title: colorectal normal mucosa, sample 4

description: colorectal normal mucosa biopsy

value: syntethic miRNA pool of 954 miRNA sequences from human, mouse, rat, and virus

source_name: colorectal normal mucosa biopsy sample 4


title: SW480

status: Public on Aug 30 2013

type: genomic

city: BALTIMORE

first: hari

last: easwaran

state: MD

address: 1650 Orleans Street, CRB1, Room 530

department: Oncology

country: USA

institute: Johns Hopkins University

hyb_protocol: Bisulfite-converted genomic DNA was analyzed using Illumina’s Infinium Human Methylation27 Beadchip Kit (WG-311-1202). Beadchip contains 27,578 CpG loci covering more than 14,000 human RefSeq genes at single-nucleotide resolution. Chip process and data analysis were performed by using reagents provided in the kit and following manufacturer’s manual. Briefly, 4 ml of bisulfite-converted genomic DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer for 20-24 hours at 37oC. Samples were fragmented using a kit-provided reagents and buffer at 37oC for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95oC for 20 minutes. 12 ml of each sample was loaded onto a 12-sample chip and the chips were assembled into hybridization chamber as instructed in the manual. After incubation at 48oC for 16-20 hours, chips were washed with wash buffers provided in the kit and assembled and placed into a fluid flow-through station for primer-extension reaction and staining with reagents and buffers provided in the kit.

scan_protocol: Polymer-coated chips were image- processed in Illumina’s iScan scanner.  Data were extracted and analyzed using BeadStudio v3.0 software.

data_processing: Data were extracted and analyzed using BeadStudio v3.0 software.  The methylation status of each CpG site is presented as b (beta) value based on following definition and calculation:  b value = (signal intensity of methylation-detection probe)/(signal intensity of methylation- detection probe + signal intensity of non-methylation-detection probe + 100).

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: SW480 cell line

label_protocol: Primer extension

growth_protocol: Cells were grown on serum supplemented medium (SW480 and HCT116 grown on MCCoy's 5a and RKO was frown on MEM). Cells were grown to 70% confluency, harvested and DNA was extracted.

extract_protocol: DNA was extracted usign Phenol-Chloroform extraction method. Genomic DNA quality was assessed by low agarose gel (0.5%) electrophoresis under low power voltage. Only samples with good genomic DNA integrity were used in chip assay. Bisulfite conversion of genomic DNA was done with EZ DNA methylation Kit (Zymo Research, D5002) by following manufacturer’s protocol with modifications for Illumina Infinium Methylation Assay. Briefly, one microgram of genomic DNA was first mixed with 5 ml of M-Dilution Buffer and incubate at 37oC for 15 minutes and then mixed with 100 ml of CT Conversion Reagent prepared as instructed in the protocol. Mixtures were incubated in a thermocycler for 16 cycles at 95oC for 30 seconds and 50oC for 60 minutes. Bisulfite-converted DNA samples were loaded onto 96-column plates provided in the kit for desulphonation and purification as instructed in the protocol. Concentration of eluted DNA was measured using Nanodrop-1000. Bisulfite-converted samples were used for chip analysis without any delay.

tag: cell type

value: Colon cancer

tag: cell line


title: Patient 4,21st post-op day sample

type: RNA

city: Helsinki

first: Kristo

middle: Juhana

last: Nuutila

address: Haartmaninkatu 8, Biomedicum 1

department: Institute of Biomedicine

country: Finland

institute: University of Helsinki

hyb_protocol: According to Illumina Hybridization, Wash and Stain Kit

scan_protocol: Illumina Bead scan

data_processing: Data analysis was performed with GeneSpring GX software, version 11.0.1 (Agilent Technologies), normalized to the median, filtered by expression, and presented as gene expression-

label: Biotin

molecule: total RNA

source_name: Biopsy from donor site wound

label_protocol: According to Illumina HT12 Expression Kit

growth_protocol: No treatment, clinical patient samples from normal wound healing process.

extract_protocol: The skin samples were homogenized using the Precellys 24 tissue homogenizer with a Cryolys temperature controller unit (Bertin Technologies SA, Montigny-le-Bretonneux, France).Total RNA was extracted from the homogenized tissue samples with an RNeasy® mini kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: The skin biopsies were immediately immersed in RNAlater® (Qiagen) buffer, were incubated at +4°C for one day, and stored thereafter at -80°C until RNA isolation.

tag: sample type

value: Wound

tag: time

value: 21 days post-op


title: NAFLD liver biopsy tissue 15012

city: Durham

first: Cynthia

last: Moylan

state: NC

address: 595 LaSalle Street, GSRB1, DUMC 3256

department: Gastroenterology

institute: Duke University Medical Center

description: Gene expression data from mild NAFLD patient

hyb_protocol: Affymetrix GeneChip  hybridization Oven 645

scan_protocol: Affymetrix GeneChip Scanner 7G

data_processing: GC-RMA

label: biotin

source_name: NAFLD liver biopsy tissue

label_protocol: Ambion MessageAmp Premier as described by the manufacturer

extract_protocol: Qiagen Micro Kit according to manufacturer's instructions

tag: Stage

value: mild (fibrosis stage 0-1)

tag: tissue

value: liver


title: HCT116

source_name: HCT116 cell line


title: colorectal normal mucosa, sample 3

city: Brest

first: Laurent

last: Corcos

address: 22, Avenue Camille Desmoulins

department: Faculty of Medicine

country: France

institute: INSERM U1078-ECLA

description: colorectal normal mucosa biopsy

hyb_protocol: The fluorescently labeled samples were hybridized overnight to miRXplore TM Microarrays using the a-HybTM Hybridization Station (Miltenyi Biotec).

scan_protocol: Image capture and signal quantification of hybridized miRXplore (TM) microarrays were done with the Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA) and ImaGene software Version 9.0 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification of the scanned miRXplore TM microarrays was done using ImaGene software Version 9.0 (BioDiscovery, Los Angeles, CA, USA). Local background was subtracted from the signal to obtain the net signal intensity and the ratio of Cy5/Cy3. Subsequently, the mean of the ratios of 4 corresponding spots representing the same miRNA was computed. The mean ratios were normalised using the calibration oligos.

organism: synthetic construct

source_name: Universal Reference provided by Miltenyi Biotec GmbH

label_protocol: 1.5 - 2 µg of respective total RNA as well as 2 fmol of the Universal Reference were each mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer. The total RNA and Universal Reference mix was hybridized in a dual colour approach to microarrays.

extract_protocol: Total RNA was extracted with the AllPrep DNA/RNA Mini kit (Qiagen, Courtabœuf, France) from homogenized tissue samples (20 mg), according to the manufacturer’s instructions. RNA purity and integrity were determined by measuring the optical density ratio (A260/A280) and the RNA integrity number (RIN) using the RNA 6000 Nano LabChip (Agilent, Massy, France) and the 2100 Bioanalyzer (Agilent). Only RNA samples with a 28S/18S ratio > 1.0 and RIN ≥ 7.0 were used for microarray analyses.

source_name: colorectal normal mucosa biopsy sample 3

value: normal mucosa

tag: localisation

value: colon


title: Patient 3, intact skin sample

source_name: Biopsy from intact skin

value: Intact skin


title: Patient 4, intact skin sample


title: Patient 3,14th post-op day sample

value: 14 days post-op


title: Patient 4,14th post-op day sample


title: Patient 3,21st post-op day sample


title: Patient 2, intact skin sample


title: colorectal normal mucosa, sample 2

description: colorectal normal mucosa biopsy

source_name: colorectal normal mucosa biopsy sample 2

value: sigmoid colon


title: Patient 1,21st post-op day sample


title: Patient 2,21st post-op day sample


title: colorectal normal mucosa, sample 1

description: colorectal normal mucosa biopsy

source_name: colorectal normal mucosa biopsy sample 1

value: left colon


title: Patient 1,14th post-op day sample


title: Patient 1, intact skin sample


title: Patient 2,14th post-op day sample


title: genomic DNA from SCLC sample 36

status: Public on Aug 29 2013

city: Koto

first: YUICHI

last: SAITO

state: Tokyo

address: 3-8-31 Ariake

department: Pathology

country: Japan

institute: The Cancer Institute of Japanese Foundation Cancer Research

description: Normal Lung Tissue sample  Sample name: 36

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
GenomeStudio software v2010.3 with the Methylation module.  The signal_intensities matrix reporting unmethylated and methylated signal intensities is linked as a supplementary file on the Series record.
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted aaccording to standard protocaols and DNA purity and concentration determined by spechtrophotometry.

