-ALL


title: MILES stage 2 data N2_1073

value: AML with t(8;21)


title: MILES stage 2 data N2_1067


title: MILES stage 2 data N2_1072


title: MILES stage 2 data N2_1064


title: MILES stage 2 data N2_1066


title: MILES stage 2 data N2_1065


title: MILES stage 2 data N2_1071


title: MILES stage 2 data N2_1063


title: MILES stage 2 data N2_1070


title: MILES stage 2 data N2_1068


title: MILES stage 2 data N2_1062


title: MILES stage 2 data N2_1055


title: MILES stage 2 data N2_1056


title: MILES stage 2 data N2_1053


title: MILES stage 2 data N2_1058


title: MILES stage 2 data N2_1060


title: MILES stage 2 data N2_1059


title: MILES stage 2 data N2_1054


title: MILES stage 2 data N2_1052


title: MILES stage 2 data N2_1069


title: MILES stage 2 data N2_1061


title: MILES stage 2 data N2_1057


title: MILES stage 2 data N2_1045


title: MILES stage 2 data N2_1044


title: MILES stage 2 data N2_1050


title: MILES stage 2 data N2_1048


title: MILES stage 2 data N2_1049


title: MILES stage 2 data N2_1046


title: MILES stage 2 data N2_1047


title: MILES stage 2 data N2_1043


title: MILES stage 2 data N2_1051


title: MILES stage 2 data N2_1042


title: MILES stage 2 data N2_1037


title: MILES stage 2 data N2_1038


title: MILES stage 2 data N2_1036


title: MILES stage 2 data N2_1041


title: MILES stage 2 data N2_1034


title: MILES stage 2 data N2_1039


title: MILES stage 2 data N2_1134


title: MILES stage 2 data N2_1035


title: MILES stage 2 data N2_1033


title: MILES stage 2 data N2_1027


title: MILES stage 2 data N2_1028


title: MILES stage 2 data N2_1029


title: MILES stage 2 data N2_1032


title: MILES stage 2 data N2_1031


title: MILES stage 2 data N2_1030


title: MILES stage 2 data N2_1026


title: MILES stage 2 data N2_1040


title: MILES stage 2 data N2_1025


title: MILES stage 2 data N2_1024


title: MILES stage 2 data N2_1023


title: MILES stage 2 data N2_1019


title: MILES stage 2 data N2_1022


title: MILES stage 2 data N2_1020


title: MILES stage 2 data N2_1018


title: MILES stage 2 data N2_1015


title: MILES stage 2 data N2_1021


title: MILES stage 2 data N2_1014


title: MILES stage 2 data N2_1012


title: MILES stage 2 data N2_1013


title: MILES stage 2 data N2_1011


title: MILES stage 2 data N2_1005


title: MILES stage 2 data N2_1007


title: MILES stage 2 data N2_1006


title: MILES stage 2 data N2_1010


title: MILES stage 2 data N2_1009


title: MILES stage 2 data N2_1016


title: MILES stage 2 data N2_1008


title: MILES stage 2 data N2_1017


title: MILES stage 2 data N2_1004


title: MILES stage 2 data N2_0997


title: MILES stage 2 data N2_0999


title: MILES stage 2 data N2_0998


title: MILES stage 2 data N2_0996


title: MILES stage 2 data N2_1002


title: MILES stage 2 data N2_0995


title: MILES stage 2 data N2_1003


title: MILES stage 2 data N2_0994


title: MILES stage 2 data N2_1001


title: MILES stage 2 data N2_0989


title: MILES stage 2 data N2_0992


title: MILES stage 2 data N2_0991


title: MILES stage 2 data N2_0990


title: MILES stage 2 data N2_0993


title: MILES stage 2 data N2_1000


title: MILES stage 2 data N2_0988


title: MILES stage 2 data N2_0987


title: MILES stage 2 data N2_0986


title: MILES stage 2 data N2_0985


title: MILES stage 2 data N2_0981


title: MILES stage 2 data N2_0982


title: MILES stage 2 data N2_0983


title: MILES stage 2 data N2_0979


title: MILES stage 2 data N2_0977


title: MILES stage 2 data N2_0978


title: MILES stage 2 data N2_0974


title: MILES stage 2 data N2_0984


title: MILES stage 2 data N2_0976


title: MILES stage 2 data N2_0975


title: MILES stage 2 data N2_0973


title: MILES stage 2 data N2_0970


title: MILES stage 1 data N1_0745


title: MILES stage 2 data N2_0971


title: MILES stage 1 data N1_0743


title: MILES stage 1 data N1_0748


title: MILES stage 2 data N2_0972


title: MILES stage 2 data N2_0980


title: MILES stage 1 data N1_0735


title: MILES stage 1 data N1_0741


title: MILES stage 2 data N2_0969


title: MILES stage 2 data N2_0967

value: ALL with t(1;19)


title: MILES stage 2 data N2_0968


title: MILES stage 2 data N2_0966

value: CML


title: MILES stage 2 data N2_0963


title: MILES stage 2 data N2_0965


title: MILES stage 1 data N1_0739


title: MILES stage 2 data N2_0964


title: MILES stage 2 data N2_0962

value: c-ALL/Pre-B-ALL with t(9;22)


title: MILES stage 2 data N2_0961


title: MILES stage 2 data N2_0960


title: MILES stage 2 data N2_0959


title: MILES stage 2 data N2_0957


title: MILES stage 2 data N2_0952

value: AML with t(11q23)/MLL


title: MILES stage 2 data N2_0955


title: MILES stage 2 data N2_0956


title: MILES stage 1 data N1_0723

value: c-ALL/Pre-B-ALL without t(9;22)


