title: AML sample #8

first: Hans-Ulrich

last: Klein

institute: Columbia University Medical Center

description: AML samples investigated according to WHO 2008 classification

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

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

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

value: AML-NOS

value: AML-NOS plus AML-MLD-sole


title: myocyte_serum free media_adeno-bGal_sample1

status: Public on Jan 01 2011

type: RNA

city: cincinnati

first: izhak

last: kehat

state: OH

address: 3333 burnet ave

country: USA

institute: CCHMC

description: Gene expression data from cardiomyocytes in serum free media, infected with adeno-beta-galactosidase

hyb_protocol: Hybridization cocktail for a single probe array contained 2.5 ?g of fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 7% DMSO, and 1X Hybridization Buffer.  GeneChip Rat Gene 1.0 ST Array– Affymetrix was hybridized at 45?C for 18 hours in the GeneChip Hybridization Oven 640 (Affymetrix)

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

data_processing: The data were analyzed with GeneSpring version 7.3 using RMA normalization, then normalized to median of all samples.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Primary culture of neonatal rat ventricular cardiomyocytes, serum free media

label_protocol: The Affymetrix Whole Transcript Sense Target Labeling Assay (Affymetrix) is used to create biotin – labeled sense -strand cDNA targets for hybridization to the Gene 1.0 ST Arrays.

extract_protocol: RNA was extracted using RNeasy Fibrous Tissue kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Neonatal cardiomyocytes were isolated from 1-3 day old Sprague Dawley rat pups using the Neonatal Cardiomyocyte Isolation System (Worthington) according to the manufacturer’s instructions. Briefly, hearts were rinsed with ice cold HBSS, and trypsinised for 16 hrs at 4oC. Hearts were incubated with trypsin inhibitor at 37°C, and then incubated for 60 minutes with a collagenase solution at 37°C with gentle mixing. Cell pellet was triturated and resuspended in M199 media (invitrogen) containing 10% fetal calf serum.  Cells were then pre-plated for 1 hr to deplete culture of fibroblasts, and non adherent cells were plated on gelatin coated culture dishes. Following plating cells were washed twice with serum free culture media, infected with adenovirus encoding for beta galactosidase and grown for 48 hrs.

tag: tissue

value: Neonatal cardiomyocytes


title: Control-2

city: Minato-ku

first: Yukihiro

last: Kobayashi

state: Tokyo

department: Department of Marine Biosciences

country: Japan

institute: Tokyo University of Marine Science and Technology

description: gene expression data from liver of rat fed a high-fat diet without mulberry leaves

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using statistical language R and MAS 5.0 software in Affy package.

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

extract_protocol: RNAiso extraction (Takara Bio) of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Rats fed a high-fat diet were orally administrated dried mulberry leaf powder suspended in 0.5% carboxymethylcellulose at 0 or 500 mg/kg body weight/day. The administration was performed on a 6 weekly basis by gastric probe after fasting overnight. After 7 weeks, rats were anesthetized and killed by exsanguination. Parts of liver of each rat was taken and immediately immersed in RNAlater (Applied Biosystems).

tag: strain

value: Wistar/ST


title: cell25_not stim._90min_rep2

city: Munich

first: Wolfgang

last: Hammerschmidt

address: Marchioninistr. 25

department: Gene Vectors

country: Germany

institute: Helmholtz Zentrum München

description: This sample is of the lymphoblastoid cell line 2525. It is the second of three technical replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen as described in 'NimbleChip Arrays Uer's Guide: Gene Expression Analysis v2.0'. See www.nimblegen.com

scan_protocol: Scanning was performed by NimbleGen as described in 'NimbleChip Arrays Uer's Guide: Gene Expression Analysis v2.0'. See www.nimblegen.com

data_processing: The raw .call data was subjected to Multi-Lowess normalization.

organism: Homo sapiens

source_name: human lymphoblastoid cell line 2525 BCR not stimulated

label_protocol: Labeling was performed by NimbleGen as described in 'NimbleChip Arrays Uer's Guide: Gene Expression Analysis v2.0'. See www.nimblegen.com

growth_protocol: LCLs 2525 and 3696.10 were cultivated in RPMI-1640 media supplemented with 10% fetal bovine serum, penicillin (100U/ml), streptomycin (100μg/ml), sodium selenit (100nM), sodium pyruvate (1mM), bathocuproinedisulfonic acid (40nM) and 0.87‰ α-thioglycerol

extract_protocol: Total RNA was extracted, using the RNeasy mini Kit (Qiagen), followed by DNase digest for 90min at 37°C; mRNA was transcribed into cDNA by NimbleGen

treatment_protocol: Cells were seeded at 10^7 per 3ml and left untreated or stimulated for 90 min; BCR stimulation: 25ug/ml goat-anti-human IgG/M (dianova); LMP2A:mCD69 stimulation: 1ug/ml armenian hamster-anti-murineCD69 + 5ug/ml goat-anti-armenian hamster IgG (dianova)

tag: cell type

value: primary human b cells infected with EBV mutant 2525

tag: genotype/variation

value: wtLMP2A knockout


title: 900_24_CSA_3

city: Halle

first: Bayram

last: Edemir

address: Ernst-Grube-Str. 20

institute: University Hospital Halle (Saale)

hyb_protocol: Samples were hybridized with GeneChip Rat Gene 1.0 ST Arrays (Affymetrix) and scanned at the University Hospital Muenster IFG Microarray Core Facility.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G was used.

