title: Primary Lung Adenocarcinoma Sample_A44

city: Brisbane

first: Jill

middle: Everland

last: Larsen

state: Queensland

address: Rode Road, Chermside

department: Thoracic Medicine

country: Australia

institute: The Prince Charles Hospital

description: Synthesis of the labelled first strand cDNA was conducted using Amersham CyScribe Post-Labelling kit with starting material of 20 ug of total RNA. The amino-allyl labeled dNTP mix was added to the reaction to generate amino-allyl labelled second strand cDNA. Following the hydrolysis reaction, single-stranded cDNA probes were purified using Amersham GFX columns. Dye coupling reactions were performed by mixing the cDNA samples with Amersham Cy3 (reference) or Cy5 (tumour) and incubating in the dark. The reactions were purified with Amersham GFX columns to remove the unincorporated/quenched dyes. After the purification samples were combined for hybridization, the labeled cDNAs were co-hybridized to 22K oligo microarrays. Slides were scanned on GMS418 confocal scanner (Agilent).

data_processing: Raw images were imported into Imagene V5.1 (BioDiscovery, CA, USA) to extract pixel intensities and to flag spots with poor/absent signal. The raw background subtracted signal median for each probe was imported into GeneSpring GX V7.3 (Agilent Technologies, Inc., CA, USA) for analysis. Data was normalized (Lowess: per spot and per chip; per chip to the 50th percentile) and probe signals filtered on pixel intensity (for both red and green channels any spots less than 20 units or greater than 65,000 units were excluded) and consistent spot morphology. Only spots flagged present in at least 80% of samples were included. For each probe, the logarithm to the base 2 of the ratio between the intensity in the tumor sample (red) channel and the reference (green) channel was used as the expression value for the probe.

source_name: Universal Reference RNA

tag: The reference sample used for this experiment was commercially available Universal Reference RNA (Stratagene)

source_name: Tumour sample A44

tag: Primary adenocarcinoma of the lung. Total RNA extracted from fresh-frozen tissue using Trizol and RNeasy clean-up.


title: Primary Lung Adenocarcinoma Sample_A47

status: Public on May 01 2007

type: RNA

molecule: total RNA

organism: Homo sapiens

source_name: Tumour sample A47


title: 9442

type: genomic

city: Nijmegen

first: Roland

middle: P.

last: Kuiper

address: Geert Grooteplein 10

department: Human Genetics

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

description: primary ALL diagnosis sample

hyb_protocol: Hybridizations were performed according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix) using an Affymetrix hybridisation oven 640 and an Affymetrix Fluidic station 450.

scan_protocol: Scanning performed according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix) using an Affymetrix scanner 3000.

data_processing: copy number detection using CNAG2.0 software (http://www.genome.umin.jp/)

label: biotin

molecule: genomic DNA

source_name: Bone marrow with 90% blasts

label_protocol: Biotinylated DNA was prepared according to the standard Affymetrix protocol from 250 ng genomic DNA (Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix).

extract_protocol: QiaAmp purification kit (Qiagen)

tag: Immunotype

value: common ALL; Age:3.2 yrs; Gender:F


title: Primary Lung Adenocarcinoma Sample_A41

source_name: Tumour sample A41


title: Primary Lung Adenocarcinoma Sample_A43

source_name: Tumour sample A43


title: Primary Lung Adenocarcinoma Sample_A38

source_name: Tumour sample A38


title: male ref pool_50kHind

description: pool of 10 male individuals

source_name: Peripheral blood

tag: control sample


title: Primary Lung Adenocarcinoma Sample_A32

source_name: Tumour sample A32


title: Primary Lung Adenocarcinoma Sample_A31

source_name: Tumour sample A31


title: Primary Lung Adenocarcinoma Sample_A45

source_name: Tumour sample A45


title: 9256

description: primary ALL diagnosis sample

source_name: Bone marrow with 86% blasts

value: common ALL; Age:3.5 yrs; Gender:M


title: Primary Lung Adenocarcinoma Sample_A35

source_name: Tumour sample A35


title: female ref pool_50kXba

description: pool of 10 female individuals


title: 9314

description: primary ALL diagnosis sample

source_name: Bone marrow with 96% blasts

value: common ALL; Age:4.6 yrs; Gender:F


title: 9225

description: primary ALL diagnosis sample

source_name: Bone marrow with 87% blasts

value: pro-B ALL; Age:1.4 yrs; Gender:F


title: Primary Lung Adenocarcinoma Sample_A25

source_name: Tumour sample A25


title: Primary Lung Adenocarcinoma Sample_A21

source_name: Tumour sample A21


title: Primary Lung Adenocarcinoma Sample_A33

source_name: Universal Reference RNA

source_name: Tumour sample A33


title: Primary Lung Adenocarcinoma Sample_A16

source_name: Tumour sample A16


title: Primary Lung Adenocarcinoma Sample_A26

source_name: Tumour sample A26


title: Primary Lung Adenocarcinoma Sample_A18

source_name: Tumour sample A18


title: Primary Lung Adenocarcinoma Sample_A20

source_name: Tumour sample A20


title: Primary Lung Adenocarcinoma Sample_A13

source_name: Tumour sample A13


title: Primary Lung Adenocarcinoma Sample_A4

source_name: Tumour sample A4


title: Primary Lung Adenocarcinoma Sample_A15

source_name: Tumour sample A15


title: Primary Lung Adenocarcinoma Sample_A1

source_name: Tumour sample A1


title: Primary Lung Adenocarcinoma Sample_A14

source_name: Tumour sample A14


title: Primary Lung Adenocarcinoma Sample_A6

source_name: Tumour sample A6


title: Primary Lung Adenocarcinoma Sample_A3

source_name: Tumour sample A3


title: Primary Lung SCC Carcinoma Sample_S7

source_name: Tumour sample S7

tag: Primary SCC carcinoma of the lung. Total RNA extracted from fresh-frozen tissue using Trizol and RNeasy clean-up.


title: Primary Lung SCC Carcinoma Sample_S8

source_name: Tumour sample S8


title: Primary Lung Adenocarcinoma Sample_A5

source_name: Tumour sample A5


title: Primary Lung SCC Carcinoma Sample_S6

source_name: Tumour sample S6


title: Primary Lung Adenocarcinoma Sample_A2

source_name: Universal Reference RNA

source_name: Tumour sample A2


title: 9385

description: primary ALL diagnosis sample

source_name: Bone marrow with 97% blasts

value: common ALL; Age:4.3 yrs; Gender:M


title: 9150

description: primary ALL diagnosis sample

value: common ALL; Age:11 yrs; Gender:M


title: 9317

description: primary ALL diagnosis sample

source_name: Bone marrow with 98% blasts

value: common ALL; Age:9.5 yrs; Gender:F


title: Primary Lung SCC Carcinoma Sample_S2

source_name: Tumour sample S2


title: 9194

description: primary ALL diagnosis sample

source_name: Bone marrow with 96% blasts

value: common ALL; Age:9.2 yrs; Gender:F


title: Primary Lung SCC Carcinoma Sample_S3

source_name: Tumour sample S3


title: 9176

description: primary ALL diagnosis sample

source_name: Bone marrow with 90% blasts

value: common ALL; Age:1.9 yrs; Gender:F


title: Primary Lung SCC Carcinoma Sample_S1

source_name: Tumour sample S1


title: 9351

description: primary ALL diagnosis sample

source_name: Bone marrow with 93% blasts

value: common ALL; Age:5.4 yrs; Gender:M


title: 9127

description: primary ALL diagnosis sample

source_name: Bone marrow with 89% blasts

value: common ALL; Age:3.3 yrs; Gender:M


title: 9327

description: primary ALL diagnosis sample

source_name: Bone marrow with 49% blasts

value: T-ALL; Age:4.3 yrs; Gender:M


title: 9191

description: primary ALL diagnosis sample

source_name: Bone marrow with 95% blasts

value: common ALL; Age:5.8 yrs; Gender:F


title: Primary Lung SCC Carcinoma Sample_S5

source_name: Tumour sample S5


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 11 week of age, replicate 1

city: Newark

first: Larry

middle: Albert

last: Cogburn

state: DE

address: 531 South College Ave.

department: Animal and Food Sciences

country: USA

institute: University of Delaware

description: Liver from high growth (HG) and low growth (LG) chickens, 11 week of age, replicate 1

hyb_protocol: A cDNA spotted glass slide (Del-Mar 14K Chicken Integrated Systems microarray) was pre-treated for 45 min at 42 degree celsius in pre-hybridization solution containing 5x SSC, 0.1 % SDS and 1 % BSA and followed by dipping for 5 min in deionized water and dry spinning for 5 min at 1,000 x g. The labeled cDNA was dried down (Speed Vac) and reconstituted prior to hybridization in a 30 microliter volume of pre-warm DIG Easy Hyb solution (Roche Diagnostics Corporation; Indianapolis, IN). The two target samples (Alexa 555 and Alexa 647 labeled) were pooled and mixed with 2.5 microliter of 10 mg/ml Yeast tRNA, 2.5 microliter of 10 mg/ml salmon testes DNA (Sigma, Louis, MO) and 2.5 microliter of 1 microgram/microliter of pSport 6.1 vector (PCR amplified product from “empty” pSport 6.1 vector sequence). The target mixture was denatured for 2 min at 94 degree Celsius, cooled at room temperature, carefully loaded onto the middle of a pre-treated mircoarray slide held in a hybridization chamber (Corning #2551, Lowell, MA) and overlaid with a 22 x 65 mm LifterSlip (Erie Scientific, Portsmouth, NH). The sealed hybridization chamber was incubated overnight at 42 degrees Celsius in a water bath under a light-tight box. On the following day, slides were sequentially washed with 1 x SSC, 0.2% SDS, and 0.5% DTT at 55 degrees C for 10 min, then 0.1 x SSC, 0.2% SDS, and 0.5% DTT for 5 min at room temperature, and finally 0.1 x SSC and 0.5% DTT for 1 min at room temperature, with nitrogen gas bubbled through each of the washes to prevent interference of ozone. The slides were subsequently rinsed in dH2O and dried by centrifugation. Before scanning, slides were stored in individual 50 ml tubes covered in aluminum foil and filled with nitrogen gas.

scan_protocol: Each microarray slide was scanned using a GenePix 4000B microarray scanner (Molecular Devices; Sunnyvale, CA) set at 635 nm for Alexa647 and 532 nm for Alexa555 after adjustment of the PMT count ratio (635/532) to 1. Two high-resolution TIFF images (embedded in a single file) were generated for each slide.

data_processing: Image analysis was performed on high-resolution TIFF images using GenePix Pro 4.1 (Molecular Devices, Sunnyvale, CA). The results of image analysis [GenePix Report (GPR) files] were automatically merged with Excel files containing the clone identification number/plate address and gene name/function (from the highest BLAST score). Data in the VALUE column is based on the loess-normalized ratio of the loess-normalized log2 Alexa 555 and Alexa 647 values. The values are based on non-background corrected median intensity values for Alexa 555 and Alexa 647.

label: Alexa Flour 555

organism: Gallus gallus

label_protocol: Twenty micrograms of total RNA were indirectly labeled following the SuperScript Plus Indirect cDNA Labeling System (Invitrogen, Carlsbad, CA). Briefly, the first strand cDNA synthesis was performed in a 30 microliter final volume containing 1x first-strand buffer, 5 micrograms of anchored oligo(dT)20, DTT, dNTP Mix (including aminoallyl- and aminohexyl-modified nucleotides), 40 U of RNaseOUT and 800 U of SuperScript III reverse transcriptase with an incubation at 46 degree Celsius for 3 hours. The original RNA was destroyed by NaOH hydrolysis and followed by neutralization with HCl. The cDNAs were purified using a low-elution volume spin cartridge (Invitrogen; Carlsbad, CA) and labeled with either Alexa Fluor 555 or Alexa Fluor 647 succinimidyl ester in the dark at room temperature for 2 hours. After purification of labeled cDNAs with a low-elution-volume spin cartridge, the efficiency of dye incorporation was determined using the Microarray Module on the NanoDrop ND-1000 spectrophotometer and the Base:Dye Ratio Calculator on the Invitrogen website.