title: MILES stage 2 data N2_0950


title: MILES stage 1 data N1_0721


title: MILES stage 2 data N2_0946


title: MILES stage 1 data N1_0710


title: MILES stage 1 data N1_0722


title: MILES stage 1 data N1_0727


title: MILES stage 2 data N2_0954


title: MILES stage 2 data N2_0948


title: MILES stage 2 data N2_0949


title: MILES stage 2 data N2_0953


title: MILES stage 1 data N1_0732


title: MILES stage 2 data N2_0951


title: MILES stage 1 data N1_0714


title: MILES stage 1 data N1_0718


title: MILES stage 1 data N1_0725


title: MILES stage 2 data N2_0945


title: MILES stage 2 data N2_0947


title: MILES stage 1 data N1_0720


title: MILES stage 1 data N1_0711


title: MILES stage 2 data N2_0942


title: MILES stage 1 data N1_0706


title: MILES stage 1 data N1_0707


title: MILES stage 2 data N2_0944


title: MILES stage 1 data N1_0704


title: MILES stage 2 data N2_0940


title: MILES stage 2 data N2_0934


title: MILES stage 2 data N2_0941


title: MILES stage 2 data N2_0933


title: MILES stage 2 data N2_0932


title: MILES stage 1 data N1_0700


title: MILES stage 2 data N2_0936


title: MILES stage 2 data N2_0935


title: MILES stage 2 data N2_0958


title: MILES stage 2 data N2_0937


title: MILES stage 2 data N2_0938


title: MILES stage 2 data N2_0939


title: MILES stage 2 data N2_0930


title: MILES stage 2 data N2_0924


title: MILES stage 2 data N2_0925


title: MILES stage 2 data N2_0926


title: MILES stage 2 data N2_0931


title: MILES stage 2 data N2_0928


title: MILES stage 2 data N2_0927


title: MILES stage 1 data N1_0694


title: MILES stage 2 data N2_0929


title: MILES stage 1 data N1_0698


title: MILES stage 1 data N1_0688


title: MILES stage 2 data N2_0920


title: MILES stage 2 data N2_0923


title: MILES stage 2 data N2_0922


title: MILES stage 2 data N2_0921


title: MILES stage 1 data N1_0691


title: MILES stage 2 data N2_0919


title: MILES stage 1 data N1_0690


title: MILES stage 2 data N2_0918


title: MILES stage 1 data N1_0686


title: MILES stage 2 data N2_0916


title: MILES stage 1 data N1_0685


title: MILES stage 2 data N2_0917


title: MILES stage 2 data N2_0913


title: MILES stage 2 data N2_0912


title: MILES stage 2 data N2_0914


title: MILES stage 2 data N2_0915


title: MILES stage 1 data N1_0680


title: MILES stage 1 data N1_0677


title: MILES stage 2 data N2_0909


title: MILES stage 2 data N2_0906


title: MILES stage 2 data N2_0911


title: MILES stage 2 data N2_0907

value: Pro-B-ALL with t(11q23)/MLL


title: MILES stage 2 data N2_0910


title: MILES stage 1 data N1_0674

value: bone marrow


title: MILES stage 1 data N1_0673


title: MILES stage 1 data N1_0663


title: MILES stage 1 data N1_0668


title: MILES stage 2 data N2_0903


title: MILES stage 1 data N1_0662


title: MILES stage 1 data N1_0667


title: MILES stage 2 data N2_0908


title: MILES stage 2 data N2_0901

value: MDS


title: MILES stage 2 data N2_0904

value: peripheral blood


title: MILES stage 2 data N2_0905


title: MILES stage 1 data N1_0665


title: MILES stage 2 data N2_0900


title: MILES stage 2 data N2_0898

value: AML with normal karyotype + other abnormalities


title: MILES stage 2 data N2_0899


title: MILES stage 2 data N2_0897


title: MILES stage 2 data N2_0896


title: MILES stage 2 data N2_0893


title: MILES stage 2 data N2_0892


title: MILES stage 2 data N2_0895

value: AML complex aberrant karyotype


title: MILES stage 2 data N2_0943


title: MILES stage 1 data N1_0660


title: MILES stage 1 data N1_0658


title: MILES stage 2 data N2_0894


title: MILES stage 1 data N1_0656


title: MILES stage 2 data N2_0891


title: MILES stage 1 data N1_0659


title: MILES stage 2 data N2_0890


title: MILES stage 1 data N1_0654


title: MILES stage 2 data N2_0889


title: MILES stage 2 data N2_0886


title: MILES stage 2 data N2_0887


title: MILES stage 2 data N2_0888


title: MILES stage 2 data N2_0884


title: MILES stage 2 data N2_0885


title: MILES stage 1 data N1_0652


title: MILES stage 2 data N2_0881


title: MILES stage 1 data N1_0649


title: MILES stage 2 data N2_0883


title: MILES stage 2 data N2_0882


title: MILES stage 1 data N1_0646


title: MILES stage 2 data N2_0878


title: MILES stage 2 data N2_0880


title: MILES stage 2 data N2_0877


title: MILES stage 2 data N2_0879

value: mature B-ALL with t(8;14)


title: MILES stage 2 data N2_0876


title: MILES stage 1 data N1_0642


title: MILES stage 2 data N2_0874

value: CLL


title: MILES stage 2 data N2_0873


title: MILES stage 2 data N2_0869


title: MILES stage 2 data N2_0870


title: MILES stage 2 data N2_0875


title: MILES stage 2 data N2_0872


title: MILES stage 1 data N1_0640


title: MILES stage 1 data N1_0633


title: MILES stage 2 data N2_0867


title: MILES stage 1 data N1_0634


title: MILES stage 2 data N2_0868


title: MILES stage 2 data N2_0866


title: MILES stage 2 data N2_0864


title: MILES stage 2 data N2_0871


title: MILES stage 1 data N1_0630


title: MILES stage 1 data N1_0632


title: MILES stage 1 data N1_0629


title: MILES stage 2 data N2_0862


title: MILES stage 2 data N2_0863


title: MILES stage 2 data N2_0859

value: ALL with hyperdiploid karyotype


title: MILES stage 2 data N2_0857


title: MILES stage 2 data N2_0858


title: MILES stage 2 data N2_0865


title: MILES stage 2 data N2_0861


title: MILES stage 2 data N2_0860


title: MILES stage 1 data N1_0620


title: MILES stage 2 data N2_0855


title: MILES stage 1 data N1_0619


title: MILES stage 1 data N1_0625


title: MILES stage 1 data N1_0618


title: MILES stage 2 data N2_0853

value: AML with t(15;17)