tag: disease state

value: Normal Lung Tissue sample

tag: tumor/control

value: Tumor

tag: cpg island methylator phenotype (cimp) subgroup

value: CIMP-high


title: genomic DNA from SCLC sample 40

description: Normal Lung Tissue sample  Sample name: 40


title: genomic DNA from SCLC sample 30

description: Normal Lung Tissue sample  Sample name: 30


title: genomic DNA from SCLC sample 31

description: Normal Lung Tissue sample  Sample name: 31


title: genomic DNA from SCLC sample 37

description: Normal Lung Tissue sample  Sample name: 37


title: genomic DNA from SCLC sample 38

description: Normal Lung Tissue sample  Sample name: 38


title: genomic DNA from SCLC sample 22

description: SCLC Tumor sample  Sample name: 22

value: SCLC Tumor sample


title: genomic DNA from SCLC sample 24

description: SCLC Tumor sample  Sample name: 24


title: genomic DNA from SCLC sample 20

description: SCLC Tumor sample  Sample name: 20


title: genomic DNA from SCLC sample 33

description: Normal Lung Tissue sample  Sample name: 33


title: genomic DNA from SCLC sample 27

description: SCLC Tumor sample  Sample name: 27


title: genomic DNA from SCLC sample 26

description: SCLC Tumor sample  Sample name: 26


title: genomic DNA from SCLC sample 25

description: SCLC Tumor sample  Sample name: 25


title: genomic DNA from SCLC sample 29

description: Normal Lung Tissue sample  Sample name: 29


title: genomic DNA from SCLC sample 39

description: Normal Lung Tissue sample  Sample name: 39


title: genomic DNA from SCLC sample 35

description: Normal Lung Tissue sample  Sample name: 35


title: genomic DNA from SCLC sample 34

description: Normal Lung Tissue sample  Sample name: 34


title: genomic DNA from SCLC sample 28

description: SCLC Tumor sample  Sample name: 28


title: genomic DNA from SCLC sample 41

description: Normal Lung Tissue sample  Sample name: 41


title: genomic DNA from SCLC sample 19

description: SCLC Tumor sample  Sample name: 19


title: genomic DNA from SCLC sample 21

description: SCLC Tumor sample  Sample name: 21


title: genomic DNA from SCLC sample 15

description: SCLC Tumor sample  Sample name: 15


title: genomic DNA from SCLC sample 32

description: Normal Lung Tissue sample  Sample name: 32


title: genomic DNA from SCLC sample 18

description: SCLC Tumor sample  Sample name: 18


title: genomic DNA from SCLC sample 23

description: SCLC Tumor sample  Sample name: 23


title: genomic DNA from SCLC sample 17

description: SCLC Tumor sample  Sample name: 17


title: genomic DNA from SCLC sample 16

description: SCLC Tumor sample  Sample name: 16


title: genomic DNA from SCLC sample 14

description: SCLC Tumor sample  Sample name: 14


title: genomic DNA from SCLC sample 13

description: SCLC Tumor sample  Sample name: 13


title: genomic DNA from SCLC sample 11

description: SCLC Tumor sample  Sample name: 11


title: genomic DNA from SCLC sample 9

description: SCLC Tumor sample  Sample name: 9


title: genomic DNA from SCLC sample 12

description: SCLC Tumor sample  Sample name: 12


title: genomic DNA from SCLC sample 6

description: SCLC Tumor sample  Sample name: 6


title: genomic DNA from SCLC sample 4

description: SCLC Tumor sample  Sample name: 4


title: genomic DNA from SCLC sample 10

description: SCLC Tumor sample  Sample name: 10


title: genomic DNA from SCLC sample 2

description: SCLC Tumor sample  Sample name: 2


title: genomic DNA from SCLC sample 7

description: SCLC Tumor sample  Sample name: 7


title: genomic DNA from SCLC sample 3

description: SCLC Tumor sample  Sample name: 3


title: genomic DNA from SCLC sample 5

description: SCLC Tumor sample  Sample name: 5


title: 4953087046_H: Control

city: Cincinnati

first: Scott

middle: M

last: Langevin

state: OH

address: 160 Panzeca Way, ML0056

department: Department of Environmental Health

institute: University of Cincinnati College of Medicine

data_processing: BeadStudio software v3.2

source_name: Control

extract_protocol: genomic DNA was extracted DNeasy blood and tissue kit according to standard instructions

value: Peripheral Blood Leukocytes

tag: diagnosis

value: Healthy


title: 4953087046_B: Bladder cancer case

source_name: Bladder cancer case

value: Bladder cancer


title: 4953087046_D: Control


title: 4953087046_J: Control


title: 4953087046_C: Bladder cancer case


title: 4953087043_G: Bladder cancer case


title: 4953087043_J: Bladder cancer case


title: 4953087046_A: Control


title: 4953087046_F: Bladder cancer case


title: 4953087043_D: Control


title: 4953087046_L: Bladder cancer case


title: 4953087043_F: Bladder cancer case


title: genomic DNA from SCLC sample 1

description: SCLC Tumor sample  Sample name: 1


title: genomic DNA from SCLC sample 8

description: SCLC Tumor sample  Sample name: 8


title: 4953087043_L: Control


title: 4953087043_E: Bladder cancer case


title: 4953087043_H: Control


title: 4953087046_G: Bladder cancer case


title: Expose Bacillus VOC-6h rep3

city: Daejeon

first: Choong-Min

last: Ryu

address: 125 Gwahak-ro Yuseong

country: South Korea

institute: KRIBB

description: replication 3 of 4

hyb_protocol: 7.5 µg of labeled sample RNA and 7.5 µg of labeled reference RNA were fragmented in total 250 µl mixture (50 µl of 10X blocking agent, 10 µl of 25X fragmentation buffer, H2O) at 60°C for 30 min, then put it on ice for 1 min. 250 µl of fragmentation mix and 250 µl of GE hybridization buffer HI-RPM were mixed and spinned for 1 min at RT at 13,000 rpm, and put on ice. 490 µl of the hybridization mix was applied to the slide in chamber, and put in a hybridization oven at 65°C for 17 hrs. After hybridization, the slide was washed sequentially in GE wash buffer 1 (twice) and 2.

scan_protocol: The arrays were scanned by Microarray Scanner (Agilent Technologies, Santa Clara, CA). Signal intensities and local backgrounds were determined by Feature Extraction software (Agilent Technologies).

data_processing: Cy3 and Cy5 intensities were normalized by scaling so that the 75th percentile in the Cy3 and Cy5 channels were equal.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: control 6h

label_protocol: 1.5 µg of total RNA were directly labeled with 1.5 µl of Kreatech  dye (Cy3 or Cy5) at 95°C for 5 min, then put it on ice. The solutions were purified by KREApure column.

extract_protocol: Total RNAs were extracted using RNeasy mini kit (Qiagen, #74104) following manufacture's instruction

tag: treatment

value: control

value: 6 h

tag: strain

source_name: expose Bacillus VOC 6h

value: Bacillus volatile organic compounds (VOCs)