growth_protocol: Standard broiler chicken growth protocol

extract_protocol: Total RNA was extracted using a RNeasy Midi kit according to the manufacture’s protocol (Qiagen; Valencia, CA). The RNA concentration was determined with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies; Wilmington, DE). RNA integrity was examined using a RNA 6000 Nano Assay kit and the Model 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA).

treatment_protocol: Divergently selected for high body weight (HG genotype) at 8 and 32 weeks of age

tag: Liver HG cockerel, 11 week of age

label: Alexa Flour 647

label_protocol: Twenty micrograms of total RNA were indirectly labeled following the SuperScript Plus Indirect cDNA Labeling System (Invitrogen life technologies, Carlsbad, CA). Briefly, the first strand cDNA synthesis was performed in a 30 microliter final volume containing 1x First-Strand buffer, 5 micrograms of anchored oligo(dT)20, DTT, dNTP Mix (including aminoallyl- and aminohexyl-modified nucleotides), 40 U of RNaseOUT and 800 U of SuperScript III reverse transcriptase with an incubation at 46 degree celsius for 3 hours. After purification of labeled cDNAs with a low-elution-volume spin cartridge, the efficiency of dye incorporation was determined using the Microarray Module on the NanoDrop ND-1000 spectrophotometer and the Base:Dye Ratio Calculator on the Invitrogen website.

extract_protocol: Total RNA was extracted using the RNeasy Midi kit according to the manufacture’s protocol (Qiagen; Valencia, CA). The RNA concentration was determined by NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Rockland, DE). The RNA integrity was examined using the RNA 6000 Nano Assay kit and Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Divergently selected for low body weight (LG genotype) at 8 and 32 weeks of age

tag: Liver LG cockerel, 11 week of age


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 11 week of age, replicate 4

description: Liver from high growth (HG) and low growth (LG) chickens, 11 week of age, replicate 4


title: 9095

description: primary ALL diagnosis sample

value: pre-B ALL; Age:3 yrs; Gender:F


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 9 week of age, replicate 4

description: Liver from high growth (HG) and low growth (LG) chickens, 9 week of age, replicate 4

tag: Liver LG cockerel, 9 week of age

tag: Liver HG cockerel, 9 week of age


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 11 week of age, replicate 2

description: Liver from high growth (HG) and low growth (LG) chickens, 11 week of age, replicate 2


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 11 week of age, replicate 3

description: Liver from high growth (HG) and low growth (LG) chickens, 11 week of age, replicate 3


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 9 week of age, replicate 1

description: Liver from high growth (HG) and low growth (LG) chickens, 9 week of age, replicate 1


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 5 week of age, replicate 3

description: Liver from high growth (HG) and low growth (LG) chickens, 5 week of age, replicate 3

tag: Liver LG cockerel, 5 week of age

tag: Liver HG cockerel, 5 week of age


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 9 week of age, replicate 2

description: Liver from high growth (HG) and low growth (LG) chickens, 9 week of age, replicate 2


title: 9161

description: primary ALL diagnosis sample

value: common ALL; Age:6.6 yrs; Gender:M


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 9 week of age, replicate 3

description: Liver from high growth (HG) and low growth (LG) chickens, 9 week of age, replicate 3


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 7 week of age, replicate 1

description: Liver from high growth (HG) and low growth (LG) chickens, 7 week of age, replicate 1

tag: Liver LG cockerel, 7 week of age

tag: Liver HG cockerel, 7 week of age


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 7 week of age, replicate 2

description: Liver from high growth (HG) and low growth (LG) chickens, 7 week of age, replicate 2


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 7 week of age, replicate 4

description: Liver from high growth (HG) and low growth (LG) chickens, 7 week of age, replicate 4


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 5 week of age, replicate 4

description: Liver from high growth (HG) and low growth (LG) chickens, 5 week of age, replicate 4


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 7 week of age, replicate 3

description: Liver from high growth (HG) and low growth (LG) chickens, 7 week of age, replicate 3


title: Primary Lung SCC Carcinoma Sample_S4

source_name: Tumour sample S4


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 5 week of age, replicate 1

description: Liver from high growth (HG) and low growth (LG) chickens, 5 week of age, replicate 1


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 5 week of age, replicate 2

description: Liver from high growth (HG) and low growth (LG) chickens, 5 week of age, replicate 2


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 3 week of age, replicate 12

description: Liver from high growth (HG) and low growth (LG) chickens, 3 week of age, replicate 12

tag: Liver LG cockerel, 3 week of age

tag: Liver HG cockerel, 3 week of age


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 3 week of age, replicate 10

description: Liver from high growth (HG) and low growth (LG) chickens, 3 week of age, replicate 10

treatment_protocol: Divergently selected for low body weight (LG genotype)  at 8 and 32 weeks of age


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 3 week of age, replicate 11

description: Liver from high growth (HG) and low growth (LG) chickens, 3 week of age, replicate 11


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 3 week of age, replicate 5

description: Liver from high growth (HG) and low growth (LG) chickens, 3 week of age, replicate 5


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 3 week of age, replicate 4

description: Liver from high growth (HG) and low growth (LG) chickens, 3 week of age, replicate 4


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 3 week of age, replicate 1

description: Liver from high growth (HG) and low growth (LG) chickens, 3 week of age, replicate 1


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 3 week of age, replicate 3

description: Liver from high growth (HG) and low growth (LG) chickens, 3 week of age, replicate 3


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 3 week of age, replicate 2

description: Liver from high growth (HG) and low growth (LG) chickens, 3 week of age, replicate 2


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 3 week of age, replicate 9

description: Liver from high growth (HG) and low growth (LG) chickens, 3 week of age, replicate 9


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 1 week of age, replicate 12

description: Liver from high growth (HG) and low growth (LG) chickens, 1 week of age, replicate 12

tag: Liver LG cockerel, 1 week of age

tag: Liver HG cockerel, 1 week of age


title: phoU_3

city: Baltimore

first: Yanqin

last: Yang

state: MD

address: 600 N. Wolfe Street

institute: The Johns Hopkins University

description: phoU gene mutant

hyb_protocol: Fragmented, biotinylated cDNA was hybridized to E. coli Genome 2.0  GeneChips for 16hours at 45oC and 60rpm.  Washing/staining was performed according to Affymetrix recommended Prokaryotic protocol, in a FS450 automated fluidics station.

scan_protocol: GeneChips were scanned in an Affymetrix GCS3000 scanner with autoloader.

data_processing: The data were analyzed with GCOS 1.4 software.  All probe sets scaling was performed with a target signal value of 500.  No normalization was performed.

label: Biotin

organism: Escherichia coli

source_name: phoU gene mutant

label_protocol: 10 ug total RNA was processed according to the Affymetrix recommended protocol for prokaryotic targets.  cDNA was fragmented and endlabeled with biotin.

growth_protocol: Overnight culture

extract_protocol: MasterPure RNA purification Kit

tag: phoU gene mutant; minimal medium


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 1 week of age, replicate 3

description: Liver from high growth (HG) and low growth (LG) chickens, 1 week of age, replicate 3


title: phoU_1

description: phoU gene mutant


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 3 week of age, replicate 6

description: Liver from high growth (HG) and low growth (LG) chickens, 3 week of age, replicate 6


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 1 week of age, replicate 10

description: Liver from high growth (HG) and low growth (LG) chickens, 1 week of age, replicate 10


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 1 week of age, replicate 11

description: Liver from high growth (HG) and low growth (LG) chickens, 1 week of age, replicate 11


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 3 week of age, replicate 8

description: Liver from high growth (HG) and low growth (LG) chickens, 3 week of age, replicate 8


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 3 week of age, replicate 7

description: Liver from high growth (HG) and low growth (LG) chickens, 3 week of age, replicate 7


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 1 week of age, replicate 7

description: Liver from high growth (HG) and low growth (LG) chickens, 1 week of age, replicate 7


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 1 week of age, replicate 4

description: Liver from high growth (HG) and low growth (LG) chickens, 1 week of age, replicate 4


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 1 week of age, replicate 2

description: Liver from high growth (HG) and low growth (LG) chickens, 1 week of age, replicate 2


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 1 week of age, replicate 9

description: Liver from high growth (HG) and low growth (LG) chickens, 1 week of age, replicate 9


title: phoU_2

description: phoU gene mutant


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 1 week of age, replicate 6

description: Liver from high growth (HG) and low growth (LG) chickens, 1 week of age, replicate 6


title: WT3110_3

description: E.coli WT3110

tag: wildtype strain; minimal medium


title: Fruit6_woolly_rep5

status: Public on Apr 30 2007

city: Santiago

first: Mauricio

last: Gonzalez

state: Region Metropolitana

address: Santa Rosa 11610

country: Chile

institute: Instituto de Investigaciones Agropecuarias

description: Woolly fruit (0% juice)

hyb_protocol: Pre-hybridization in 5 ml of hybridization buffer (5X SSC, 5 X Denhardt solution, 1% SDS, and 50% formamide) for 1-3 h at 42 ºC. Hybridization was performed in the same buffer for 16-18 h at 42 ºC.

scan_protocol: After washing, the membranes were sealed with a plastic film and exposed for 72-96 h to Phosphor screens (Kodak).

data_processing: Quantification of the signal intensity was performed using the VersArray Analyzer software (BioRad). Raw values were measured as the volume of pixels within a circle encompassing the spot. Local background values were measured in the corners of spot and were subtracted from the signal intensity values for each spot. Spots that showed: (1) Signal Mean < (Background Mean + (1 x Background Standard Deviation; and (2) qcom < 0.8, were considered as low-quality spots and were removed. Qcom values were calculated as described in Wang et al., 2001. Then, the net intensity value of each spot was normalized by that of dap, a spike mRNA control.

molecule: polyA RNA

organism: Prunus persica

source_name: Mesocarp tissue of O´Henry cultivar peach

label_protocol: The 32P-labeled target DNA samples were prepared from poly(A)+ RNAs by incorporation of [α-32P]dCTP during first-strand cDNA synthesis, according to the protocol described by Bernard et al. (1996), unincorporated radioactive nucleotides were removed using the QIAquick Nucleotide Removal according to the manufacturer’s instructions (Qiagen).

extract_protocol: mRNA was purified using an Oligotex Mini kit (Qiagen), following manufacturer recommendations

treatment_protocol: Peach sampled from commercial harvest and exposed 7 days at 21 ºC after 15 days at 4ºC

tag: Woolly fruit (0% juice)


title: Fruit6_woolly_rep4

description: Woolly fruit (0% juice)


title: WT3110_2

description: E.coli WT3110


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 1 week of age, replicate 8

description: Liver from high growth (HG) and low growth (LG) chickens, 1 week of age, replicate 8