title: MILES stage 2 data N2_0854


title: MILES stage 2 data N2_0852


title: MILES stage 2 data N2_0850

value: ALL with t(12;21)


title: MILES stage 1 data N1_0611


title: MILES stage 2 data N2_0849


title: MILES stage 2 data N2_0851


title: MILES stage 2 data N2_0856


title: MILES stage 2 data N2_0902


title: MILES stage 2 data N2_0848


title: MILES stage 2 data N2_0847


title: MILES stage 2 data N2_0845


title: MILES stage 2 data N2_0846


title: MILES stage 1 data N1_0617


title: MILES stage 1 data N1_0609


title: MILES stage 2 data N2_0839

value: AML with t(8;21)


title: MILES stage 2 data N2_0843


title: MILES stage 2 data N2_0841


title: MILES stage 2 data N2_0836


title: MILES stage 2 data N2_0840

value: Non-leukemia and healthy bone marrow


title: MILES stage 2 data N2_0838

value: T-ALL


title: MILES stage 2 data N2_0844


title: MILES stage 1 data N1_0607


title: MILES stage 2 data N2_0835


title: MILES stage 2 data N2_0834


title: MILES stage 1 data N1_0605


title: MILES stage 2 data N2_0833


title: MILES stage 2 data N2_0832


title: MILES stage 2 data N2_0831


title: MILES stage 1 data N1_0601


title: MILES stage 1 data N1_0604


title: MILES stage 2 data N2_0830


title: MILES stage 2 data N2_0829


title: MILES stage 2 data N2_0828


title: MILES stage 2 data N2_0822


title: MILES stage 2 data N2_0821

value: c-ALL/Pre-B-ALL with t(9;22)


title: MILES stage 2 data N2_0823


title: MILES stage 2 data N2_0826


title: MILES stage 2 data N2_0820


title: MILES stage 2 data N2_0825


title: MILES stage 2 data N2_0819


title: MILES stage 2 data N2_0817

value: AML with t(11q23)/MLL


title: MILES stage 2 data N2_0827


title: MILES stage 2 data N2_0818


title: MILES stage 1 data N1_0591

value: c-ALL/Pre-B-ALL without t(9;22)