title: 4953087046_I: Bladder cancer case


title: 4953087033_L: Control


title: 4953087043_B: Control


title: 4953087043_C: Bladder cancer case


title: 4953087033_I: Control


title: 4953087033_F: Control


title: 4953087033_K: Control


title: 4953087033_J: Control


title: 4953087033_D: Control


title: 4953087033_C: Control


title: 4953087024_K: Bladder cancer case


title: 4953087033_A: Control


title: 4953087024_H: Bladder cancer case


title: 4953087024_C: Bladder cancer case


title: 4953087024_F: Bladder cancer case


title: 4953087024_I: Control


title: 4953087024_D: Control


title: 4953087024_B: Bladder cancer case


title: 4953087024_J: Bladder cancer case


title: 4953087024_E: Control


title: 4953087024_A: Bladder cancer case


title: 4948000036_K: Bladder cancer case


title: 4948000036_L: Bladder cancer case


title: 4948000036_G: Control


title: 4948000036_H: Bladder cancer case


title: 4953087024_G: Control


title: 4948000036_F: Bladder cancer case


title: 4953087033_H: Control


title: 4948000036_J: Bladder cancer case


title: 4948000036_I: Control


title: 4948000036_A: Control


title: 4948000036_C: Bladder cancer case


title: 4948000035_L: Bladder cancer case


title: 4948000035_F: Control


title: 4948000036_D: Bladder cancer case


title: 4948000035_J: Bladder cancer case


title: 4948000036_B: Bladder cancer case


title: 4948000035_I: Bladder cancer case


title: 4948000035_C: Bladder cancer case


title: 4948000035_D: Bladder cancer case


title: 4948000035_G: Control


title: 4948000035_H: Bladder cancer case


title: 4948000012_J: Bladder cancer case


title: 4948000035_E: Bladder cancer case


title: 4948000012_F: Bladder cancer case


title: 4948000035_K: Bladder cancer case


title: 4948000012_B: Control


title: 4948000012_H: Bladder cancer case


title: 4948000012_C: Control


title: 4948000012_D: Control


title: 4948000012_A: Control


title: 4948000012_K: Bladder cancer case


title: 4948000012_L: Bladder cancer case


title: 4948000012_E: Bladder cancer case


title: 4948000010_K: Bladder cancer case


title: 4948000010_J: Control


title: 4948000010_I: Bladder cancer case


title: 4948000012_I: Control


title: 4948000010_B: Bladder cancer case


title: 4948000010_H: Bladder cancer case


title: 4948000010_A: Control


title: 4948000010_C: Control


title: 4868501165_J: Bladder cancer case


title: 4948000010_E: Bladder cancer case


title: 4948000010_F: Bladder cancer case


title: 4868501165_I: Control


title: 4948000010_L: Control


title: 4868501165_H: Control


title: 4948000010_G: Control


title: 4868501165_L: Control


title: 4868501165_G: Bladder cancer case


title: 4868501165_E: Control


title: 4868501165_B: Control


title: 4868501165_K: Control


title: 4868501165_C: Control


title: 4868501165_D: Bladder cancer case


title: 4868501146_I: Control


title: 4868501146_K: Control


title: 4868501146_J: Control


title: 4868501146_B: Control


title: 4776148054_L: Control


title: 4868501146_E: Bladder cancer case


title: 4776148054_F: Bladder cancer case


title: 4776148054_E: Control


title: 4776148054_I: Bladder cancer case


title: 4868501146_H: Bladder cancer case


title: 4776148054_A: Control


title: 4776148054_G: Bladder cancer case


title: 4868501146_A: Bladder cancer case


title: 4868501146_D: Bladder cancer case


title: 4868501165_A: Control


title: 4868501146_C: Bladder cancer case


title: 4776148054_J: Bladder cancer case


title: 4776148054_D: Bladder cancer case


title: 4776148051_L: Control


title: 4776148054_B: Bladder cancer case


title: 4776148051_K: Bladder cancer case


title: 4868501146_F: Bladder cancer case


title: 4776148054_H: Control


title: 4776148051_I: Control


title: 4776148051_J: Control


title: 4776148054_C: Control


title: 4776148051_G: Bladder cancer case


title: 4776148051_H: Bladder cancer case


title: 4776148050_K: Control


title: 4776148050_J: Control


title: 4776148051_B: Bladder cancer case


title: 4776148050_F: Bladder cancer case


title: 4776148051_D: Bladder cancer case


title: 4776148051_A: Control


title: 4776148050_I: Control


title: 4776148049_K: Bladder cancer case


title: 4776148050_H: Control


title: 4776148051_E: Control


title: 4776148050_L: Control


title: 4776148050_G: Bladder cancer case


title: 4776148051_C: Control


title: 4776148050_D: Bladder cancer case


title: 4776148050_A: Control


title: 4776148049_J: Control


title: 4776148050_E: Control


title: 4776148049_D: Bladder cancer case


title: 4776148049_F: Control


title: 4776148050_B: Bladder cancer case


title: 4776148049_C: Bladder cancer case


title: 4776148049_H: Control


title: 4776148049_G: Bladder cancer case


title: 4776148049_B: Control


title: 4776148049_E: Control


title: 4776148049_A: Bladder cancer case


title: 4776148047_F: Control


title: 4776148047_K: Control


title: 4776148047_A: Control


title: 4776148044_F: Control


title: 4776148043_L: Bladder cancer case


title: 4776148044_K: Control


title: 4776148047_G: Control


title: 4776148047_I: Bladder cancer case


title: 4776148047_H: Bladder cancer case


title: 4776148044_D: Control


title: 4776148047_C: Control


title: 4776148044_E: Bladder cancer case


title: 4776148043_K: Bladder cancer case


title: 4776148047_L: Bladder cancer case


title: 4776148047_E: Control


title: 4776148047_D: Control


title: 4776148044_I: Control


title: 4776148044_J: Control


title: 4776148047_B: Bladder cancer case


title: 4776148043_H: Control


title: 4776148044_C: Bladder cancer case


title: 4776148044_B: Control


title: 4776148043_I: Control


title: 4776148043_G: Control


title: 4776148043_F: Bladder cancer case


title: 4776148043_J: Control


title: 4776148043_C: Control


title: 4776148043_E: Control


title: 4776148043_B: Control


title: 4776148043_D: Control


title: 4776148036_J: Bladder cancer case


title: 4776148036_E: Control


title: 4776148035_K: Bladder cancer case


title: 4776148036_G: Bladder cancer case


title: 4776148035_E: Bladder cancer case


title: 4776148035_I: Bladder cancer case


title: 4776148036_L: Bladder cancer case


title: 4776148034_K: Bladder cancer case


title: 4776148036_A: Control


title: 4776148036_H: Control


title: 4776148035_L: Control


title: 4776148036_K: Bladder cancer case


title: 4776148035_H: Bladder cancer case


title: 4776148034_H: Bladder cancer case


title: 4776148034_L: Control


title: 4776148036_D: Bladder cancer case


title: 4776148036_I: Bladder cancer case


title: 4776148035_A: Control


title: 4776148034_I: Bladder cancer case


title: 4776148035_C: Control


title: 4776148036_F: Bladder cancer case


title: 4776148035_G: Bladder cancer case


title: 4776148034_G: Control


title: 4776148034_B: Control


title: 4776148034_A: Bladder cancer case


title: 4776148034_J: Bladder cancer case


title: 4776148036_B: Bladder cancer case


title: 4776148034_E: Bladder cancer case


title: 4776148033_L: Bladder cancer case


title: 4776148033_K: Bladder cancer case


title: 4776148033_I: Bladder cancer case


title: 4776148033_J: Bladder cancer case


title: 4776148033_G: Control


title: 4776148033_E: Bladder cancer case


title: 4776148035_J: Bladder cancer case


title: 4776148033_H: Control


title: 4776148033_F: Control


title: 4776148032_J: Bladder cancer case


title: 4776148032_I: Control


title: 4776148033_C: Bladder cancer case


title: 4776148031_G: Control


title: 4776148032_B: Bladder cancer case


title: 4776148031_A: Control


title: 4776148032_H: Bladder cancer case


title: 4776148031_C: Bladder cancer case


title: 4776148031_H: Control


title: 4776148032_K: Bladder cancer case


title: 4776148032_L: Bladder cancer case


title: 4776148031_F: Control


title: 4776148032_C: Control


title: 4776148032_E: Bladder cancer case


title: 4776148031_J: Bladder cancer case


title: 4776148031_L: Bladder cancer case


title: 4776148031_D: Bladder cancer case


title: 4776148031_E: Bladder cancer case


title: 4776148032_A: Control


title: 4776148033_B: Bladder cancer case


title: 4776148032_F: Bladder cancer case


title: 4776148030_I: Control


title: 4776148030_J: Bladder cancer case


title: 4776148030_E: Bladder cancer case


title: 4776148030_L: Bladder cancer case


title: 4776148030_H: Control


title: 4776148030_A: Control