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 1 week of age, replicate 5

description: Liver from high growth (HG) and low growth (LG) chickens, 1 week of age, replicate 5


title: Fruit6_woolly_rep6

description: Woolly fruit (0% juice)


title: Fruit6_woolly_rep3

description: Woolly fruit (0% juice)


title: Chicken liver, high growth (HG) versus low growth (LG) lines, 1 week of age, replicate 1

description: Liver from high growth (HG) and low growth (LG) chickens, 1 week of age, replicate 1


title: WT3110_1

description: E.coli WT3110


title: Fruit4_woolly_rep6

description: Woolly fruit (0% juice)


title: Fruit4_woolly_rep5

description: Woolly fruit (0% juice)


title: Fruit6_woolly_rep2

description: Woolly fruit (0% juice)


title: Fruit5_woolly_rep4

description: Woolly fruit (0% juice)


title: Fruit5_woolly_rep3

description: Woolly fruit (0% juice)


title: Fruit6_woolly_rep1

description: Woolly fruit (0% juice)


title: Fruit3_juice_rep6

description: Non-woolly fruit (24-30% juice)

treatment_protocol: Peach sampled from commercial harvest and exposed 7 days at 21 ºC.

tag: Non-woolly fruit (24-30% juice)


title: Fruit5_woolly_rep5

description: Woolly fruit (0% juice)


title: Fruit3_juice_rep4

description: Non-woolly fruit (24-30% juice)


title: Fruit5_woolly_rep2

description: Woolly fruit (0% juice)


title: Fruit3_juice_rep5

description: Non-woolly fruit (24-30% juice)


title: Fruit4_woolly_rep4

description: Woolly fruit (0% juice)


title: Fruit3_juice_rep1

description: Non-woolly fruit (24-30% juice)


title: Fruit3_juice_rep3

description: Non-woolly fruit (24-30% juice)


title: Fruit4_woolly_rep3

description: Woolly fruit (0% juice)


title: Fruit4_woolly_rep2

description: Woolly fruit (0% juice)


title: F1 chloromethane treated sample biological replicate 3

city: Corvallis

first: barbara

last: gvakharia

state: OR

address: Cordley Hall 4097

department: Botany and Plant Pathology

institute: OSU

description: Gene expression data from chloromethane treated cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Nitrosomonas Genome Array in Affymetrix geneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GenChip Scanner 3000

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

organism: Nitrosomonas europaea

source_name: Nitrosomonas europaea culture at late exponential phase.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA according to the Affymetrix prokaryotic target preparation protocol

growth_protocol: Nitrosomonas europaea cells grown in batch cultures with 25 mM (NH4)2SO4, to OD600 close to 0.07

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's protocol. RNA extracts were further  purified using RNeasy Mini kit (QIAGEN), and on-column DNase digestion was performed.

treatment_protocol: cells grown to late exponential phase were washed and innoculated into medium with 5 mM (NH4)2SO4, placed on the orbital shaker. Cells were treated with 3.2 mM chloromethane for one hour. 150 mls of cells were collected  for RNA extraction by centrifugation.

tag: strain ATCC 19718


title: Fruit5_woolly_rep6

description: Woolly fruit (0% juice)


title: Fruit4_woolly_rep1

description: Woolly fruit (0% juice)


title: Fruit2_juice_rep6

description: Non-woolly fruit (24-30% juice)


title: E1 chloromethane treated sample biological replicate 2


title: Primary Lung Adenocarcinoma Sample_A27

description: Synthesis of the labelled first strand cDNA was conducted using Amersham CyScribe Post-Labelling kit with starting material of 20 ug of total RNA. The amino-allyl labeled dNTP mix was added to the reaction to generate amino-allyl labelled second strand cDNA. Following the hydrolysis reaction, single-stranded cDNA probes were purified using Amersham GFX columns. Dye coupling reactions were performed by mixing the cDNA samples with Amersham Cy3 (reference) or Cy5 (tumour) and incubating in the dark. The reactions were purified with Amersham GFX columns to remove the unincorporated/quenched dyes. After the purification samples were combined for hybridization, the labeled cDNAs were co-hybridized to 22K oligo microarrays. Slides were scanned on GMS418 confocal scanner (Agilent).

source_name: Universal Reference RNA

tag: The reference sample used for this experiment was commercially available Universal Reference RNA (Stratagene)

source_name: Tumour sample A27

tag: Primary adenocarcinoma of the lung. Total RNA extracted from fresh-frozen tissue using Trizol and RNeasy clean-up.


title: D2 untreated control biological replicate 1

description: Gene expression data from  untreated cells


title: E2 untreated control biological replicate2


title: Fruit3_juice_rep2

description: Non-woolly fruit (24-30% juice)


title: F2 untreated control biological replicate 3


title: Fruit2_juice_rep4

description: Non-woolly fruit (24-30% juice)


title: Fruit2_juice_rep3

description: Non-woolly fruit (24-30% juice)


title: C2 chloroform treated sample biological replicate3

description: Gene expression data from  chloroform treated cells

treatment_protocol: cells grown to late exponential phase were washed and innoculated into medium with 5 mM (NH4)2SO4, placed on the orbital shaker. Cells were treated with 7 uM chloroform for one hour. 150 mls of cells were collected  for RNA extraction by centrifugation.


title: Fruit2_juice_rep5

description: Non-woolly fruit (24-30% juice)


title: Fruit2_juice_rep2

description: Non-woolly fruit (24-30% juice)


title: Fruit2_juice_rep1

description: Non-woolly fruit (24-30% juice)


title: Fruit1_juice_rep4

description: Non-woolly fruit (24-30% juice)


title: Fruit1_juice_rep5

description: Non-woolly fruit (24-30% juice)


title: Fruit1_juice_rep6

description: Non-woolly fruit (24-30% juice)

data_processing: Quantification of the signal intensity was performed using the VersArray Analyzer software (BioRad). Raw values were measured as the volume of pixels within a circle encompassing the spot. Local background values were measured in the corners of spot and were subtracted from the signal intensity values for each spot. Spots that showed: (1) Signal Mean < (Background Mean + (1 x Background Standard Deviation; (2) qcom < 0.8; and (3) inter-membranes coefficient of variation (CV) > 0.5, were considered as low-quality spots and were removed. Qcom values were calculated as described in Wang et al., 2001. Then, the net intensity value of each spot was normalized by that of dap, a spike mRNA control.


title: Listeria_prfAstar and prfA

status: Public on Apr 28 2007

city: Ithaca

first: Patrick

last: Mc Gann

state: NY

address: 412 Stocking Hall

department: Food Science

institute: Cornell University

description: Due to the small number of targeted genes, two complete arrays were printed on each microarray slide. As two different probes, printed in duplicate, were used for each gene on a single array, the microarray design generated eight replicate spots for each gene per slide. Expression profiles were measured from three independent RNA extractions, resulting in twenty-four replicate spots per gene (twelve from each probe).

hyb_protocol: Before hybridization, microarray slides were treated for 10 min in a methyl pyrrilidone solution containing 0.18 M succinic anhydride, and 40 mM sodium borate (pH 8.0) and then washed in fresh methyl pyrrilidone for 10 min. Slides were successively washed for 1 min each in (i) nanopure H2O, (ii) 0.1% sodium dodecyl sulfate (SDS) (3 washes), (iii) nanopure water (5 washes), and (iv) 95% EtOH (1 wash). The slides were dried by centrifugation and immersed for 1 h in blocking solution (0.1% BSA, 5X SSC, 0.1% SDS) at 42oC. After blocking, the slides were washed for one minute each in nanopure H2O (5 washes) and in 95% EtOH (2 washes) and then dried by centrifugation. For the strains to be compared, labeled cDNA was resuspended in 50μl of hybridization buffer (5× SSC, 0.1% SDS, 1mM dithiothreitol (DTT), 0.5X formamide, 600μg/ml salmon sperm DNA ), denatured at 95oC for 5 min then applied to the slides using mSeries LifterSlips™ (Erie Scientific, Portsmouth, NH). Hybridization was conducted in a water bath at 42°C overnight. After hybridization, the slides were washed in 2X SSC+0.1% SDS (5 min at 42˚C), with subsequent washes at room temperature in 2X SSC+0.1% SDS (5 min), 2X SSC (5 min), 0.2X SSC (5 min), 0.05X SSC (1 min), followed by final rinse in nanopure H2O. The slides were dried by centrifugation.

scan_protocol: All images were scanned using a GenePix 4000b scanner (Axon Instruments Inc., Foster City, CA, USA). Acquired images were analyzed using GenePix 6.0 (Molecular Devices Corp., Sunnyvale, CA, USA).

data_processing:
Analyses of microarray data were performed in R (http://www.R-project.org) with Bioconductor (Gentleman et al., 2004) using LIMMA software (Wettenhall & Smyth, 2004). To correct for background noise, the background intensity was subtracted from the foreground intensity for each spot (Yang et al., 2001). For normalization within arrays, the data were weighted for the housekeeping genes and genomic DNA controls and normalized using a print-tip loess (Smyth & Speed, 2003). A linear model was fitted to the normalized log ratios and four B-statistics, t-statistics and P-values were generated for each gene

The VALUE column represents normalized log2 (CH1/CH2) ratios derived from 6 arrays (3 upper arrays & 3 lower arrays).  The 6 corresponding gpr files have been linked below as supplementary raw data files.

label: Alexa Flour 635

organism: Listeria monocytogenes

source_name: Listeria monocytogenes prfA null mutant

label_protocol: cDNA was synthesized from 10 μg purified total RNA and labeled with Alexa Fluor dyes using the SuperScript Plus Indirect cDNA labeling system (Invitrogen Inc., Carlsbad, CA, USA).

extract_protocol: RNA was isolated from frozen bacterial pellets with the RNeasy kit (Qiagen) according to the manufacturer’s protocol for enzymic and mechanical disruption, except that cells were sonicated on ice for three 30 s bursts at 18–21 W.C ontaminating DNA was removed using Turbo DNase according to the manufacturer’s instructions (Ambion Inc., TX, USA). Purified RNA was precipitated and stored at –80oC

tag: Listeria monocytogenes prfA null mutant FSL B2-046 (Wong & Freitag, 2004)

label: Alexa Flour 532

source_name: Listeria monocytogenes PrfA* strain

tag: Listeria monocytogenes NF-L753 prfA* (Shetron-Rama et al., 2003)


title: Listeria_WT and sigBprfA

hyb_protocol: Before hybridization, microarray slides were treated for 10 min in a methyl pyrrilidone solution containing 0.18 M succinic anhydride, and 44 mM sodium borate (pH 8.0) and then washed in fresh methyl pyrrilidone for 10 min. Slides were successively washed for 1 min each in (i) nanopure H2O, (ii) 0.1% sodium dodecyl sulfate (SDS) (3 washes), (iii) nanopure water (5 washes), and (iv) 95% EtOH (1 wash). The slides were dried by centrifugation and immersed for 1 h in blocking solution (0.1% BSA, 5X SSC, 0.1% SDS) at 42oC. After blocking, the slides were washed for one minute each in nanopure H2O (5 washes) and in 95% EtOH (2 washes) and then dried by centrifugation. For the strains to be compared, labeled cDNA was resuspended in 50μl of hybridization buffer (5× SSC, 0.1% SDS, 0.1mM dithiothreitol (DTT), 0.5X formamide, 600μg/ml salmon sperm DNA ), denatured at 95oC for 5 min then applied to the slides using mSeries LifterSlips™ (Erie Scientific, Portsmouth, NH). Hybridization was conducted in a water bath at 42°C overnight. After hybridization, the slides were washed in 2X SSC+0.1% SDS (5 min at 42˚C), with subsequent washes at room temperature in 2X SSC+0.1% SDS (5 min), 2X SSC (5 min), 0.2X SSC (5 min), 0.05X SSC (1 min), followed by final rinse in nanopure H2O. The slides were dried by centrifugation.