title: MILES stage 2 data N2_0816


title: MILES stage 1 data N1_0587


title: MILES stage 2 data N2_0814


title: MILES stage 2 data N2_0813


title: MILES stage 2 data N2_0824


title: MILES stage 1 data N1_0584


title: MILES stage 2 data N2_0837


title: MILES stage 2 data N2_0815


title: MILES stage 2 data N2_0810


title: MILES stage 2 data N2_0808


title: MILES stage 1 data N1_0581


title: MILES stage 2 data N2_0807


title: MILES stage 2 data N2_0809


title: MILES stage 2 data N2_0806


title: MILES stage 2 data N2_0812


title: MILES stage 2 data N2_0805


title: MILES stage 1 data N1_0578


title: MILES stage 1 data N1_0572


title: MILES stage 2 data N2_0803


title: MILES stage 2 data N2_0811


title: MILES stage 2 data N2_0804


title: MILES stage 1 data N1_0568


title: MILES stage 2 data N2_0802


title: MILES stage 1 data N1_0566


title: MILES stage 2 data N2_0801


title: MILES stage 2 data N2_0842


title: MILES stage 2 data N2_0800


title: MILES stage 2 data N2_0799


title: MILES stage 1 data N1_0563


title: MILES stage 2 data N2_0796


title: MILES stage 2 data N2_0797


title: MILES stage 2 data N2_0798


title: MILES stage 2 data N2_0793


title: MILES stage 2 data N2_0791


title: MILES stage 1 data N1_0561


title: MILES stage 2 data N2_0792


title: MILES stage 1 data N1_0558


title: MILES stage 1 data N1_0556


title: MILES stage 2 data N2_0790


title: MILES stage 1 data N1_0555


title: MILES stage 1 data N1_0554


title: MILES stage 2 data N2_0795


title: MILES stage 2 data N2_0788


title: MILES stage 2 data N2_0787


title: MILES stage 1 data N1_0553


title: MILES stage 2 data N2_0794


title: MILES stage 2 data N2_0786

value: CML


title: MILES stage 2 data N2_0785

value: bone marrow


title: MILES stage 1 data N1_0547


title: MILES stage 1 data N1_0549


title: MILES stage 2 data N2_0789


title: MILES stage 2 data N2_0784


title: MILES stage 2 data N2_0783


title: MILES stage 1 data N1_0548


title: MILES stage 2 data N2_0778


title: MILES stage 2 data N2_0781


title: MILES stage 2 data N2_0782


title: MILES stage 2 data N2_0780


title: MILES stage 2 data N2_0779

value: MDS


title: MILES stage 2 data N2_0777


title: MILES stage 1 data N1_0540


title: MILES stage 1 data N1_0541


title: MILES stage 1 data N1_0539


title: MILES stage 2 data N2_0771

value: peripheral blood


title: MILES stage 2 data N2_0770


title: MILES stage 2 data N2_0769


title: MILES stage 2 data N2_0773


title: MILES stage 2 data N2_0772


title: MILES stage 2 data N2_0776


title: MILES stage 2 data N2_0775


title: MILES stage 2 data N2_0774


title: MILES stage 1 data N1_0532


title: MILES stage 1 data N1_0529


title: MILES stage 1 data N1_0525


title: MILES stage 2 data N2_0768


title: MILES stage 2 data N2_0767


title: MILES stage 1 data N1_0528


title: MILES stage 1 data N1_0535


title: MILES stage 2 data N2_0765


title: MILES stage 1 data N1_0526


title: MILES stage 2 data N2_0764


title: MILES stage 2 data N2_0762


title: MILES stage 2 data N2_0761


title: MILES stage 1 data N1_0523


title: MILES stage 1 data N1_0524


title: MILES stage 2 data N2_0757


title: MILES stage 2 data N2_0760

value: AML with normal karyotype + other abnormalities


title: MILES stage 2 data N2_0759


title: MILES stage 2 data N2_0756


title: MILES stage 1 data N1_0520


title: MILES stage 1 data N1_0521


title: MILES stage 2 data N2_0766


title: MILES stage 1 data N1_0519


title: MILES stage 2 data N2_0763


title: MILES stage 2 data N2_0755


title: MILES stage 2 data N2_0754


title: MILES stage 2 data N2_0753


title: MILES stage 2 data N2_0758


title: MILES stage 2 data N2_0751


title: MILES stage 2 data N2_0749


title: MILES stage 2 data N2_0746


title: MILES stage 2 data N2_0748


title: MILES stage 2 data N2_0752


title: MILES stage 2 data N2_0747


title: MILES stage 2 data N2_0743


title: MILES stage 2 data N2_0744


title: MILES stage 2 data N2_0745


title: MILES stage 2 data N2_0750


title: MILES stage 2 data N2_0741


title: MILES stage 2 data N2_0742


title: MILES stage 2 data N2_0739


title: MILES stage 2 data N2_0737


title: MILES stage 2 data N2_0735


title: MILES stage 2 data N2_0736


title: MILES stage 2 data N2_0730


title: MILES stage 2 data N2_0740


title: MILES stage 2 data N2_0734


title: MILES stage 2 data N2_0728


title: MILES stage 2 data N2_0733


title: MILES stage 2 data N2_0732


title: MILES stage 2 data N2_0738


title: MILES stage 2 data N2_0729


title: MILES stage 2 data N2_0731


title: MILES stage 2 data N2_0720


title: MILES stage 2 data N2_0718


title: MILES stage 2 data N2_0719


title: MILES stage 2 data N2_0716


title: MILES stage 2 data N2_0723


title: MILES stage 2 data N2_0717


title: MILES stage 2 data N2_0724


title: MILES stage 2 data N2_0722


title: MILES stage 2 data N2_0726


title: MILES stage 2 data N2_0715


title: MILES stage 2 data N2_0727


title: MILES stage 2 data N2_0725

value: ALL with t(1;19)