title: 4776148030_C: Bladder cancer case


title: 4776148030_F: Bladder cancer case


title: 4776148030_B: Bladder cancer case


title: 4776148024_L: Bladder cancer case


title: 4776148024_I: Control


title: 4776148024_C: Bladder cancer case


title: 4776148021_K: Control


title: 4776148021_I: Bladder cancer case


title: 4776148024_F: Control


title: 4776148021_F: Bladder cancer case


title: 4776148024_G: Control


title: 4776148020_K: Bladder cancer case


title: 4776148024_D: Control


title: 4776148021_J: Bladder cancer case


title: 4776148024_B: Bladder cancer case


title: 4776148021_A: Bladder cancer case


title: 4776148020_L: Bladder cancer case


title: 4776148021_G: Bladder cancer case


title: 4776148021_B: Control


title: 4776148024_K: Bladder cancer case


title: 4776148021_E: Control


title: 4776148020_G: Control


title: 4776148020_F: Control


title: 4776148020_H: Bladder cancer case


title: 4776148024_E: Bladder cancer case


title: 4776148020_J: Bladder cancer case


title: 4776148020_E: Control


title: 4776148020_D: Bladder cancer case


title: 4776148020_A: Bladder cancer case


title: 4776148019_L: Control


title: 4776148020_B: Control


title: 4776148020_C: Bladder cancer case


title: 4776148019_H: Control


title: 4776148019_I: Bladder cancer case


title: 4776148019_A: Control


title: 4776148019_G: Bladder cancer case


title: 4776148019_F: Control


title: 4776148018_H: Control


title: 4776148019_C: Bladder cancer case


title: 4776148019_J: Bladder cancer case


title: 4776148018_K: Bladder cancer case


title: 4776148018_A: Control


title: 4776148018_D: Control


title: 4776148019_B: Bladder cancer case


title: 4776148018_L: Bladder cancer case


title: 4776148018_F: Bladder cancer case


title: 4776148019_K: Bladder cancer case


title: 4776148017_J: Bladder cancer case


title: 4776148017_L: Bladder cancer case


title: 4776148018_I: Bladder cancer case


title: 4776148018_G: Control


title: 4776148018_E: Bladder cancer case


title: 4776148017_K: Control


title: 4776148018_J: Control


title: 4776148018_C: Bladder cancer case


title: 4776148017_E: Bladder cancer case


title: 4776148017_I: Bladder cancer case


title: 4776148017_F: Control


title: 4776148017_H: Control


title: 4776148031_I: Bladder cancer case


title: 4776148017_D: Bladder cancer case


title: 4776148016_I: Control


title: 4776148017_C: Control


title: 4776148017_A: Bladder cancer case


title: 4776148016_J: Control


title: 4776148016_B: Bladder cancer case


title: 4776148016_L: Control


title: 4776148016_K: Bladder cancer case


title: 4776148016_F: Control


title: 4776148012_H: Bladder cancer case


title: 4776148012_J: Bladder cancer case


title: 4776148016_G: Control


title: 4776148016_D: Control


title: 4776148011_J: Bladder cancer case


title: 4776148012_K: Control


title: 4776148011_I: Bladder cancer case


title: 4776148012_E: Bladder cancer case


title: 4776148012_D: Control


title: 4776148016_C: Control


title: 4776148016_E: Control


title: 4776148012_C: Control


title: 4776148012_G: Bladder cancer case


title: 4776148012_L: Bladder cancer case


title: 4776148016_A: Bladder cancer case


title: 4776148012_A: Control


title: 4776148012_F: Bladder cancer case


title: 4776148012_B: Bladder cancer case


title: 4776148011_H: Bladder cancer case


title: 4776148011_G: Control


title: 4776148021_C: Bladder cancer case


title: 4776148011_F: Bladder cancer case


title: 4776148011_D: Bladder cancer case


title: 4776148011_A: Control


title: 4776148011_B: Control


title: 4776148009_H: Control


title: 4776148009_K: Bladder cancer case


title: 4776148011_E: Bladder cancer case


title: 4776148011_C: Bladder cancer case


title: 4776148009_J: Bladder cancer case


title: 4776148009_G: Control


title: 4776148009_B: Control


title: 4776148009_L: Bladder cancer case


title: 4763072066_B: Bladder cancer case


title: 4763072066_L: Control


title: 4763072066_C: Control


title: 4763072066_G: Control


title: 4763072066_K: Control


title: 4763072066_F: Control


title: 4763072066_D: Control


title: 4763072066_A: Bladder cancer case


title: 4763072066_J: Bladder cancer case


title: 4776148009_I: Control


title: 4776148009_F: Bladder cancer case


title: 4776148024_A: Bladder cancer case


title: 4763072066_I: Bladder cancer case


title: 4763072052_I: Control


title: 4776148009_E: Bladder cancer case


title: 4763072052_K: Bladder cancer case


title: 4763072052_E: Control


title: 4763072052_H: Bladder cancer case


title: 4763072052_D: Bladder cancer case


title: 4763072052_F: Control


title: 4763072052_C: Bladder cancer case


title: 4763072052_A: Control


title: 4763072052_L: Control


title: 4763072040_L: Control


title: 4763072040_G: Control


title: 4763072040_I: Control


title: 4763072040_E: Control


title: 4763072040_H: Bladder cancer case


title: 4763072040_C: Control


title: 4763072040_A: Control


title: 4763072027_I: Control


title: 4763072040_J: Bladder cancer case


title: 4763072040_B: Control


title: 4763072027_H: Control


title: 4763072027_K: Bladder cancer case


title: 4763072027_L: Bladder cancer case


title: 4763072052_G: Control


title: 4763072027_E: Bladder cancer case


title: 4763072027_G: Bladder cancer case


title: 4763072027_F: Bladder cancer case


title: 4763072027_C: Bladder cancer case


title: 4763072027_J: Control


title: 4763072027_A: Bladder cancer case


title: 4763072027_B: Control


title: 4763072025_H: Control


title: 4763072025_G: Bladder cancer case


title: 4763072025_B: Control


title: 4763072025_I: Bladder cancer case


title: 4763072025_A: Control


title: 4763072025_C: Control


title: 4763072022_J: Bladder cancer case


title: 4763072022_D: Control


title: 4763072022_L: Bladder cancer case


title: 4763072025_F: Control


title: 4763072025_J: Bladder cancer case


title: 4763072022_F: Bladder cancer case


title: 4763072021_L: Control


title: 4763072022_C: Control


title: 4763072022_B: Bladder cancer case


title: 4763072022_I: Bladder cancer case


title: 4763072021_I: Bladder cancer case


title: 4763072022_K: Bladder cancer case


title: 4763072025_D: Control


title: 4763072040_K: Control


title: 4763072022_E: Control


title: 4763072021_H: Control


title: 4763072021_D: Control


title: 4763072021_K: Control


title: 4763072021_F: Control


title: 4763072021_J: Control


title: 4763072022_H: Bladder cancer case


title: 4763072021_G: Bladder cancer case


title: 4763072011_H: Bladder cancer case


title: 4763072021_E: Control


title: 4763072011_I: Control


title: 4763072021_A: Control


title: 4763072011_E: Control


title: 4763072011_L: Bladder cancer case


title: 4763072011_F: Bladder cancer case


title: 4763072011_A: Bladder cancer case


title: 4763072021_B: Bladder cancer case


title: 4763072011_D: Control


title: 4763072011_C: Control


title: 4763072011_G: Control


title: 4763072011_B: Control


title: 4763072066_H: Control


title: WholeBlood_Sample988

city: Greifswald

first: Uwe

last: Völker

address: Friedrich-Ludwig-Jahn-Str. 15A

department: Interfakultäres Institut für Genetik und Funktionelle Genomforschung

country: Germany

hyb_protocol: Altogether 3000 ng of cRNA were hybridized to Illumina HumanHT-12 v3 Expression BeadChips, followed by washing steps, as described in the Illumina protocol (Performed at the Helmholtz Zentrum München).

scan_protocol: Scanning and image acquisition was carried out as described in the Illumina protocol (Performed at the Helmholtz Zentrum München).

data_processing: The data were quantile normalized and log2-transformed using the lumi 1.12.4 package from the Bioconductor open source software (http://www.bioconductor.org/)

source_name: RNA from whole blood under fasting conditions (>10h)

label_protocol: Altogether 500 ng of RNA were reverse transcribed into cDNA which served as the template in the subsequent in vitro transcription that produced biotin-UTP-labeled cRNA using the Illumina TotalPrep-96 RNA Amplification Kit (Ambion) as described in the Illumina protocol (Performed at the Helmholtz Zentrum München).

extract_protocol: Total RNA was prepared using a QIAcube device in combination with the Blood miRNA Kit (both from Qiagen, Hilden, Germany) according to manufacturer’s protocols from whole-blood samples collected in PAXgene tubes (BD).