tag: Listeria monocytogenes sigBprfA double mutant (this study)

organism: Listeria monocytogenes 10403S

source_name: Listeria monocytogenes 10403S

tag: Listeria monocytogenes 10403S (serotype 1/2a;Bishop & Hinrichs, 1987)


title: Fruit1_juice_rep2

description: Non-woolly fruit (24-30% juice)


title: B2 chloroform treated sample biological replicate2

description: Gene expression data from chloroform treated cells


title: Fruit1_juice_rep3

description: Non-woolly fruit (24-30% juice)


title: B1 untreated control biological replicate 2

description: Gene expression data from untreated cells


title: Listeria_wt and prfA

data_processing:
Analyses of microarray data were performed in R (http://www.R-project.org) with Bioconductor (Gentleman et al., 2004) using LIMMA software (Wettenhall & Smyth, 2004). To correct for background noise, the background intensity was subtracted from the foreground intensity for each spot (Yang et al., 2001). For normalization within arrays, the data were weighted for the housekeeping genes and genomic DNA controls and normalized using a print-tip loess (Smyth & Speed, 2003). A linear model was fitted to the normalized log ratios and four B-statistics, t-statistics and P-values were generated for each gene

The VALUE column represents normalized log2 (CH1/CH2) ratios derived from 4 arrays (2 upper arrays & 2 lower arrays).  The 4 corresponding gpr files have been linked below as supplementary raw data files.

tag: Listeria monocytogenes 10403S (serotype 1/2a;(Bishop & Hinrichs, 1987)


title: C1 untreated control biological replicate 3


title: D1 chloromethane treated sample biological replicate1


title: Listeria_wt and sigB

hyb_protocol: ). Before hybridization, microarray slides were treated for 10 min in a methyl pyrrilidone solution containing 0.18 M succinic anhydride, and 40 mM sodium borate (pH 8.0) and then washed in fresh methyl pyrrilidone for 10 min. Slides were successively washed for 1 min each in (i) nanopure H2O, (ii) 0.1% sodium dodecyl sulfate (SDS) (3 washes), (iii) nanopure water (5 washes), and (iv) 95% EtOH (1 wash). The slides were dried by centrifugation and immersed for 1 h in blocking solution (0.1% BSA, 5X SSC, 0.1% SDS) at 42oC. After blocking, the slides were washed for one minute each in nanopure H2O (5 washes) and in 95% EtOH (2 washes) and then dried by centrifugation. For the strains to be compared, labeled cDNA was resuspended in 50μl of hybridization buffer (5× SSC, 0.1% SDS, 1mM dithiothreitol (DTT), 0.5X formamide, 600μg/ml salmon sperm DNA ), denatured at 95oC for 5 min then applied to the slides using mSeries LifterSlips™ (Erie Scientific, Portsmouth, NH). Hybridization was conducted in a water bath at 42°C overnight. After hybridization, the slides were washed in 2X SSC+0.1% SDS (5 min at 42˚C), with subsequent washes at room temperature in 2X SSC+0.1% SDS (5 min), 2X SSC (5 min), 0.2X SSC (5 min), 0.05X SSC (1 min), followed by final rinse in nanopure H2O. The slides were dried by centrifugation.

source_name: Listeria monocytogenes sigB null mutant

tag: Listeria monocytogenes sigB null mutant FSL A1-254 (Wiedmann et al., 1998).

label: Alexa flour 532

source_name: Listeria monocytogenes 10403s


title: A2 chloroform treated sample biological replicate1


title: A1 untreated control biological replicate 1


title: 22 weeks old BALB-neuT mouse MA0019Z

status: Public on Apr 19 2007

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description: 22 weeks old BALB-neuT mouse with progressive stages of mammary carcinogenesis

hyb_protocol: Arrays were then prehybridized at 55°C for 1 hour in hybridization buffer, denaturant and blocking reagent. For each sample, 15µg of DIG-labeled cRNA were fragmented by incubating with fragmentation buffer at 60°C for 30 min, mixed with hybridization controls and internal control target (ICT, 24-mer oligo labeled with LIZ fluorescent dye) and hybridized to each microarray in a 1.5-ml volume at 55°C for 16 hr. After hybridization, arrays were washed with hybridization wash buffer and chemiluminescence rinse buffer according to manufacturer’s protocol (Applied Biosystems Chemiluminescence Detection Kit). Chemiluminescence detection process consisted of antibody binding (anti-digoxigenin-Alkaline-Phosphatase) to the microarrays and chemiluminescence enhancing solution and substrate addition.

scan_protocol: According to the standard procedure for Applied Biosystems 1700 Chemiluminescent Microarray Analyzer

data_processing: Raw intensity data were quantile normalized using the ABarray Bioconductor package Version: 1.2.0

label: Digoxigenin

organism: Mus musculus

source_name: 22 weeks old BALB-neuT mouse mammary gland

label_protocol: All steps in sample and microarray processing (cRNA preparation, microarray hybridization, chemiluminescence detection, images acquisition and analysis) were performed following manufacturer’s protocol. Briefly, reverse transcription has been performed to generate first strand cDNA with T7-oligo(dT) primers at 42°C for 2 hours, followed by cDNA second strand synthesis at 16°C for 2 hours. After cDNA purification, cRNA has been produced and labeled by IVT reaction and DIG-UTP incorporation for 9 hours at 37°C (Applied Biosystems Chemiluminescent RT-IVT Labeling Kit).

extract_protocol:
RNA isolation was done as described in Quaglino et al. J Clin Invest. 2004 113:709-717
Quality and quantity of RNA was determined using  Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA)

treatment_protocol: Whole-mount for BALB-neuT animals were prepared as described in Quaglino et al. J Clin Invest. 2004 113:709-717

tag: BALB-neuT mouse


title: Fruit5_woolly_rep1

description: Woolly fruit (0% juice)


title: 22 weeks old BALB-neuT mouse MA001CU


title: Fruit1_juice_rep1

description: Non-woolly fruit (24-30% juice)


title: 22 weeks old BALB-neuT mouse MA001HW


title: 22 weeks old BALB-neuT mouse MA001HY


title: 19 weeks old BALB-neuT mouse MA001D0

description: 19 weeks old BALB-neuT mouse with progressive stages of mammary carcinogenesis

source_name: 19 weeks old BALB-neuT mouse mammary gland


title: 19 weeks old BALB-neuT mouse MA001I7

source_name: 19 weeks old BALB-neuT mouse mamamry gland


title: 19 weeks old BALB-neuT mouse MA001CZ


title: 15 weeks old BALB-neuT mouse MA001I9

description: 15 weeks old BALB-neuT mouse with progressive stages of mammary carcinogenesis

source_name: 15 weeks old BALB-neuT mouse mammary gland


title: 10 weeks old BALB-neuT mouse MA001IB

description: 10 weeks old BALB-neuT mouse with progressive stages of mammary carcinogenesis

source_name: 10 weeks old BALB-neuT mouse mammary gland


title: 10 weeks old BALB-neuT mouse MA001CV


title: 15 weeks old BALB-neuT mouse MA0019Y


title: exp5_1_2005101211

status: Public on Apr 15 2007

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Array-CGH of patient with T-ALL

hyb_protocol: For each hybridisation, 3 mg each of the Cy5- and Cy3- labeled probes, with a specific activity of 40 were mixed together with 100 µg Cot-1 DNA (Invitrogen, Carlsbad, CA). Probe preparation, pre-blocking and washing of the slides was performed as described previously (Van Buggenhout G, et al. 2004. J. Med. Genet. 41: 691-698).

scan_protocol: Arrays were scanned at 532 nm (Cy3) and 635 nm (Cy5) using the Genepix 4 scanner (Amersham Biosciences, Buckinghamshire, UK) and acquired images were analysed using the ArrayVision software (Imaging Research Inc., Ontario, Canada).

data_processing: Spot intensities were corrected for local background and only those spots with Cy5 as well as Cy3 signal intensities at least 1.7-fold above the local background, were further analysed. For each clone, a ratio of Cy3 to Cy5 fluorescent intensity was calculated. Normalization of the data was achieved by dividing the fluorescent intensity ratio of each spot by the mean of the ratios of the autosomes. Finally, the normalized ratio values of the duplicates were averaged and a log2 value was calculated. Datapoints for which the variation between the two intensity ratios was larger than 10% were excluded from the analysis.

label_protocol: Genomic DNA was labeled with the Bioprime DNA Labeling System (Invitrogen, Carlsbad, CA) using Cy5-labelled dCTP's (Amersham Biosciences, Buckinghamshire, UK) as described by the manufacturer. The concentrations and labeling efficiencies were measured with the Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Rockland, DE).

extract_protocol: Genomic DNA from patients as well as from healthy controls was isolated from bone marrow using the Wizard Genomic DNA purification Kit (Promega, Madison, WI) and using manufacture's protocol.

tag: Normal male DNA

label_protocol: Genomic DNA was labeled with the Bioprime DNA Labeling System (Invitrogen, Carlsbad, CA) using Cy3-labelled dCTP's (Amersham Biosciences, Buckinghamshire, UK) as described by the manufacturer. The concentrations and labeling efficiencies were measured with the Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Rockland, DE).


title: exp6_1_2005101227

description: Array-CGH of patient with T-ALL


title: exp6_2_2005101237

description: Array-CGH of patient with T-ALL


title: 10 weeks old BALB-neuT mouse MA001HX


title: exp3_2_2005101224

description: Array-CGH of patient with T-ALL


title: exp9_1_2005101231

description: Array-CGH of patient with T-ALL


title: exp8_2_2005101235

description: Array-CGH of patient with T-ALL


title: exp9_2_2005101236

description: Array-CGH of patient with T-ALL


title: 19 weeks old BALB-neuT mouse MA000UR


title: 10 weeks old BALB-neuT mouse MA001D2


title: exp4_2_2005101225

description: Array-CGH of patient with T-ALL


title: exp7_1_2005101228

description: Array-CGH of patient with T-ALL


title: exp7_2_2005101233

description: Array-CGH of patient with T-ALL


title: exp8_1_2005101230

description: Array-CGH of patient with T-ALL


title: exp5_2_2005101226

description: Array-CGH of patient with T-ALL


title: exp4_1_2005101210

description: Array-CGH of patient with T-ALL


title: exp3_1_2005101209

description: Array-CGH of patient with T-ALL


title: exp25_1_2006011134

description: Array-CGH of patient with T-ALL

tag: failure karyotype


title: exp25_2_2006011149

description: Array-CGH of patient with T-ALL


title: exp26_1_2006011136

description: Array-CGH of patient with T-ALL

tag: Normal female DNA


title: exp24_2_2006011148

description: Array-CGH of patient with T-ALL


title: exp2_2_2005101223

description: Array-CGH of patient with T-ALL


title: exp26_2_2006011151

description: Array-CGH of patient with T-ALL


title: exp27_1_2006011153

description: Array-CGH of patient with T-ALL


title: 10 weeks old BALB-neuT mouse MA001I1


title: exp2_1_2005101208

description: Array-CGH of patient with T-ALL


title: exp24_1_2006011133

description: Array-CGH of patient with T-ALL


title: exp23_2_2006011141

description: Array-CGH of patient with T-ALL


title: exp21_2_2006011143

description: Array-CGH of patient with T-ALL


title: exp20_2_2006011142

description: Array-CGH of patient with T-ALL


title: exp23_1_2006011125

description: Array-CGH of patient with T-ALL


title: exp22_1_2006011124

description: Array-CGH of patient with T-ALL


title: exp19_1_2006011106

description: Array-CGH of patient with T-ALL


title: exp1_1_2005101207

description: Array-CGH of patient with T-ALL


title: exp15_2_2006011107

description: Array-CGH of patient with T-ALL


title: exp18_2_2006011110

description: Array-CGH of patient with T-ALL


title: exp19_2_2006011111

description: Array-CGH of patient with T-ALL


title: exp21_1_2006011127

description: Array-CGH of patient with T-ALL


title: exp16_2_2006011108

description: Array-CGH of patient with T-ALL


title: exp17_2_2006011109

description: Array-CGH of patient with T-ALL


title: exp1_2_2005101222

description: Array-CGH of patient with T-ALL


title: exp27_2_2006011152

description: Array-CGH of patient with T-ALL


title: exp17_1_2006011104

description: Array-CGH of patient with T-ALL


title: exp18_1_2006011105

description: Array-CGH of patient with T-ALL


title: exp20_1_2006011126

description: Array-CGH of patient with T-ALL


title: exp16_1_2005101255

description: Array-CGH of patient with T-ALL


title: exp22_2_2006011140

description: Array-CGH of patient with T-ALL


title: exp12_2_2005101243

description: Array-CGH of patient with T-ALL


title: exp13_2_2005101244

description: Array-CGH of patient with T-ALL


title: exp12_1_2005101247

description: Array-CGH of patient with T-ALL


title: exp10_2_2005101241

description: Array-CGH of patient with T-ALL


title: exp14_2_2005101238

description: Array-CGH of patient with T-ALL


title: exp10_1_2005101245

description: Array-CGH of patient with T-ALL


title: exp14_1_2005101253

description: Array-CGH of patient with T-ALL


title: SUP-B15 untreated

status: Public on Apr 03 2007

city: Los Angeles

first: Markus

last: Müschen

state: CA

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

description: SUP-B15 cells were cultured without STI571

hyb_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)

data_processing: GCOS 1.3

source_name: Cell line SUP-B15

label_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site.