title: MILES stage 2 data N2_0714


title: MILES stage 2 data N2_0713


title: MILES stage 2 data N2_0712


title: MILES stage 2 data N2_0711


title: MILES stage 2 data N2_0710


title: MILES stage 2 data N2_0721


title: MILES stage 2 data N2_0708


title: MILES stage 2 data N2_0709


title: MILES stage 2 data N2_0706


title: MILES stage 2 data N2_0707


title: MILES stage 2 data N2_0704


title: MILES stage 2 data N2_0705


title: MILES stage 1 data N1_0490


title: MILES stage 1 data N1_0478


title: MILES stage 2 data N2_0703


title: MILES stage 1 data N1_0466


title: MILES stage 2 data N2_0697


title: MILES stage 1 data N1_0462


title: MILES stage 2 data N2_0696


title: MILES stage 2 data N2_0699


title: MILES stage 2 data N2_0694


title: MILES stage 2 data N2_0695


title: MILES stage 2 data N2_0688


title: MILES stage 2 data N2_0689


title: MILES stage 2 data N2_0693


title: MILES stage 2 data N2_0701


title: MILES stage 2 data N2_0684


title: MILES stage 2 data N2_0702


title: MILES stage 2 data N2_0692


title: MILES stage 2 data N2_0690


title: MILES stage 2 data N2_0700


title: MILES stage 2 data N2_0687


title: MILES stage 2 data N2_0686

value: mature B-ALL with t(8;14)