tag: ethnicity

value: White Europeans from North-Eastern Germany

value: whole blood


title: WholeBlood_Sample989


title: WholeBlood_Sample987


title: WholeBlood_Sample985


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title: WholeBlood_Sample979


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title: WholeBlood_Sample976


title: WholeBlood_Sample990


title: WholeBlood_Sample981


title: WholeBlood_Sample980


title: WholeBlood_Sample982


title: WholeBlood_Sample991


title: WholeBlood_Sample984


title: WholeBlood_Sample965


title: WholeBlood_Sample966


title: WholeBlood_Sample974


title: WholeBlood_Sample971


title: WholeBlood_Sample972


title: WholeBlood_Sample961


title: WholeBlood_Sample967


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title: WholeBlood_Sample975


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title: WholeBlood_Sample968


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title: WholeBlood_Sample942


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title: WholeBlood_Sample918


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title: WholeBlood_Sample919


title: WholeBlood_Sample921


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title: WholeBlood_Sample923


title: WholeBlood_Sample912


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title: WholeBlood_Sample925


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title: WholeBlood_Sample906


title: WholeBlood_Sample908


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title: WholeBlood_Sample902


title: WholeBlood_Sample903


title: WholeBlood_Sample901


title: WholeBlood_Sample897


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title: WholeBlood_Sample909


title: WholeBlood_Sample910


title: WholeBlood_Sample892


title: WholeBlood_Sample905


title: WholeBlood_Sample895


title: WholeBlood_Sample904


title: WholeBlood_Sample889


title: WholeBlood_Sample893


title: WholeBlood_Sample898


title: WholeBlood_Sample900


title: WholeBlood_Sample894


title: WholeBlood_Sample891


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title: WholeBlood_Sample337


title: WholeBlood_Sample351


title: WholeBlood_Sample341


title: WholeBlood_Sample332


title: WholeBlood_Sample346


title: WholeBlood_Sample326


title: WholeBlood_Sample349


title: WholeBlood_Sample347


title: WholeBlood_Sample331


title: WholeBlood_Sample333


title: WholeBlood_Sample329


title: WholeBlood_Sample330


title: WholeBlood_Sample335


title: WholeBlood_Sample324


title: WholeBlood_Sample322


title: WholeBlood_Sample328


title: WholeBlood_Sample317


title: WholeBlood_Sample320


title: WholeBlood_Sample323


title: WholeBlood_Sample327


title: WholeBlood_Sample315


title: WholeBlood_Sample325


title: WholeBlood_Sample314


title: WholeBlood_Sample319


title: WholeBlood_Sample318


title: WholeBlood_Sample321


title: WholeBlood_Sample312


title: WholeBlood_Sample306


title: WholeBlood_Sample309


title: WholeBlood_Sample308


title: WholeBlood_Sample304


title: WholeBlood_Sample313


title: WholeBlood_Sample310


title: WholeBlood_Sample303


title: WholeBlood_Sample307


title: WholeBlood_Sample311


title: WholeBlood_Sample316


title: WholeBlood_Sample305


title: WholeBlood_Sample301


title: WholeBlood_Sample299


title: WholeBlood_Sample302


title: WholeBlood_Sample300


title: WholeBlood_Sample298


title: WholeBlood_Sample297


title: WholeBlood_Sample294


title: WholeBlood_Sample295


title: WholeBlood_Sample296


title: WholeBlood_Sample348


title: WholeBlood_Sample290


title: WholeBlood_Sample293


title: WholeBlood_Sample292


title: WholeBlood_Sample284


title: WholeBlood_Sample280


title: WholeBlood_Sample283


title: WholeBlood_Sample288


title: WholeBlood_Sample278


title: WholeBlood_Sample271


title: WholeBlood_Sample276


title: WholeBlood_Sample291


title: WholeBlood_Sample289


title: WholeBlood_Sample279


title: WholeBlood_Sample281


title: WholeBlood_Sample270


title: WholeBlood_Sample282


title: WholeBlood_Sample272


title: WholeBlood_Sample286


title: WholeBlood_Sample274


title: WholeBlood_Sample287


title: WholeBlood_Sample273


title: WholeBlood_Sample285


title: WholeBlood_Sample275


title: WholeBlood_Sample265


title: WholeBlood_Sample268


title: WholeBlood_Sample269


title: WholeBlood_Sample266


title: WholeBlood_Sample277


title: WholeBlood_Sample267


title: WholeBlood_Sample262


title: WholeBlood_Sample259


title: WholeBlood_Sample258


title: WholeBlood_Sample264


title: WholeBlood_Sample250


title: WholeBlood_Sample263


title: WholeBlood_Sample252


title: WholeBlood_Sample254


title: WholeBlood_Sample253


title: WholeBlood_Sample249


title: WholeBlood_Sample260


title: WholeBlood_Sample257


title: WholeBlood_Sample261


title: WholeBlood_Sample241


title: WholeBlood_Sample255


title: WholeBlood_Sample247


title: WholeBlood_Sample239


title: WholeBlood_Sample235


title: WholeBlood_Sample243


title: WholeBlood_Sample245


title: WholeBlood_Sample256


title: WholeBlood_Sample237


title: WholeBlood_Sample242


title: WholeBlood_Sample236


title: WholeBlood_Sample244


title: WholeBlood_Sample246


title: WholeBlood_Sample240


title: WholeBlood_Sample238


title: WholeBlood_Sample248


title: WholeBlood_Sample251


title: WholeBlood_Sample231


title: WholeBlood_Sample226


title: WholeBlood_Sample234


title: WholeBlood_Sample219


title: WholeBlood_Sample221


title: WholeBlood_Sample228


title: WholeBlood_Sample229


title: WholeBlood_Sample224


title: WholeBlood_Sample218


title: WholeBlood_Sample215


title: WholeBlood_Sample212


title: WholeBlood_Sample213


title: WholeBlood_Sample208


title: WholeBlood_Sample220


title: WholeBlood_Sample223


title: WholeBlood_Sample222


title: WholeBlood_Sample206


title: WholeBlood_Sample233


title: WholeBlood_Sample210


title: WholeBlood_Sample214


title: WholeBlood_Sample232


title: WholeBlood_Sample227


title: WholeBlood_Sample230


title: WholeBlood_Sample209


title: WholeBlood_Sample216


title: WholeBlood_Sample205


title: WholeBlood_Sample217


title: WholeBlood_Sample211


title: WholeBlood_Sample207


title: WholeBlood_Sample199


title: WholeBlood_Sample201


title: WholeBlood_Sample194


title: WholeBlood_Sample203


title: WholeBlood_Sample187


title: WholeBlood_Sample196


title: WholeBlood_Sample193


title: WholeBlood_Sample200


title: WholeBlood_Sample202


title: WholeBlood_Sample189


title: WholeBlood_Sample198


title: WholeBlood_Sample195


title: WholeBlood_Sample186


title: WholeBlood_Sample204


title: WholeBlood_Sample180


title: WholeBlood_Sample183


title: WholeBlood_Sample178


title: WholeBlood_Sample182


title: WholeBlood_Sample179


title: WholeBlood_Sample197


title: WholeBlood_Sample192


title: WholeBlood_Sample184


title: WholeBlood_Sample188


title: WholeBlood_Sample191


title: WholeBlood_Sample185


title: WholeBlood_Sample190


title: WholeBlood_Sample181


title: WholeBlood_Sample176


title: WholeBlood_Sample177


title: WholeBlood_Sample172


title: WholeBlood_Sample171


title: WholeBlood_Sample166


title: WholeBlood_Sample173


title: WholeBlood_Sample167


title: WholeBlood_Sample168


title: WholeBlood_Sample225


title: WholeBlood_Sample159


title: WholeBlood_Sample165


title: WholeBlood_Sample157


title: WholeBlood_Sample175


title: WholeBlood_Sample152


title: WholeBlood_Sample161


title: WholeBlood_Sample160


title: WholeBlood_Sample174


title: WholeBlood_Sample154


title: WholeBlood_Sample169


title: WholeBlood_Sample164


title: WholeBlood_Sample162


title: WholeBlood_Sample158


title: WholeBlood_Sample163


title: WholeBlood_Sample150


title: WholeBlood_Sample153


title: WholeBlood_Sample155


title: WholeBlood_Sample156


title: WholeBlood_Sample149


title: WholeBlood_Sample151


title: WholeBlood_Sample147


title: WholeBlood_Sample141


title: WholeBlood_Sample144


title: WholeBlood_Sample145


title: WholeBlood_Sample140


title: WholeBlood_Sample143


title: WholeBlood_Sample146


title: WholeBlood_Sample148


title: WholeBlood_Sample139


title: WholeBlood_Sample142


title: WholeBlood_Sample138


title: WholeBlood_Sample132


title: WholeBlood_Sample123


title: WholeBlood_Sample136


title: WholeBlood_Sample137


title: WholeBlood_Sample135


title: WholeBlood_Sample134


title: WholeBlood_Sample128


title: WholeBlood_Sample129


title: WholeBlood_Sample131


title: WholeBlood_Sample133


title: WholeBlood_Sample130


title: WholeBlood_Sample126


title: WholeBlood_Sample125


title: WholeBlood_Sample127


title: WholeBlood_Sample124


title: WholeBlood_Sample121


title: WholeBlood_Sample122


title: WholeBlood_Sample119


title: WholeBlood_Sample120


title: WholeBlood_Sample114


title: WholeBlood_Sample116


title: WholeBlood_Sample115


title: WholeBlood_Sample112


title: WholeBlood_Sample170


title: WholeBlood_Sample106


title: WholeBlood_Sample111


title: WholeBlood_Sample118


title: WholeBlood_Sample117


title: WholeBlood_Sample113


title: WholeBlood_Sample109


title: WholeBlood_Sample104


title: WholeBlood_Sample101


title: WholeBlood_Sample107


title: WholeBlood_Sample110


title: WholeBlood_Sample102


title: WholeBlood_Sample108


title: WholeBlood_Sample103


title: WholeBlood_Sample97


title: WholeBlood_Sample96


title: WholeBlood_Sample100


title: WholeBlood_Sample105


title: WholeBlood_Sample94


title: WholeBlood_Sample99


title: WholeBlood_Sample98


title: WholeBlood_Sample95


title: WholeBlood_Sample93


title: WholeBlood_Sample89


title: WholeBlood_Sample90


title: WholeBlood_Sample92


title: WholeBlood_Sample88


title: WholeBlood_Sample91


title: WholeBlood_Sample87


title: WholeBlood_Sample85


title: WholeBlood_Sample81


title: WholeBlood_Sample83


title: WholeBlood_Sample78


title: WholeBlood_Sample79


title: WholeBlood_Sample74


title: WholeBlood_Sample77


title: WholeBlood_Sample84


title: WholeBlood_Sample70


title: WholeBlood_Sample68


title: WholeBlood_Sample73


title: WholeBlood_Sample80


title: WholeBlood_Sample76


title: WholeBlood_Sample75


title: WholeBlood_Sample67


title: WholeBlood_Sample66


title: WholeBlood_Sample71


title: WholeBlood_Sample82


title: WholeBlood_Sample61


title: WholeBlood_Sample63


title: WholeBlood_Sample62


title: WholeBlood_Sample59


title: WholeBlood_Sample64


title: WholeBlood_Sample65


title: WholeBlood_Sample72


title: WholeBlood_Sample86


title: WholeBlood_Sample69


title: WholeBlood_Sample58


title: WholeBlood_Sample48


title: WholeBlood_Sample50


title: WholeBlood_Sample53


title: WholeBlood_Sample56


title: WholeBlood_Sample46


title: WholeBlood_Sample60


title: WholeBlood_Sample51


title: WholeBlood_Sample55


title: WholeBlood_Sample41


title: WholeBlood_Sample49


title: WholeBlood_Sample38


title: WholeBlood_Sample36


title: WholeBlood_Sample47


title: WholeBlood_Sample43


title: WholeBlood_Sample44


title: WholeBlood_Sample37


title: WholeBlood_Sample54


title: WholeBlood_Sample34


title: WholeBlood_Sample33


title: WholeBlood_Sample35


title: WholeBlood_Sample52


title: WholeBlood_Sample39


title: WholeBlood_Sample31


title: WholeBlood_Sample29


title: WholeBlood_Sample40


title: WholeBlood_Sample42


title: WholeBlood_Sample45


title: WholeBlood_Sample30


title: WholeBlood_Sample32


title: WholeBlood_Sample27


title: WholeBlood_Sample23


title: WholeBlood_Sample18


title: WholeBlood_Sample19


title: WholeBlood_Sample22


title: WholeBlood_Sample25


title: WholeBlood_Sample12


title: WholeBlood_Sample21


title: WholeBlood_Sample28


title: WholeBlood_Sample7


title: WholeBlood_Sample17


title: WholeBlood_Sample6


title: WholeBlood_Sample8


title: WholeBlood_Sample24


title: WholeBlood_Sample11


title: WholeBlood_Sample4


title: WholeBlood_Sample10


title: WholeBlood_Sample5


title: WholeBlood_Sample20


title: WholeBlood_Sample15


title: WholeBlood_Sample26


title: WholeBlood_Sample13


title: WholeBlood_Sample3


title: WholeBlood_Sample2


title: WholeBlood_Sample1


title: WholeBlood_Sample16


title: WholeBlood_Sample14


title: WholeBlood_Sample9


title: WholeBlood_Sample57


title: Wnt regulated gene expression in normal B cells (Normal3_treated2)

city: Boston

first: Lili

last: Wang

state: MA

address: 77 Ave Louis Pasteur

institute: Dana Farber Cancer Instutute

description: Wnt targets.

hyb_protocol: Samples were hybridized to a microarray chip overnight at 45 degree in a solution containg several biotinylated control oligonucleotides

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