extract_protocol: Extraction Method: Qiagen_RNeasy_Kit

tag: human B cell precursor leukemia


title: SUP-B15 treated

description: SUP-B15 cells were cultured with 10 μmol/l STI571 for 16 hours

scan_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)


title: exp11_1_2005101246

description: Array-CGH of patient with T-ALL


title: exp11_2_2005101242

description: Array-CGH of patient with T-ALL


title: BV-173 treated

description: BV-173 cells were cultured with 10 μmol/l STI571 for 16 hours

source_name: Cell line BV-173


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. TAF1-(delta)TAND Y13.2 w/ pCALF-T(V161E) (1-119-680680)

status: Public on Apr 01 2007

first: B. Franklin

last: Pugh

email: fp265@cornell.edu, bfp2@psu.edu

address: 465 Biotechnology Bldg.

department: Molecular Biology and Genetics

description: one of at least 2 independent biological replicates, Test/Ref with Ref=WT strain with M1stop mutant

hyb_protocol: Chitikila et al.  2002. Mol Cell. 10:871-82

data_processing: MeanFRG- MedianBCK>S.D. BCK, <26% saturation.  Log2 Ratio of Test/Ref; see publication for normalized data

organism: Saccharomyces cerevisiae

growth_protocol: Transformants carrying the TBP plasmids were grown in CSM-Leu-Trp + 3% raffinose liquid media until they reached an OD600 = 0.65-0.8. Expression of the TBP was induced by addition of galactose to a final concentration of 2%.

treatment_protocol: Galactose induction (see below)

tag: WT Y13.2 derivative strain transformed with pCALF-T(M1Stop)(Gal10) plasmid

tag: TAF1-(delta)TAND Y13.2 derivative strain transformed with pCALF-T(V161E)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. TAF1-(delta)TAND Y13.2 w/ pCALF-T(K145E F182V) (1-084-740700)

scan_protocol: Chitikila et al.  2002. Mol Cell. 10:871-82

tag: TAF1-(delta)TAND Y13.2 derivative strain transformed with pCALF-T(K145E F182V)(Gal10) plasmid


title: TAF1-(delta)TAND Y13.2 deriv w/ pCALF-T(K145E F182V) vs. WT Y13.2 w/ pCALF-T(M1Stop) (1-034-710700)

label_protocol: Chitikila et al.  2002. Mol Cell. 10:871-82


title: TAF1-(delta)TAND Y13.2 deriv w/ pCALF-T(V161E) vs. WT Y13.2 w/ pCALF-T(M1Stop) (1-102-690700)

extract_protocol: Chitikila et al.  2002. Mol Cell. 10:871-82


title: TAF1-(delta)TAND Y13.2 deriv w/ pCALF-T(K145E V161R F182V) vs. WT Y13.2 w/ pCALF-T(M1Stop) (1-080-730700)

tag: TAF1-(delta)TAND Y13.2 derivative strain transformed with pCALF-T(K145E V161R F182V)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. TAF1-(delta)TAND Y13.2 w/ pCALF-T(V161R) (1-115-750670)

tag: TAF1-(delta)TAND Y13.2 derivative strain transformed with pCALF-T(V161R)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. TAF1-(delta)TAND Y13.2 w/ pCALF-T(wt) (1-063-630650)

tag: TAF1-(delta)TAND Y13.2 derivative strain transformed with pCALF-T(wt)(Gal10) plasmid


title: TAF1-(delta)TAND Y13.2 deriv w/ pCALF-T(V161R) vs. WT Y13.2 w/ pCALF-T(M1Stop) (1-111-710710)


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. TAF1-(delta)TAND Y13.2 w/ pCALF-T(V161R F182V) (1-082-730700)

tag: TAF1-(delta)TAND Y13.2 derivative strain transformed with pCALF-T(V161R F182V)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. TAF1-(delta)TAND Y13.2 w/ pCALF-T(V161R) (1-064-610628)


title: BV-173 untreated

description: BV-173 cells were cultured without STI571


title: exp15_1_2005101254

description: Array-CGH of patient with T-ALL


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. TAF1-(delta)TAND Y13.2 w/ pCALF-T(M1Stop) (1-062-630645)

tag: TAF1-(delta)TAND Y13.2 derivative strain transformed with pCALF-T(M1Stop)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. TAF1-(delta)TAND Y13.2 w/ pCALF-T(K145E) (1-030-740710)

tag: TAF1-(delta)TAND Y13.2 derivative strain transformed with pCALF-T(K145E)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. TAF1-(delta)TAND Y13.2 w/ pCALF-T(F182V) (1-031-740700)

tag: TAF1-(delta)TAND Y13.2 derivative strain transformed with pCALF-T(F182V)(Gal10) plasmid


title: TAF1-(delta)TAND Y13.2 deriv w/ pCALF-T(V161R F182V) vs. WT Y13.2 w/ pCALF-T(M1Stop) (1-033-720700)


title: TAF1-(delta)TAND Y13.2 deriv w/ pCALF-T(V161R) vs. WT Y13.2 w/ pCALF-T(M1Stop) (1-024-700735)


title: TAF1-(delta)TAND Y13.2 deriv w/ pCALF-T(wt) vs. WT Y13.2 w/ pCALF-T(M1Stop) (1-023-700755)


title: TAF1-(delta)TAND Y13.2 deriv w/ pCALF-T(F182V) vs. WT Y13.2 w/ pCALF-T(M1Stop) (1-028-680650)


title: TAF1-(delta)TAND Y13.2 deriv w/ pCALF-T(K145E V161R) vs. WT Y13.2 w/ pCALF-T(M1Stop) (1-029-690650)

tag: TAF1-(delta)TAND Y13.2 derivative strain transformed with pCALF-T(K145E V161R)(Gal10) plasmid


title: TAF1-(delta)TAND Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(M1Stop) (1-022-710745)

tag: WT Y13.2 derivative strain= WT Y13.2 derivative strain transformed with pCALF-T(M1Stop)(Gal10) plasmid


title: TAF1-(delta)TAND Y13.2 deriv w/ pCALF-T(K145E) vs. WT Y13.2 w/ pCALF-T(M1Stop) (1-027-680650)


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(K145E V161E F182V) (2-122-720700)

source_name: WT_pCALF-T(K145E V161E F182V)(Gal10)

tag: WT Y13.2 derivative strain transformed with pCALF-T(K145E V161E F182V)(Gal10) plasmid


title: exp13_1_2005101248

description: Array-CGH of patient with T-ALL

tag: Normal male DNA


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(K145E V161E) (2-120-700700)

source_name: WT_pCALF-T(K145E V161E)(Gal10)

tag: WT Y13.2 derivative strain transformed with pCALF-T(K145E V161E)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(V161E F182V) (2-121-710700)

source_name: WT_pCALF-T(V161E F182V)(Gal10)

tag: WT Y13.2 derivative strain transformed with pCALF-T(V161E F182V)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(N2-1) vs. WT Y13.2 w/ pCALF-T(M1Stop) (3-063-670670)

tag: WT Y13.2 derivative strain transformed with pCALF-T(N2-1)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(R107E) vs. WT Y13.2 w/ pCALF-T(M1Stop) (3-062-670670)

tag: WT Y13.2 derivative strain transformed with pCALF-T(R107E)(Gal10) plasmid

tag: WT Y13.2 derivative strain transformed with pCALF-T(M1Stop)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. TAF1-(delta)TAND Y13.2 w/ pCALF-T(K145E V161R F182V) (1-085-740700)


title: WT Y13.2 deriv w/ pCALF-T(V161E F182V) vs. WT Y13.2 w/ pCALF-T(M1Stop) (3-065-660680)


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-Toa2-TBP(N2-1) (2-119-700700)

tag: WT Y13.2 derivative strain transformed with pCALF-Toa2-TBP(N2-1)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(K145E V161E) vs. WT Y13.2 w/ pCALF-T(M1Stop) (3-064-660680)


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(R107E) (2-117-720700)


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(N2-1) (2-118-700700)


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(V161R) (2-065-600600)

tag: WT Y13.2 derivative strain transformed with pCALF-T(V161R)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-Toa2-TBP(wt) vs. WT Y13.2 w/ pCALF-T(M1Stop) (2-113-700700)

tag: WT Y13.2 derivative strain transformed with pCALF-Toa2-TBP(wt)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(E93R) (2-116-700730)

tag: WT Y13.2 derivative strain transformed with pCALF-T(E93R)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(V161R) vs. WT Y13.2 w/ pCALF-T(M1Stop) (2-061-600600)


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(V161E) (2-056-600640)

tag: WT Y13.2 derivative strain transformed with pCALF-T(V161E)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(K145E V161E F182V) vs. WT Y13.2 w/ pCALF-T(M1Stop) (2-115-700700)


title: WT Y13.2 deriv w/ pCALF-T(E93R) vs. WT Y13.2 w/ pCALF-T(M1Stop) (3-061-660670)


title: WT Y13.2 deriv w/ pCALF-Toa2-TBP(N2-1) vs. WT Y13.2 w/ pCALF-T(M1Stop) (2-114-700700)


title: WT Y13.2 deriv w/ pCALF-T(V161E) vs. WT Y13.2 w/ pCALF-T(M1Stop) (2-052-590625)


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(M1Stop) (2-055-590600)


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(K145E V161R F182V) (1-141-680680)

source_name: WT_pCALF-T(K145E V161R F182V)(Gal10)

tag: WT Y13.2 derivative strain transformed with pCALF-T(K145E V161R F182V)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(M1Stop) (2-051-580605)


title: WT Y13.2 deriv w/ pCALF-T(K145E V161R F182V) vs. WT Y13.2 w/ pCALF-T(M1Stop) (1-136-700680)


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(K145E F182V) (1-140-680700)

source_name: WT_pCALF-T(K145E F182V)(Gal10)

tag: WT Y13.2 derivative strain transformed with pCALF-T(K145E F182V)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(K145E F182V) vs. WT Y13.2 w/ pCALF-T(M1Stop) (1-135-730660)