title: MILES stage 2 data N2_0698

value: CLL


title: MILES stage 2 data N2_0691


title: MILES stage 2 data N2_0681


title: MILES stage 2 data N2_0685


title: MILES stage 2 data N2_0682


title: MILES stage 2 data N2_0679


title: MILES stage 2 data N2_0680


title: MILES stage 2 data N2_0678


title: MILES stage 1 data N1_0452


title: MILES stage 2 data N2_0683


title: MILES stage 1 data N1_0444


title: MILES stage 1 data N1_0439


title: MILES stage 1 data N1_0451


title: MILES stage 2 data N2_0673


title: MILES stage 1 data N1_0437


title: MILES stage 2 data N2_0677


title: MILES stage 2 data N2_0675


title: MILES stage 2 data N2_0674


title: MILES stage 2 data N2_0676


title: MILES stage 2 data N2_0671


title: MILES stage 1 data N1_0436


title: MILES stage 2 data N2_0672


title: MILES stage 2 data N2_0667


title: MILES stage 2 data N2_0666


title: MILES stage 2 data N2_0670


title: MILES stage 2 data N2_0665


title: MILES stage 2 data N2_0668


title: MILES stage 2 data N2_0664


title: MILES stage 2 data N2_0669


title: MILES stage 2 data N2_0663


title: MILES stage 2 data N2_0661


title: MILES stage 2 data N2_0662

value: AML complex aberrant karyotype


title: MILES stage 2 data N2_0660


title: MILES stage 1 data N1_0432


title: MILES stage 2 data N2_0656


title: MILES stage 2 data N2_0658


title: MILES stage 2 data N2_0651


title: MILES stage 2 data N2_0653


title: MILES stage 2 data N2_0654


title: MILES stage 1 data N1_0425


title: MILES stage 2 data N2_0649


title: MILES stage 2 data N2_0650


title: MILES stage 1 data N1_0420


title: MILES stage 2 data N2_0648


title: MILES stage 1 data N1_0419


title: MILES stage 1 data N1_0422


title: MILES stage 2 data N2_0646


title: MILES stage 1 data N1_0418


title: MILES stage 2 data N2_0659


title: MILES stage 2 data N2_0645


title: MILES stage 2 data N2_0657


title: MILES stage 1 data N1_0417


title: MILES stage 2 data N2_0655


title: MILES stage 2 data N2_0643


title: MILES stage 2 data N2_0652


title: MILES stage 2 data N2_0644


title: MILES stage 2 data N2_0642


title: MILES stage 2 data N2_0647


title: MILES stage 1 data N1_0411


title: MILES stage 1 data N1_0404


title: MILES stage 2 data N2_0640


title: MILES stage 2 data N2_0641


title: MILES stage 2 data N2_0639


title: MILES stage 2 data N2_0636


title: MILES stage 2 data N2_0638


title: MILES stage 2 data N2_0637


title: MILES stage 2 data N2_0635


title: MILES stage 1 data N1_0403


title: MILES stage 2 data N2_0631


title: MILES stage 2 data N2_0629


title: MILES stage 2 data N2_0630


title: MILES stage 2 data N2_0632


title: MILES stage 2 data N2_0633


title: MILES stage 2 data N2_0634


title: MILES stage 1 data N1_0398


title: MILES stage 2 data N2_0627


title: MILES stage 2 data N2_0628


title: MILES stage 2 data N2_0624


title: MILES stage 2 data N2_0625


title: MILES stage 2 data N2_0623


title: MILES stage 1 data N1_0400