All expression profiles were processed using RMA implemented by the PreprocessDataset module in GenePattern, and Affymetrix probes were collapsed to unique genes (Gene Symbol) by selecting the probe with the maximal average expression for each gene. Batch effects were removed using ComBat, implemented by the ComBat module in GenePattern.
Complete table of RMA signals shown below. RMA signals, collapsed  to unique genes, are linked as supplementary files on the Series record.

source_name: B cells

label_protocol: Samples were enzymatically fragmented and end-labled with a biotinylated nucleotide analog

extract_protocol: RNA were extracted using Trizol and further purified by RNeasy kit from Qiagen

treatment_protocol: For identification of Wnt targets, cells were treated with Wnt3a at 5ng/ml and 50ng/ml for 48 hours before harvest for RNA

value: peripheral lymphocytes

tag: cd status

value: CD19 positive


title: Wnt regulated gene expression in CLL-B cells (CLL3_untreated)

description: Wnt targets.

source_name: leukemia cells

value: CD19 CD5 positive


title: Wnt regulated gene expression in normal B cells (Normal3_treated1)

description: Wnt targets.


title: Wnt regulated gene expression in CLL-B cells (CLL1_treated1)

description: Wnt targets.


title: Wnt regulated gene expression in CLL-B cells (CLL2_treated1)

description: Wnt targets.


title: Wnt regulated gene expression in normal B cells (Normal2_untreated)

description: Wnt targets.


title: Wnt regulated gene expression in CLL-B cells (CLL2_treated2)

description: Wnt targets.


title: Wnt regulated gene expression in CLL-B cells (CLL2_untreated)

description: Wnt targets.


title: Wnt regulated gene expression in CLL-B cells (CLL1_treated2)

description: Wnt targets.


title: Wnt regulated gene expression in normal B cells (Normal1_treated2)

description: Wnt targets.


title: Wnt pathway gene expression in CLL-B cells (CLL176)

description: Wnt pathway genes.


title: Wnt regulated gene expression in CLL-B cells (CLL3_treated2)

description: Wnt targets.


title: Wnt regulated gene expression in normal B cells (Normal3_untreated)

description: Wnt targets.


title: Wnt pathway gene expression in CLL-B cells (CLL177)

description: Wnt pathway genes.


title: Wnt regulated gene expression in normal B cells (Normal1_treated1)

description: Wnt targets.


title: Wnt regulated gene expression in CLL-B cells (CLL1_untreated)

description: Wnt targets.


title: Wnt regulated gene expression in normal B cells (Normal2_treated2)

description: Wnt targets.


title: Wnt regulated gene expression in normal B cells (Normal2_treated1)

description: Wnt targets.


title: Wnt pathway gene expression in CLL-B cells (CLL178)

description: Wnt pathway genes.


title: Wnt regulated gene expression in CLL-B cells (CLL3_treated1)

description: Wnt targets.


title: Wnt pathway gene expression in CLL-B cells (CLL173)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL179)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL172)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL170)

description: Wnt pathway genes.


title: Wnt regulated gene expression in normal B cells (Normal1_untreated)

description: Wnt targets.


title: Wnt pathway gene expression in CLL-B cells (CLL168)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL175)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL171)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL174)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL167)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL169)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL162)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL165)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL150)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL161)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL163)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL166)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL160)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL151)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL144)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL159)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL157)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL147)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL153)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL155)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL154)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL140)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL158)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL141)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL156)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL138)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL146)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL145)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL164)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL152)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL149)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL143)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL148)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL137)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL142)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL139)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL133)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL135)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL128)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL131)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL136)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL130)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL129)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL126)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL132)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL127)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL134)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL122)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL113)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL118)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL116)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL120)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL111)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL123)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL112)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL109)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL121)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL117)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL110)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL124)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL115)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL119)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL108)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL125)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL114)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL107)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL104)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL105)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL99)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL102)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL106)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL100)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL96)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL103)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL101)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL98)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL97)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL93)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL87)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL94)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL95)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL86)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL90)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL81)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL88)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL89)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL84)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL92)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL91)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL80)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL79)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL83)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL76)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL75)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL78)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL77)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL70)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL74)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL73)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL68)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL72)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL67)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL64)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL63)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL59)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL61)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL53)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL62)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL71)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL60)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL55)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL57)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL51)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL69)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL56)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL54)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL50)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL47)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL52)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL45)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL41)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL46)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL48)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL40)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL49)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL37)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL58)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL39)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL44)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL35)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL42)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL33)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL43)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL36)

description: Wnt pathway genes.


title: B6 mESCs treated with LIF

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

country: China

institute: Anhui University

description: replicate 1

hyb_protocol: Standard Illumina scanning protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalized.The cut-off: The detection pval of LIF or LIF/CHIR99021 <0.05.

organism: Mus musculus

source_name: Inner cell mass

label_protocol: Standard Illumina hybridization protocol

growth_protocol: B6 mESCs were cutlured in serum medium in thre presence of LIF/CHIR99021

extract_protocol: Standard illumina RNA extraction protocol

treatment_protocol: With or without  CHIR99021 for 12 h

tag: developmental stage

value: E3.5 embryo


title: B6 mESCs treated with LIF/CHIR99021

description: replicate 1


title: Wnt pathway gene expression in CLL-B cells (CLL38)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL32)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL82)

description: Wnt pathway genes.


title: LN_Clodronate_VSV0h_rep2

city: Milan

first: Elena

last: Tonti

address: Via Olgettina 58

country: Italy

institute: San Raffaele Scientific Institute

description: Gene expression data from lymph node pre-treated with Clodronate

hyb_protocol: Standard Affymetrix protocols for mouse HT arrays

data_processing: cel files were RMA normalized using R

source_name: Clodronate-treated whole popliteal lymph node before infection with VSV_rep2

extract_protocol: Whole lymph nodes were lysed in 600 μL of QIAzol (Qiagen) reagent using the TissueLyser II. Total RNA was extracted following the miRNeasy kit’s procedure (Qiagen)

treatment_protocol: C57Bl/6 mice received intrafoodpad injections of Clodronate (CLD, 2mg) or vehicle control (PBS) 3 and 1 day prior infection with 104 pfu of VSV serotype Indiana in the same footpad. The popliteal lymph nodes were harvested immediately before or 8 hours after the infection.