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(V161R F182V) (1-132-650660)

source_name: WT_pCALF-T(V161R F182V)(Gal10)

tag: WT Y13.2 derivative strain transformed with pCALF-T(V161R F182V)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(F182V) vs. WT Y13.2 w/ pCALF-T(M1Stop) (1-128-700680)

description: homotypic hyb- Used in Null data set, Test & Ref different biological samples of same genotype

tag: WT Y13.2 derivative strain transformed with pCALF-T(F182V)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(V161R F182V) vs. WT Y13.2 w/ pCALF-T(M1Stop) (1-129-680680)


title: WT Y13.2 deriv w/ pCALF-T(wt) vs. WT Y13.2 w/ pCALF-T(M1Stop) (1-020-710750)

tag: WT Y13.2 derivative strain transformed with pCALF-T(wt)(Gal10) plasmid


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(F182V) (1-130-650660)


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(wt) (1-059-660670)


title: WT Y13.2 deriv w/ pCALF-T(M1Stop) vs. WT Y13.2 w/ pCALF-T(V161R) (1-060-635655)


title: WT Y13.2 deriv w/ pCALF-T(V161R) vs. WT Y13.2 w/ pCALF-T(M1Stop) (1-021-710745)


title: Y13.2 strain w/ pCALF-T(M1Stop) vs. Y13.2 w/ pCALF-T(M1Stop) (1-114-740680)

tag: Y13.2 strain transformed with pCALF-T(M1Stop)(Gal10) plasmid


title: Methylation IP/total DNA 60932

status: Public on Apr 02 2007

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Antibody-based methylation mapping of the Arabidopsis genome. The DNA was extracted from ros1 dml2 dml3 homozygous mutant plants (Colombia background). The values are log2 signal ratios of immunoprecipitated DNA / input DNA.

hyb_protocol: Hybridization protocol provided and performed by NimbleGen. Set MAUI hybridization unit to 42 deg C and allow time for the temperature to stabilize. Based on the A_260 measurement, combine 13 micrograms each of the Test and Reference Samples into a single 1.5 ml microcentrifuge tube. Protect tube from light during handling to prevent photobleaching of the light-sensitive Cy dyes. Dry the combined contents in a Speed-Vac on low heat. Resuspend the sample in 10.9microliter VWR water and vortex to completely dissolve the sample. Spin the tube down briefly to collect the contents in the bottom. Using the NimbleGen Array Reuse Kit, add the following to the resuspended sample: 19.5 microliter 2X Hybridization Buffer, 7.8 microliter Hybridization Component A, 0.4 microliter Cy3 CPK6 50mer Oligo (50nM), 0.4 microliter Cy5 CPK6 50mer Oligo (100nM). CPK6 oligos are included in the hybridization as controls that hybridize to alignment features on the NimbleGen arrays. They are required for proper extraction of array data from the scanned image. Mix the tube briefly then spin down to collect the contents in the bottom and place at 95 deg C for 5 minutes. Immediately transfer the tube to the MAUI 42 deg C sample block and hold at this temperature until you are are ready for sample loading. Place the MAUI Mixer SL Hybridization Chamber on the array using the provided assembly/disassembly jig and carefully follow MAUI setup instructions. Use the braying tool to remove all air bubbles from the adhesive gasket around the outside of the hybridization chamber. Put the array and hybridization chamber on the MAUI and allow 30 seconds for the chips to come up to temperature. Load the sample using the pipet supplied with the MAUI Station and following manufacturer instructions. During the loading, a small amount (3-7 microliter) of the sample may flow out of the outlet port. Confirm that there are no bubbles in the chamber. If there are, very gently massage any bubbles to either of the ends, away from the center of the array. Avoid applying too much pressure since this will force liquid out of the ports. Place the loaded array into one of the four MAUI bays and let equilibrate for 30 seconds. Wipe off any sample leakage at the ports with a Kim-Wipe, and adhere MAUI stickers to both ports. Close the bay clamp and select mix mode B. Hold down the mix button to start mixing. Confirm that the mixing is in progress before closing the cover. Hybridize the sample 16-20 hours. Prior to removing the array from the MAUI Hybridization Station, prepare the following solutions. You will need two 250ml dishes of Wash I, and one each for Wash II and Wash III. One dish for Wash I should be shallow and be wide enough to accomodate the array and mixer loaded in the MAUI assembly/dissassembly jig. The lid from a 1000 microliter pipet tip box works well. Also, the buffer in the first Wash I dish should be heated to 42 deg C to help soften the adhesive on the hybridization chamber; this will help prevent braking the array. Place the remaining three wash solutions in 300 microliter Tissue-Tek slide staining dishes. Wash I: 225 ml VWR Water, 25ml 10X Wash Buffer I, 25microliter 1M DTT. Wash II: 225ml VWR Water, 25ml 10X Wash Buffer II, 25microliter 1M DTT. Wash III: 225ml VWR Water, 25microliter 10X Wash Buffer III, 25microliter 1M DTT. Remove chip from MAUI Hybridization Station, load it back into the MAUI assembly/disassembly jig, and immerse in the shallow 250ml Wash I at 42 deg C. Peel the hybridization chamber off very slowly to prevent the slide from cracking. Do not let the surface of the slide dry out at any point during washing. While the chip is submerged, carefully peel off the mixer. Gently agitate the chip in Wash I for 10-15 seconds. Transfer the slide into a slide rack in the second dish of Wash I and incubate 2 minutes with agitation. Transfer to Wash II and incubate 1 minute with agitation. Rock the disk to move the wash over the tops of the arrays. Transfer to Wash III and incubate for 15 sec with agitation. Remove array and spin dry in array-drying unit for 1 minute. Store the dried array in a dark desiccator.

scan_protocol: Sample scan protocol provided and performed by NimbleGen. Axon Scanner (model 4000B). Turn on the power of the scanner. The switch is on the back right hand side. Launch GenePix Software 10 minutes before scanning to allow lasers to warm. Open the scanner door and open the side carriage. Place chip in carriage so that array is face down and barcode end is closest to you. Move the black lever on the left side of the carriage left until the array is lying flat in the carriage. Release the lever so that the arry is pushed over gently to the right side of the carriage and held firmly. Close the carriage (you should hear a click) and slide the scanner door shut. Open the hardware settings. Select the following settings for scanning: Wavelength (532=Cy3, 635=Cy5). Set the 532 laser PMT Gain to 650 and the 635 laser PMT Gain to 750. Power=100%. Pixel Size=5m. Lines to average=1. Focus position=0micrometer. Select Image/Ratio to view both channels simultaneously. Perform a preview scan by clicking on the fast-forward icon. Stop scan once the full arry is in view by pressing the stop icon. Switch to zoom mode by clicking on the array image and pressing Z. Click and drag the mouse on the area in which you want to zoom. Center the image of the entire array area within the viewing window. Under Tools on the left side of the screen, click the Scan Area icon. Click and drag to define a box that bounds the visibile array area. The box dimensions should be stretched to create a box just slightly larger than the array area. It is critical to include all of the corner probes within the scan image. Scan chip by clicking the play icon. While scanning, set the zoom level to view the whole image and adjust the brightness and contrast of the displayed image to eliminate visible saturation. Based on the appearance of the array features, adjust the PMT setting as appropriate. The features should be mostly yellow. If your features are mostly green, either decrease the 532 PMT or raise the 635 PMT. If the features are mostly red or orange, either raise the 532 PMT or decrease the 635 PMT. Zoom the view to a region scanned under the most recent PMT settings and click on the Histogram tab at the top of the left side of the screen to check global intensity of the features. On the top left side of the screen make sure you have the 532 and 635 wavelength boxes checked so both wavelength histograms are displayed. Make sure the Log Axis box is checked. You want the red and green curves to be as close as possible to one another. If the red curve is above the green, lower the red PMT setting or raise the green PMT setting. You want the curve to have 1e-5 normalized counts at the 65,000 intensity level (saturation). This means that you have about 1% of the features saturated. The position of the two curves on top of each other is more important than hitting the 1% saturation mark.  The histogram only graphs the area of the image that is viewable in the screen on the image tab. If the histogram is no longer changing then either the chip is done scanning or the area that you can see on the image screen has been scanned. After the PMT settings are properly adjusted, stop the current scan, do not save this image. Restart the scan under the new settings and wait until the scan has completed. Save the images. Make sure you save both the 532nm and 635nm images as separate single image tif files.

data_processing: Log base 2 (ch_635/ch_532) ratios were bi-weight mean centered

organism: Arabidopsis thaliana

source_name: sonicated total genomic DNA

label_protocol: Sample labeling protocol provided by NimbleGen. Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffer, 10X TE.  Dilute Cy3 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and store at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR tube: 1 microgram LM-PCR Sample and 40 microliter Cy3-9mer Primers. Heat denature samples in thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling step after denaturation is critical for efficiency labeling. Add the following: 10 microliters 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM to force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler protected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microliter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol. Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove supernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 25 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 seconds and quick spin to collect contents at bottom of tube. Continue to vortex or let site in the dark at room temp until the pellet is completely rehydrated, then vortex again and quickly spin. Measure the A_260 in each sample. It is important to consume as little sample as possible when performing this measurement. Typical yields range from 10 to 30 micrograms per reaction.

extract_protocol: Methods are described in publication Zilberman et al. Nature Genetics 2006.

tag: Ecotype:Columbia, Age

source_name: Immunoprecipitated methylated genomic DNA

label_protocol: Sample labeling protocol provided by NimbleGen. Prepare the following three solutions: 50X dNTP Mix, Random 9mer Buffer, 10X TE.  Dilute Cy5 dye-labeled 9mers to 1 O.D./42 microliter Random 9mer Buffer. Aliquot to 40 microliter individual reaction volumes in 0.2 milliliter thin-walled PCR tubes and store at -20 degrees C. Assemble the following components in a 0.2 milliliter thin-walled PCR tube: 1 microgram LM-PCR Sample and 40 microliter Cy5-9mer Primers. Heat denature samples in thermocycler at 98 degrees C for 10 minutes. Quick chill in ice water bath. Snap-chilling step after denaturation is critical for efficiency labeling. Add the following: 10 microliters 50X dNTPmix, 8 microliters VWR deionized water, 2 microliters Kienow (50 U/microliter). Do not vortex after addition of Kienow. Mix well by pipetting 10 times. Spin down at low RPM to force contents to bottom of tube. Incubate at 37 degrees C for 2 hours in a thermocycler protected from light. Stop the reaction by addition of EDTA: 10 microliter Stop Solution (0.5 M EDTA). Transfer the reaction to a 1.5 milliliter tube. Precipitate the labeled samples by adding NaCl and isopropanol to each tube as indicated: 11.5 microliter 5M NaCl, 110 microliter Isopropanol. Vortex briefly after addition of 5M NaCl prior to addition of isopropanol. Vortex. Incubate 10 minutes at room temperature in the dark. Centrifuge at maximum speed for 10 minutes. Remove supernatant with pipette. Rinse pellet with 500 microliter 80% ice-cold ethanol. Dislodge pellet from tube wall. Centrifuge at maximum speed for 2 minutes. Remove supernatant with pipette. Speed-Vac on low heat for 5 minutes until dry, protected from light. Store labeled samples at -20 degrees C, protected from light. Rehydrate dried pellets in 25 microliter VWR deionized water. Spin tubes down briefly prior to opening. Vortex for 30 seconds and quick spin to collect contents at bottom of tube. Continue to vortex or let site in the dark at room temp until the pellet is completely rehydrated, then vortex again and quickly spin. Measure the A_260 in each sample. It is important to consume as little sample as possible when performing this measurement. Typical yields range from 10 to 30 micrograms per reaction.

tag: Ecotype

value: Columbia, Age 25 days old, Tissue:whole plant without roots


title: Y13.2 strain w/ pCALF-T(M1Stop) vs. Y13.2 w/ pCALF-T(M1Stop) (2-163-720700)


title: Y13.2 strain w/ pCALF-T(M1Stop) vs. Y13.2 w/ pCALF-T(M1Stop) (3-060-690680)


title: Y13.2 strain w/ pCALF-T(M1Stop) vs. Y13.2 w/ pCALF-T(M1Stop) (1-026-680650)


title: Y13.2 strain w/ pCALF-T(M1Stop) vs. Y13.2 w/ pCALF-T(M1Stop) (1-065-620630)


title: Y13.2 strain w/ pCALF-T(M1Stop) vs. Y13.2 w/ pCALF-T(M1Stop) (1-101-680680)


title: Normal donor_NC19

city: Scottsdale

first: Rafael

last: Fonseca

state: AZ

address: 13400 E Shea Blvd

department: Hematology-Oncology

institute: Mayo Clinic

description: Gene expression data from normal donor.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on HG-U133A GeneChip.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: CD138 selected bone marrow plasma cells from normal donor.