title: MILES stage 2 data N2_0626


title: MILES stage 1 data N1_0402


title: MILES stage 2 data N2_0622


title: MILES stage 1 data N1_0396


title: MILES stage 2 data N2_0621


title: MILES stage 2 data N2_0620


title: MILES stage 1 data N1_0386


title: MILES stage 2 data N2_0619


title: MILES stage 1 data N1_0393


title: MILES stage 2 data N2_0615


title: MILES stage 2 data N2_0617


title: MILES stage 1 data N1_0384


title: MILES stage 2 data N2_0618


title: MILES stage 1 data N1_0382


title: MILES stage 1 data N1_0392


title: MILES stage 2 data N2_0612


title: MILES stage 2 data N2_0613


title: MILES stage 2 data N2_0611


title: MILES stage 2 data N2_0608

value: ALL with hyperdiploid karyotype


title: MILES stage 2 data N2_0609


title: MILES stage 2 data N2_0616


title: MILES stage 2 data N2_0607


title: MILES stage 2 data N2_0610


title: MILES stage 2 data N2_0606


title: MILES stage 2 data N2_0614


title: MILES stage 2 data N2_0605


title: MILES stage 2 data N2_0603


title: MILES stage 1 data N1_0373


title: MILES stage 1 data N1_0380

value: ALL with t(12;21)


title: MILES stage 2 data N2_0604


title: MILES stage 1 data N1_0369


title: MILES stage 2 data N2_0598


title: MILES stage 2 data N2_0602


title: MILES stage 2 data N2_0601


title: MILES stage 2 data N2_0600


title: MILES stage 2 data N2_0597


title: MILES stage 1 data N1_0366


title: MILES stage 2 data N2_0596


title: MILES stage 1 data N1_0367


title: MILES stage 1 data N1_0365


title: MILES stage 2 data N2_0599


title: MILES stage 2 data N2_0595


title: MILES stage 2 data N2_0594


title: MILES stage 1 data N1_0363


title: MILES stage 2 data N2_0593


title: MILES stage 2 data N2_0592


title: MILES stage 2 data N2_0591


title: MILES stage 2 data N2_0590


title: MILES stage 2 data N2_0588


title: MILES stage 2 data N2_0589


title: MILES stage 2 data N2_0582


title: MILES stage 2 data N2_0581


title: MILES stage 2 data N2_0583


title: MILES stage 1 data N1_0352


title: MILES stage 2 data N2_0580


title: MILES stage 1 data N1_0357


title: MILES stage 2 data N2_0587


title: MILES stage 2 data N2_0585


title: MILES stage 2 data N2_0586


title: MILES stage 1 data N1_0347


title: MILES stage 1 data N1_0350


title: MILES stage 1 data N1_0346


title: MILES stage 2 data N2_0584


title: MILES stage 2 data N2_0576


title: MILES stage 2 data N2_0579


title: MILES stage 2 data N2_0574


title: MILES stage 2 data N2_0578


title: MILES stage 2 data N2_0571


title: MILES stage 1 data N1_0345


title: MILES stage 2 data N2_0569


title: MILES stage 2 data N2_0575


title: MILES stage 2 data N2_0577


title: MILES stage 2 data N2_0573


title: MILES stage 2 data N2_0570

value: AML with t(8;21)


title: MILES stage 2 data N2_0572


title: MILES stage 2 data N2_0564


title: MILES stage 2 data N2_0567


title: MILES stage 2 data N2_0565


title: MILES stage 2 data N2_0560