value: popliteal lymph node

tag: infection

value: Clodronate


title: Wnt pathway gene expression in CLL-B cells (CLL30)

description: Wnt pathway genes.

tag: cell type


title: LN_PBS_VSV8h_rep1

description: Gene expression data from lymph node pre-treated with PBS and infected with VSV 8h before

scan_protocol: Standard Affymetrix protocols for mouse HT arrays

source_name: PBS-treated whole popliteal lymph node 8 hours after infection with VSV_rep1

value: VSV

value: PBS


title: Wnt pathway gene expression in CLL-B cells (CLL29)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL28)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL31)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL27)

description: Wnt pathway genes.


title: LN_Clodronate_VSV8h_rep2

description: Gene expression data from lymph node pre-treated with Clodronate and infected with VSV 8 hours before

source_name: Clodronate-treated whole popliteal lymph node 8 hours after infection with VSV_rep2

label_protocol: Standard Affymetrix protocols for mouse HT arrays


title: Wnt pathway gene expression in CLL-B cells (CLL26)

description: Wnt pathway genes.


title: LN_Clodronate_VSV0h_rep1

source_name: Clodronate-treated whole popliteal lymph node before infection with VSV_rep1


title: LN_PBS_VSV8h_rep2

source_name: PBS-treated whole popliteal lymph node 8 hours after infection with VSV_rep2


title: Wnt pathway gene expression in CLL-B cells (CLL23)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL25)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL85)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL19)

description: Wnt pathway genes.


title: WT(ψw=-2.0) 25d, biological rep1

city: Viçosa

first: Humberto

middle: Henrique

last: de Carvalho

state: Minas Gerais

address: PH Rolfs

department: Biologia Vegetal

country: Brazil

institute: Universidade Federal de Viçosa

description: soybean WT leaves 25 days under dehydration

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChips Soybean Genome Array Affymetrix®. GeneChips were washed and stained in the Affymetrix

scan_protocol: GeneChips were scanned using 450 GCOS/Microarray Suite (GeneChip® Operating Software)

data_processing: The CEL files were analyzed using the R/Bioconductor and Normalization was performed using the Robust Multiarray Analysis, To identify differentially expressed genes, we used R/MAANOVA. The estimated p-values were corrected by FDR (false discover rate), and the resulting respective gene were considered differentially expressed if they yielded a corrected p-value > 0.05 and a fold-change > 1.5.

organism: Glycine max

source_name: soybean WT leaves ψw=-2.0 of dehydration

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: Soybean seeds untransformed (WT) (Glycine max cv. Conquista) and transgenic SoyBiPD were germinated and grown in a substrate normally until the third trifoliate leaf was fully expanded. Water was added until the maximum capacity of the soil after excess water to be drained by gravity, each pot was weighed and recorded. They were blocked with the following treatments: 35S :: BiP-4 irrigated, 35S :: BiP-4 under dehydration, WT and WT under irrigated under dehydration.

extract_protocol: Total RNA was extracted from leaves using TRIzol (Life Technologies Inc.) and treated with DNA'se free RNA'se (Life Technologies Inc). And mRNA was purified using the kit FastTrack ® 2.0 mRNA isolation (Life Technologies Inc.) performed according to the manufacturer's instructions.

treatment_protocol: Plants subjected to drought were added 40% of the volume of water lost each day. The water potential (ψ) was measured at predawn with Scholander chamber over the days until obtaining values near -1.0, 1.5 and 2.0 MPa. The leaves were collected immediately after the measurement of water potential, frozen in liquid nitrogen and stored at -80 ° C.

value: leaves

tag: genotype/variation

value: WT


title: LN_PBS_VSV0h_rep2

description: Gene expression data from lymph node pre-treated with PBS

source_name: PBS-treated whole popliteal lymph node before infection with VSV_rep2


title: LN_Clodronate_VSV8h_rep1

source_name: Clodronate-treated whole popliteal lymph node 8 hours after infection with VSV_rep1


title: LN_PBS_VSV0h_rep1

source_name: PBS-treated whole popliteal lymph node before infection with VSV_rep1


title: Wnt pathway gene expression in CLL-B cells (CLL22)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL24)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL21)

description: Wnt pathway genes.


title: 35S::BiP-4 (ψw=-1.6) 25d, biological rep2

description: soybean transgenic leaves 25 days under dehydration

source_name: soybean transgenic leaves  ψw=-1.6 of dehydration


title: Wnt pathway gene expression in CLL-B cells (CLL20)

description: Wnt pathway genes.


title: WT(ψw=-2.0) 25d, biological rep2


title: 35S::BiP-4 (ψw=-1.6) 25d, biological rep1


title: Wnt pathway gene expression in CLL-B cells (CLL66)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL17)

description: Wnt pathway genes.


title: WT(ψw=-1.0) 19d, biological rep2

description: soybean WT leaves 19 days under dehydration

source_name: soybean WT leaves ψw=-1.0 of dehydration


title: WT(ψw=-1.7) 23d, biological rep1

description: soybean WT leaves 23 days under dehydration

source_name: soybean WT leaves ψw=-1.7 of dehydration


title: WT(ψw=-1.7) 23d, biological rep2


title: Wnt pathway gene expression in CLL-B cells (CLL16)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL18)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL65)

description: Wnt pathway genes.


title: WT(ψw=-1.0) 19d, biological rep1


title: Wnt pathway gene expression in CLL-B cells (CLL15)

description: Wnt pathway genes.


title: 35S::BiP-4 (ψw=-1.0) 21d, biological rep1

description: soybean transgenic leaves 21 days under dehydration

source_name: soybean transgenic leaves ψw=-1.0 of dehydration


title: WT irrigated, biological rep2

description: Irrigated WT leaves

source_name: soybean WT leaves under normal irrigation


title: 35S::BiP-4 (ψw=-1.0) 21d, biological rep2


title: Wnt pathway gene expression in CLL-B cells (CLL12)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL9)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL13)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL11)

description: Wnt pathway genes.


title: 35S::BiP-4 irrigated, biological rep1

description: Irrigated transgenic leaves

source_name: soybean transgenic leaves under normal irrigation


title: Wnt pathway gene expression in CLL-B cells (CLL10)

description: Wnt pathway genes.

source_name: leukemia cells


title: Wnt pathway gene expression in CLL-B cells (CLL8)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL6)

description: Wnt pathway genes.


title: WT irrigated, biological rep1

description: Irrigated WT leaves


title: Wnt pathway gene expression in CLL-B cells (CLL7)

description: Wnt pathway genes.


title: 35S::BiP-4 irrigated, biological rep2

description: Irrigated transgenic leaves


title: Wnt pathway gene expression in CLL-B cells (CLL5)

description: Wnt pathway genes.


title: Striatum Day 60 Male 5

city: Los Angeles

first: Tuck

middle: Cheong

last: Ngun

state: CA

address: 695 Charles E Young Dr S Gonda 5524

department: Human Genetics

institute: UCLA

description: Biological Replicate 3

hyb_protocol: Standard Illumina hybridization protocol

data_processing: Microarray data were processed using the statistical software program R (http://www.r-project.org/) and Bioconductor packages. The raw intensity data were first log2 transformed and then the outlier samples were detected based on the average inter-sample correlations. Three samples with average inter-sample correlations larger than two standard deviations (SDs) from the mean across all samples were removed from follow-up analysis. Then the samples were normalized by quantile normalization. Probes were considered robustly expressed if the detection p value was <0.05 in at least 20 samples (the total number of samples for every genetic/treatment group) in the data set. 57 samples with 13776 probes were retained for differential expression analysis.

source_name: Striatum Day 60 Male 5

label_protocol: Biotinylated cRNA were prepared by the UCLA Neuroscience Genomics Core.

extract_protocol: Total RNA was isolated from the BNST/POA using Qiagen AllPrep DNA/RNA Mini Kit (catalog no. 80204).

tag: age

value: 60 days

value: Striatum


title: Wnt pathway gene expression in CLL-B cells (CLL34)

description: Wnt pathway genes.


title: Striatum Day 60 Male 4

description: Biological Replicate 2

source_name: Striatum Day 60 Male 4


title: Striatum Day 60 Male 6

description: Biological Replicate 4

source_name: Striatum Day 60 Male 6


title: Striatum Day 60 Female+T 3

description: Biological Replicate 1

source_name: Striatum Day 60 Female+T 3


title: Wnt pathway gene expression in CLL-B cells (CLL4)

description: Wnt pathway genes.