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

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

tag: Diploid

tag: Normal Chromosome 13


title: Y13.2 strain w/ pCALF-T(M1Stop) vs. Y13.2 w/ pCALF-T(M1Stop) (1-061-620630)


title: Normal donor_NC18

description: Gene expression data from normal donor.


title: MCF7 LMO4 low Replicate2

city: Irvine

first: Kevin

middle: K

last: Lin

address: 250 Sprague Hall

department: Biological Chemistry & Medicine

institute: University of California, Irvine

description: LMO4 - LIM-only protein 4

hyb_protocol: Subsequently, 10 ug of this fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix HG-U133A array.

scan_protocol: The GeneChip arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450, followed by scanning on a GeneChip Scanner 3000. The results were quantified and analyzed using GCOS 1.1.1 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity = 500; Normalization, All Probe Sets; Parameters, all set at default values).

data_processing: MAS 5.0

source_name: MCF7-LMO4-TetOff cells

label_protocol: Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+ mRNA  present in the isolated total RNA (10 ug total RNA starting material each sample reaction) using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp., Carlsbad, CA ) and poly (T)-nucleotide primers that contained a sequence recognized by T7 RNA polymerase. A portion of the resulting ds cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY).  15ug of the resulting biotin-tagged cRNA was fragmented to strands of 35-200 bases in length following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).

extract_protocol: Isolated total RNA samples were processed as recommended by Affymetrix, Inc. (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetric, Inc., Santa Clara, CA). In brief, total RNA was initially isolated using TRIzol Reagent (Gibco BRL Life Technologies, Rockville, MD), and passed through an RNeasy spin column (Qiagen, Chatsworth, CA) for further clean up. Eluted total RNAs were quantified with a portion of the recovered total RNA adjusted to a final concentration of 1 ug/ul. All starting total RNA samples were quality assessed prior to beginning target preparation/processing steps by running out a small amount of each sample (typically 25-250 ng/well) onto a RNA Lab-On-A-Chip (Caliper Technologies Corp., Mountain View, CA) that was evaluated on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

tag: Treatment with doxycycline results in low LMO4 level.


title: MCF7 LMO4 low Replicate3

description: LMO4 - LIM-only protein 4


title: MCF7 LMO4 high Replicate3

description: LMO4 - LIM-only protein 4

tag: Without doxycycline treatment results in high LMO4 level.


title: Normal donor_NC15

description: Gene expression data from normal donor.


title: MCF7 LMO4 high Replicate1

description: LMO4 - LIM-only protein 4


title: Y13.2 strain w/ pCALF-T(M1Stop) vs. Y13.2 w/ pCALF-T(M1Stop) (1-081-700700)


title: MCF7 LMO4 high Replicate2

description: LMO4 - LIM-only protein 4


title: Normal donor_NC16

description: Gene expression data from normal donor.


title: Normal donor_NC13

description: Gene expression data from normal donor.


title: Normal donor_NC12

description: Gene expression data from normal donor.


title: Normal donor_NC14

description: Gene expression data from normal donor.


title: Normal donor_NC09

description: Gene expression data from normal donor.


title: New MM_M822

description: Gene expression data from newly diagnosed myeloma.

source_name: CD138 selected bone marrow plasma cells from newly diagnosed myeloma.

tag: Hyperdiploid

tag: Chromosome 13 deletion


title: Relapsed MM_M821

description: Gene expression data from relapsed myeloma.

source_name: CD138 selected bone marrow plasma cells from relapsed myeloma.

tag: Non-hyperdiploid


title: Normal donor_NC11

description: Gene expression data from normal donor.


title: New MM_M806


title: Normal donor_NC04

description: Gene expression data from normal donor.


title: Smoldering MM_M819

description: Gene expression data from smoldering myeloma.

source_name: CD138 selected bone marrow plasma cells from smoldering myeloma.


title: New MM_M814


title: MCF7 LMO4 low Replicate1

description: LMO4 - LIM-only protein 4


title: MGUS_M817

description: Gene expression data from MGUS.

source_name: CD138 selected bone marrow plasma cells from MGUS.


title: Normal donor_NC05

description: Gene expression data from normal donor.


title: New MM_M813


title: New MM_M804


title: MGUS_M805

description: Gene expression data from MGUS.


title: Smoldering MM_M798


title: New MM_M820


title: New MM_M797


title: Relapsed MM_M694


title: Normal donor_M708

description: Gene expression data from normal donor.


title: MGUS_M722

description: Gene expression data from MGUS.


title: Relapsed MM_M789


title: New MM_M790


title: New MM_M795


title: New MM_M700


title: Smoldering MM_M682


title: New MM_M687


title: MGUS_M691

description: Gene expression data from MGUS.


title: New MM_M678


title: Smoldering MM_M692


title: New MM_M672


title: Smoldering MM_M661

tag: Ploidy unknown


title: Relapsed MM_M490


title: Relapsed MM_M459


title: New MM_M467


title: Relapsed MM_M444


title: New MM_M452


title: Smoldering MM_M658


title: B-lineage ALL 87

city: Lund

first: Thoas

middle: Anna

address: Lund University Hospital

country: Sweden

institute: Dept of Clinical Genetics

description: cDNA microarray data

hyb_protocol: Arrays were hybridized and washed as described in Andersson et al et al. (Leukemia 2005)

scan_protocol: Arrays were scanned in an Agilent Microarray scanner

data_processing: Image analysis was performed using Genepix v4.0. Resultsfile were uploaded into BASE where they were filtered, normalized using pin-based lowess,  mean centered with respect to hospital and filtered for presence (40% required)

source_name: Case 127

label_protocol: Samples were labeled using the CyScribe Post-labeling Kit (Amersham Biosciences)

extract_protocol: Trizol extraction followed by purification using RNeasy

source_name: Stratagene Universal Human Reference RNA

tag: RNA pooled from ten human cell lines


title: B-lineage ALL 86

description: cDNA microarray data

source_name: Case 126


title: B-lineage ALL 81

description: cDNA microarray data

source_name: Case 121

tag: Normal Karyotype


title: B-lineage ALL 85

description: cDNA microarray data

source_name: Case 125


title: Relapsed MM_M422


title: B-lineage ALL 84

description: cDNA microarray data

source_name: Case 124

tag: High Hyperdiploidy


title: B-lineage ALL 82

description: cDNA microarray data

source_name: Case 122

tag: BCR/ABL1 p190


title: Smoldering MM_M416


title: Smoldering MM_M428


title: New MM_M427

tag: Chromosome 13 status unknown


title: Smoldering MM_M429


title: B-lineage ALL 79

description: cDNA microarray data

source_name: Case 119


title: B-lineage ALL 78

description: cDNA microarray data

source_name: Case 118


title: T-cell ALL 11

description: cDNA microarray data

source_name: Case 115


title: Relapsed MM_M433


title: B-lineage ALL 77

description: cDNA microarray data

source_name: Case 117


title: B-lineage ALL 76

description: cDNA microarray data

source_name: Case 116


title: Normal donor_NC08

description: Gene expression data from normal donor.

source_name: CD138 selected bone marrow plasma cells from normal donor.


title: B-lineage ALL 83

description: cDNA microarray data

source_name: Case 123


title: MGUS_M403

description: Gene expression data from MGUS.


title: MGUS_M399

description: Gene expression data from MGUS.


title: New MM_M419

source_name: CD138 selected bone marrow plasma cells from newly diagnosed myeloma.


title: AML 21

description: cDNA microarray data

source_name: Case 106


title: AML 23

description: cDNA microarray data

source_name: Case 112


title: Normal donor_M436

description: Gene expression data from normal donor.


title: MGUS_M420

description: Gene expression data from MGUS.

source_name: CD138 selected bone marrow plasma cells from MGUS.


title: B-lineage ALL 75

description: cDNA microarray data

source_name: Case 113

source_name: Stratagene Universal Human Reference RNA


title: B-lineage ALL 80

description: cDNA microarray data

source_name: Case 120


title: B-lineage ALL 74

description: cDNA microarray data

source_name: Case 111


title: B-lineage ALL 73

description: cDNA microarray data

source_name: Case 110


title: AML 20

description: cDNA microarray data

source_name: Case 104


title: New MM_M410


title: Smoldering MM_M400

source_name: CD138 selected bone marrow plasma cells from smoldering myeloma.


title: Methylation IP/total DNA 60785

description: Antibody-based methylation mapping of the Arabidopsis genome.  The DNA was extracted from a wild type line in the Colombia background.  The values are log2 signal ratios of immunoprecipitated DNA / input DNA.

source_name: sonicated total genomic DNA

value: 25 days old, Tissue:whole plant without roots

source_name: Immunoprecipitated methylated genomic DNA


title: T-cell ALL 9

description: cDNA microarray data

source_name: Case 107


title: New MM_M373


title: New MM_M370


title: T-cell ALL 8

description: cDNA microarray data

source_name: Case 105


title: New MM_M380


title: B-lineage ALL 67

description: cDNA microarray data

source_name: Case 98

tag: 47-50 chromosomes


title: B-lineage ALL 70

description: cDNA microarray data

source_name: Case 101


title: T-cell ALL 10

description: cDNA microarray data

source_name: Case 114


title: Smoldering MM_M417


title: B-lineage ALL 68

description: cDNA microarray data

source_name: Case 99


title: B-lineage ALL 69

description: cDNA microarray data

source_name: Case 100


title: New MM_M359

source_name: CD138 selected bone marrow plasma cells from newly diagnosed myeloma.


title: New MM_M412


title: New MM_M390


title: B-lineage ALL 66

description: cDNA microarray data

source_name: Case 97


title: New MM_M413


title: B-lineage ALL 72

description: cDNA microarray data

source_name: Case 108

source_name: Stratagene Universal Human Reference RNA


title: AML 19

description: cDNA microarray data

source_name: Case 103


title: New MM_M356


title: New MM_M338


title: New MM_M407


title: New MM_M383


title: Relapsed MM_M351

source_name: CD138 selected bone marrow plasma cells from relapsed myeloma.


title: B-lineage ALL 65

description: cDNA microarray data

source_name: Case 94


title: New MM_M387


title: Relapsed MM_M353


title: B-lineage ALL 62

description: cDNA microarray data

source_name: Case 91


title: New MM_M307


title: New MM_M337


title: B-lineage ALL 58

description: cDNA microarray data

source_name: Case 84


title: Normal donor_M326

description: Gene expression data from normal donor.

source_name: CD138 selected bone marrow plasma cells from normal donor.