title: Striatum Day 60 Female 5

description: Biological Replicate 5

source_name: Striatum Day 60 Female 5


title: Striatum Day 60 Female+T 4

description: Biological Replicate 2

source_name: Striatum Day 60 Female+T 4


title: Striatum Day 60 Female+T 6

description: Biological Replicate 4

source_name: Striatum Day 60 Female+T 6


title: Striatum Day 60 Male 3

description: Biological Replicate 1

source_name: Striatum Day 60 Male 3


title: Wnt pathway gene expression in CLL-B cells (CLL2)

description: Wnt pathway genes.


title: Wnt pathway gene expression in normal B cells (Normal24)

description: Wnt pathway genes.

source_name: B cells


title: Striatum Day 60 Female+T 5

description: Biological Replicate 3

source_name: Striatum Day 60 Female+T 5


title: Wnt pathway gene expression in CLL-B cells (CLL3)

description: Wnt pathway genes.


title: normal mammary tissue, replicate 3

city: Chiba

first: Tatsuhiko

last: Imaoka

address: 4-9-1 Anagawa, Inage-ku

department: National Institute of Radiological Sciences

institute: National Institutes for Quantum and Radiological Science and Technology

description: Gene expression data from normal mammary tissue of rat

hyb_protocol: Labeled cRNA was placed in a hybridization mixture containing control biotinylated probes according to manufacturer’s instructions. GeneChip arrays were hybridized with labeled cRNA for 16 h at 45°C with constant rotation (60 rpm).

scan_protocol: The arrays were washed and then stained with streptavidin-phycoerythrin conjugate (Molecular Probes, Tokyo, Japan) in a Fluidics Station 450 (Affymetrix) and subsequently scanned with the GeneChip Scanner 3000 (Affymetrix).

data_processing: The scanned images were processed using Affymetrix GeneChip Analysis Suite software. Each data set was scaled such that the average intensity of all probe sets was adjusted to 500. Data were exported to flat text files and used for statistical analysis.

organism: Rattus norvegicus

source_name: normal mammary tissue of rat

label_protocol: Total RNA (8 µg) was used for the first-strand cDNA synthesis with a T7-(dT)24 primer (Proligo, Kyoto, Japan) and SuperScript III reverse transcriptase (Invitrogen Co., Carlsbad, CA, USA). Double-stranded cDNA was then synthesized with E. coli RNase, E. coli DNA polymerase and E. coli DNA ligase (Toyobo, Tokyo, Japan). Biotin-labeled fragmented cRNA was subsequently prepared with a BioArray HighYield RNA Transcript Labeling kit (Enzo, Farmingdale, NY, USA). Labeling was confirmed by formalin-containing agarose gel electrophoresis.

growth_protocol: 5-week-old female Sprague-Dawley rats were purchased, housed in autoclaved cages and maintained in a room with a controlled temperature (23 ± 1degreeC) and humidity (50 ± 5%) under a regular 12-h light, 12-h dark cycle. They were fed a standard laboratory animal diet) and sterilized water ad libitum.

extract_protocol: total RNA was isolated by the acid guanidine phenol chloroform method (Isogen; Nippon Gene, Tokyo, Japan) and further purified with a silica-gel membrane (RNeasy Mini kit; Qiagen Inc., Valencia, CA, USA). The quality of all RNA samples was assessed by formalin-containing agarose gel electrophoresis.

treatment_protocol: At 7 weeks of age, the rats were either left untreated, given a single whole-body gamma-irradiation (0, 0.2, 0.5, 1 or 2 Gy) from a Cs-137 source. Three days after irradiation, MNU (20 or 40 mg/kg) was injected intraperitoneally or PhIP-HCl (40 mg/kg/day) was given by gavage for 5 consecutive days a week for 2 weeks with a 2-day interval. All rats were fed an AIN-76A diet containing 23.5% corn oil after 9 weeks of age.

value: normal

tag: etiology

tag: h-ras

tag: background strain

value: Sprague-Dawley rats


title: Wnt pathway gene expression in normal B cells (Normal23)

description: Wnt pathway genes.


title: Striatum Day 60 Female 4

description: Biological Replicate 4

source_name: Striatum Day 60 Female 4

tag: tissue


title: Striatum Day 60 Female 2

description: Biological Replicate 2

source_name: Striatum Day 60 Female 2


title: Wnt pathway gene expression in normal B cells (Normal21)

description: Wnt pathway genes.


title: Wnt pathway gene expression in CLL-B cells (CLL1)

description: Wnt pathway genes.


title: Wnt pathway gene expression in normal B cells (Normal20)

description: Wnt pathway genes.


title: Wnt pathway gene expression in normal B cells (Normal18)

description: Wnt pathway genes.


title: Striatum Day 60 Female 3

description: Biological Replicate 3

source_name: Striatum Day 60 Female 3


title: Striatum Day 60 Female 1

description: Biological Replicate 1

source_name: Striatum Day 60 Female 1


title: normal mammary tissue, replicate 2


title: Wnt pathway gene expression in normal B cells (Normal22)

description: Wnt pathway genes.


title: Wnt pathway gene expression in normal B cells (Normal19)

description: Wnt pathway genes.


title: normal mammary tissue, replicate 1


title: Striatum Day 4 Male 5

description: Biological Replicate 5

source_name: Striatum Day 4 Male 5

value: 4 days


title: cancer, gamma rays plus PhIP, H-ras nonmutated, replicate 3

description: Gene expression data from rat mammary cancer induced by combination of radiation and PhIP

value: cancer

value: radiation + PhIP

value: nonmutated


title: Striatum Day 4 Male 3

description: Biological Replicate 3

source_name: Striatum Day 4 Male 3


title: Wnt pathway gene expression in normal B cells (Normal15)

description: Wnt pathway genes.

value: peripheral lymphocytes

value: CD19 positive


title: Wnt pathway gene expression in normal B cells (Normal16)

description: Wnt pathway genes.


title: Striatum Day 4 Male 4

description: Biological Replicate 4

source_name: Striatum Day 4 Male 4


title: cancer, gamma rays plus MNU, H-ras nonmutated, replicate 4

description: Gene expression data from rat mammary cancer induced by combination of radiation and MNU

value: radiation + MNU


title: Wnt pathway gene expression in normal B cells (Normal17)

description: Wnt pathway genes.


title: Wnt pathway gene expression in normal B cells (Normal14)

description: Wnt pathway genes.


title: cancer, gamma rays plus PhIP, H-ras nonmutated, replicate 4

source_name: rat mammary cancer induced by combination of radiation and PhIP


title: cancer, gamma rays plus PhIP, H-ras nonmutated, replicate 2


title: Striatum Day 4 Male 2

description: Biological Replicate 2

source_name: Striatum Day 4 Male 2


title: Wnt pathway gene expression in normal B cells (Normal13)

description: Wnt pathway genes.


title: Striatum Day 4 Male 1

description: Biological Replicate 1

source_name: Striatum Day 4 Male 1


title: cancer, gamma rays plus MNU, H-ras nonmutated, replicate 3

source_name: rat mammary cancer induced by combination of radiation and MNU


title: cancer, gamma rays plus PhIP, H-ras nonmutated, replicate 1


title: Striatum Day 4 Female+T 5

description: Biological Replicate 5

source_name: Striatum Day 4 Female+T 5


title: cancer, gamma rays plus MNU, H-ras mutated, replicate 5

value: mutated


title: Striatum Day 4 Female+T 3

description: Biological Replicate 3

source_name: Striatum Day 4 Female+T 3


title: cancer, gamma rays plus MNU, H-ras nonmutated, replicate 2


title: Striatum Day 4 Female+T 2

description: Biological Replicate 2

source_name: Striatum Day 4 Female+T 2


title: Wnt pathway gene expression in normal B cells (Normal11)

description: Wnt pathway genes.

source_name: B cells


title: cancer, gamma rays plus MNU, H-ras mutated, replicate 4


title: Wnt pathway gene expression in normal B cells (Normal9)

description: Wnt pathway genes.


title: Wnt pathway gene expression in normal B cells (Normal12)

description: Wnt pathway genes.


title: cancer, gamma rays plus MNU, H-ras nonmutated, replicate 1


title: cancer, gamma rays plus MNU, H-ras mutated, replicate 3


title: cancer, gamma rays plus MNU, H-ras mutated, replicate 2


title: Striatum Day 4 Female+T 4

description: Biological Replicate 4

source_name: Striatum Day 4 Female+T 4


title: cancer, PhIP, replicate 4

description: Gene expression data from PhIP-induced rat mammary cancer

source_name: PhIP-induced rat mammary cancer

value: PhIP


title: Striatum Day 4 Female 4

description: Biological Replicate 4

source_name: Striatum Day 4 Female 4


title: Striatum Day 4 Female 5

description: Biological Replicate 5

source_name: Striatum Day 4 Female 5


title: Striatum Day 4 Female 2

description: Biological Replicate 2

source_name: Striatum Day 4 Female 2


title: Striatum Day 4 Female 3

description: Biological Replicate 3

source_name: Striatum Day 4 Female 3


title: Wnt pathway gene expression in normal B cells (Normal8)

description: Wnt pathway genes.