title: B-lineage ALL 59

description: cDNA microarray data

source_name: Case 85


title: B-lineage ALL 63

description: cDNA microarray data

source_name: Case 92


title: New MM_M305


title: Relapsed MM_M398


title: B-lineage ALL 71

description: cDNA microarray data

source_name: Case 102


title: New MM_M350


title: T-cell ALL 6

description: cDNA microarray data

source_name: Case 88


title: New MM_M304


title: MGUS_M394

description: Gene expression data from MGUS.

source_name: CD138 selected bone marrow plasma cells from MGUS.


title: AML 22

description: cDNA microarray data

source_name: Case 109


title: B-lineage ALL 61

description: cDNA microarray data

source_name: Case 90


title: MGUS_M295

description: Gene expression data from MGUS.


title: MGUS_M358

description: Gene expression data from MGUS.


title: AML 18

description: cDNA microarray data

source_name: Case 96


title: New MM_M279

source_name: CD138 selected bone marrow plasma cells from newly diagnosed myeloma.


title: AML 14

description: cDNA microarray data

source_name: Case 79


title: New MM_M318


title: AML 13

description: cDNA microarray data

source_name: Case 78

source_name: Stratagene Universal Human Reference RNA


title: B-lineage ALL 55

description: cDNA microarray data

source_name: Case 77


title: T-cell ALL 7

description: cDNA microarray data

source_name: Case 95


title: B-lineage ALL 64

description: cDNA microarray data

source_name: Case 93


title: B-lineage ALL 52

description: cDNA microarray data

source_name: Case 71


title: Relapsed MM_M276

source_name: CD138 selected bone marrow plasma cells from relapsed myeloma.


title: AML 11

description: cDNA microarray data

source_name: Case 72

tag: PML/RARA


title: MGUS_M270

description: Gene expression data from MGUS.


title: New MM_M321


title: New MM_M300


title: New MM_M272


title: B-lineage ALL 47

description: cDNA microarray data

source_name: Case 66


title: MGUS_M280

description: Gene expression data from MGUS.


title: AML 16

description: cDNA microarray data

source_name: Case 86


title: Normal Bone Marrow 6

description: cDNA microarray data

source_name: Case 73


title: New MM_M310


title: B-lineage ALL 56

description: cDNA microarray data

source_name: Case 80


title: rNew MM_M288


title: T-cell ALL 5

description: cDNA microarray data

source_name: Case 81


title: B-lineage ALL 53

description: cDNA microarray data

source_name: Case 74


title: B-lineage ALL 60

description: cDNA microarray data

source_name: Case 87


title: B-lineage ALL 45

description: cDNA microarray data

source_name: Case 64


title: B-lineage ALL 54

description: cDNA microarray data

source_name: Case 75


title: B-lineage ALL 46

description: cDNA microarray data

source_name: Case 65


title: New MM_M257

source_name: CD138 selected bone marrow plasma cells from newly diagnosed myeloma.


title: Smoldering MM_M290

source_name: CD138 selected bone marrow plasma cells from smoldering myeloma.


title: B-lineage ALL 49

description: cDNA microarray data

source_name: Case 68

source_name: Stratagene Universal Human Reference RNA


title: MGUS_M261

description: Gene expression data from MGUS.

source_name: CD138 selected bone marrow plasma cells from MGUS.


title: New MM_M264


title: B-lineage ALL 57

description: cDNA microarray data

source_name: Case 82


title: New MM_M263


title: Smoldering MM_M266


title: Smoldering MM_M319


title: AML 17

description: cDNA microarray data

source_name: Case 89


title: MGUS_M269


title: B-lineage ALL 48

description: cDNA microarray data

source_name: Case 67


title: AML 15

description: cDNA microarray data

source_name: Case 83


title: MGUS_M247

description: Gene expression data from MGUS.


title: AML 10

description: cDNA microarray data

source_name: Case 60


title: New MM_M245


title: Smoldering MM_M246


title: B-lineage ALL 41

description: cDNA microarray data

source_name: Case 59


title: B-lineage ALL 50

description: cDNA microarray data

source_name: Case 69


title: New MM_M249


title: B-lineage ALL 42

description: cDNA microarray data

source_name: Case 61


title: Relapsed MM_M254

source_name: CD138 selected bone marrow plasma cells from relapsed myeloma.


title: MGUS_M237

description: Gene expression data from MGUS.


title: rNew MM_M297


title: B-lineage ALL 40

description: cDNA microarray data

source_name: Case 58


title: MGUS_M256

description: Gene expression data from MGUS.


title: B-lineage ALL 43

description: cDNA microarray data

source_name: Case 62


title: New MM_M250


title: AML 12

description: cDNA microarray data

source_name: Case 76


title: New MM_M271

source_name: CD138 selected bone marrow plasma cells from newly diagnosed myeloma.


title: B-lineage ALL 44

description: cDNA microarray data

source_name: Case 63


title: T-cell ALL 4

description: cDNA microarray data

source_name: Case 55


title: B-lineage ALL 38

description: cDNA microarray data

source_name: Case 56

source_name: Stratagene Universal Human Reference RNA


title: rNew MM_M233


title: B-lineage ALL 37

description: cDNA microarray data

source_name: Case 53


title: New MM_M227


title: Normal Bone Marrow 5

description: cDNA microarray data

source_name: Case 54


title: Relapsed MM_M229


title: B-lineage ALL 51

description: cDNA microarray data

source_name: Case 70


title: Relapsed MM_M235


title: New MM_M230


title: B-lineage ALL 39

description: cDNA microarray data

source_name: Case 57


title: B-lineage ALL 36

description: cDNA microarray data

source_name: Case 52


title: Smoldering MM_M226

source_name: CD138 selected bone marrow plasma cells from smoldering myeloma.


title: New MM_M218


title: Normal Bone Marrow 4

description: cDNA microarray data

source_name: Case 51


title: New MM_M217


title: MGUS_M213

description: Gene expression data from MGUS.

source_name: CD138 selected bone marrow plasma cells from MGUS.


title: B-lineage ALL 31

description: cDNA microarray data

source_name: Case 43


title: MGUS_M204

description: Gene expression data from MGUS.


title: New MM_M200


title: B-lineage ALL 28

description: cDNA microarray data

source_name: Case 40


title: B-lineage ALL 35

description: cDNA microarray data

source_name: Case 50


title: Normal Bone Marrow 2

description: cDNA microarray data

source_name: Case 46


title: B-lineage ALL 29

description: cDNA microarray data

source_name: Case 41


title: rNew MM_M198

source_name: CD138 selected bone marrow plasma cells from newly diagnosed myeloma.


title: MGUS_M192

description: Gene expression data from MGUS.


title: New MM_M196


title: Normal Bone Marrow 3

description: cDNA microarray data

source_name: Case 47


title: Normal Bone Marrow 1

description: cDNA microarray data

source_name: Case 45


title: New MM_M163


title: B-lineage ALL 25

description: cDNA microarray data

source_name: Case 37

source_name: Stratagene Universal Human Reference RNA


title: B-lineage ALL 27

description: cDNA microarray data

source_name: Case 39


title: Smoldering MM_M154


title: B-lineage ALL 26

description: cDNA microarray data

source_name: Case 38


title: B-lineage ALL 30

description: cDNA microarray data

source_name: Case 42


title: B-lineage ALL 33

description: cDNA microarray data

source_name: Case 48


title: Relapsed MM_M203

source_name: CD138 selected bone marrow plasma cells from relapsed myeloma.


title: New MM_M157


title: AML 9

description: cDNA microarray data

source_name: Case 35


title: B-lineage ALL 34

description: cDNA microarray data

source_name: Case 49


title: New MM_M167


title: New MM_M146


title: B-lineage ALL 24

description: cDNA microarray data

source_name: Case 36


title: New MM_M135


title: Smoldering MM_M162


title: AML 8

description: cDNA microarray data

source_name: Case 34


title: Smoldering MM_M145

source_name: CD138 selected bone marrow plasma cells from smoldering myeloma.


title: B-lineage ALL 32

description: cDNA microarray data

source_name: Case 44


title: Relapsed MM_M131


title: Relapsed MM_M123


title: MGUS_M132

description: Gene expression data from MGUS.

source_name: CD138 selected bone marrow plasma cells from MGUS.


title: Relapsed MM_M128


title: Relapsed MM_M122


title: B-lineage ALL 19

description: cDNA microarray data

source_name: Case 25


title: T-cell ALL 3

description: cDNA microarray data

source_name: Case 33


title: AML 5

description: cDNA microarray data

source_name: Case 29


title: New MM_M134

source_name: CD138 selected bone marrow plasma cells from newly diagnosed myeloma.


title: B-lineage ALL 23

description: cDNA microarray data

source_name: Case 31

source_name: Stratagene Universal Human Reference RNA


title: B-lineage ALL 22

description: cDNA microarray data

source_name: Case 28


title: AML 7

description: cDNA microarray data

source_name: Case 32

tag: CBP/MORF


title: AML 4

description: cDNA microarray data

source_name: Case 23


title: AML 6

description: cDNA microarray data

source_name: Case 30


title: B-lineage ALL 17

description: cDNA microarray data

source_name: Case 22


title: New MM_M142


title: Relapsed MM_M113

source_name: CD138 selected bone marrow plasma cells from relapsed myeloma.


title: B-lineage ALL 20

description: cDNA microarray data

source_name: Case 26


title: B-lineage ALL 18

description: cDNA microarray data

source_name: Case 24


title: Smoldering MM_M103

source_name: CD138 selected bone marrow plasma cells from smoldering myeloma.


title: B-lineage ALL 21

description: cDNA microarray data

source_name: Case 27


title: Relapsed MM_M105


title: Smoldering MM_M097


title: Relapsed MM_M082


title: Relapsed MM_M064


title: Smoldering MM_M111


title: B-lineage ALL 13

description: cDNA microarray data

source_name: Case 17


title: New MM_M061


title: B-lineage ALL 16

description: cDNA microarray data

source_name: Case 21


title: New MM_M073


title: T-cell ALL 2

description: cDNA microarray data

source_name: Case 19


title: New MM_M058


title: Relapsed MM_M051


title: B-lineage ALL 8

description: cDNA microarray data

source_name: Case 11


title: New MM_M059

source_name: CD138 selected bone marrow plasma cells from newly diagnosed myeloma.


title: B-lineage ALL 9

description: cDNA microarray data

source_name: Case 13


title: B-lineage ALL 14

description: cDNA microarray data

source_name: Case 18

source_name: Stratagene Universal Human Reference RNA


title: AML 3

description: cDNA microarray data

source_name: Case 12


title: New MM_M037


title: Relapsed MM_M029


title: B-lineage ALL 7

description: cDNA microarray data

source_name: Case 10


title: B-lineage ALL 11

description: cDNA microarray data

source_name: Case 15


title: B-lineage ALL 10

description: cDNA microarray data

source_name: Case 14


title: B-lineage ALL 12

description: cDNA microarray data

source_name: Case 16


title: New MM_M025


title: Smoldering MM_M087


title: Smoldering MM_M047


title: New MM_M032


title: New MM_M024


title: B-lineage ALL 5

description: cDNA microarray data

source_name: Case 8


title: T-cell ALL 1

description: cDNA microarray data

source_name: Case 5


title: B-lineage ALL 3

description: cDNA microarray data

source_name: Case 6


title: Relapsed MM_M003

source_name: CD138 selected bone marrow plasma cells from relapsed myeloma.


title: B-lineage ALL 6

description: cDNA microarray data

source_name: Case 9


title: B-lineage ALL 4

description: cDNA microarray data

source_name: Case 7


title: MGUS_M004

description: Gene expression data from MGUS.

source_name: CD138 selected bone marrow plasma cells from MGUS.


title: B-lineage ALL 15

description: cDNA microarray data

source_name: Case 20


title: B-lineage ALL 2

description: cDNA microarray data

source_name: Case 3