data_processing: Data were processed using XRAY software. Background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized and log transformed.

source_name: IMCD cultivated at 600 mosmol/kg challenged for 24h with 900 mosmol/kg CSA rep.9

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Rat primary cultured inner medullary collecting duct cells cultivated at different osmolalities

extract_protocol: Extraction of total RNA was performed using Qiagen RNeasy kit according to the manufacturer's instructions.

treatment_protocol: Treated with 5 µM Cyclosporin A for 24h as indicated.

value: Renal inner medulla

value: collecting duct cells

tag: culture condition

value: 600 mosmol/kg

tag: treatment group

value: challenged for 24h with 900 mosmol/kg + Cyclosporin A


title: 900_24_CSA_2

description: Rat primary cultured inner medullary collecting duct cells

source_name: IMCD cultivated at 600 mosmol/kg challenged for 24h with 900 mosmol/kg CSA rep.2


title: AML sample #7

city: New York

state: NY

department: Neurology

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

label: Biotin

source_name: mononuclear cells after Ficoll purification

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

treatment_protocol: Samples are from untreated AML patients.

tag: sample id

tag: analysis i

tag: analysis ii


title: cell25_stimulated_90min_rep1

description: This sample is of the lymphoblastoid cell line 2525. It is the first of three technical replicates used in this experiment, each from separate cultures.

source_name: human lymphoblastoid cell line 2525 BCR stimulated for 90 min


title: AML sample #5


title: AML sample #6

value: not included

value: AML-MRC


title: Control-4

source_name: liver of rat fed a high-fat diet without mulberry leaves


title: 900_24_CSA_1

source_name: IMCD cultivated at 600 mosmol/kg challenged for 24h with 900 mosmol/kg + CSA rep.1


title: cell25_stimulated_90min_rep2


title: patient 5 oral mucosal fibroblasts 6h post serum treatment

city: Cardiff

first: Philip

last: Stephens

state: South Glamorgan

address: Dental Drive, Heath Park

department: Dental School

country: United Kingdom

institute: Cardiff University

description: Gene expression data from human oral mucosal fibroblasts 6 hours following serum stimulation

hyb_protocol: 10 μg fragmented cRNA was then hybridised overnight to the human HG-U133A GeneChip

scan_protocol: GeneChips were scanned using the Agilent Gene Array Scanner controlled by Microarray Suite 5.0.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling (TGT 100) as normalization method.

source_name: oral mucosal fibroblast, patient 5, serum + 6h

label_protocol: 5 μg RNA was used to generate double-stranded cDNA by using a T7-linked oligo(dT) primer. Biotinylated cRNA was synthesised using the T7 RNA transcript labelling kit (Enzo Diagnostics, Farmingdale NY, USA)

growth_protocol: Primary cell cultures (derived from 6mm biopsies) of oral mucosal (normal, non-diseased buccal mucosa) fibroblasts and patient-matched skin fibroblasts were grown under standard mammalian tissue culture conditions (37 degrees celcius and 5% carbon dioxide) in fibroblast-serum containing medium (F-SCM) as previously described (Stephens P, Davies KJ, al-Khateeb, et al. , J Dent Res, 1996; 75: 1358-64).

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

treatment_protocol: Cells were seeded at a density of 1x104 cells/cm2 in 10cm diameter dishes, cultured in normal growth medium for 24 hours, then serum starved (0.1% FCS) for 48 hours prior to stimulation with 10% FCS. Samples were taken at 0h and 6h following serum stimulation of both oral mucosal and skin fibroblast cultures derived from each patient.

value: oral mucosal fibroblast

tag: post serum time point

value: 6 hours

tag: patient number


title: AML sample #1


title: 600_24_CSA_2

source_name: IMCD cultivated at 300 mosmol/kg challenged for 24h with 600 mosmol/kg CSA rep.2

value: 300 mosmol/kg

value: challenged for 24h with 600 mosmol/kg + Cyclosporin A


title: patient 6 oral mucosal fibroblasts 6h post serum treatment

source_name: oral mucosal fibroblast, patient 6, serum + 6h


title: patient 3 skin fibroblasts 6h post serum treatment

description: Gene expression data from human skin fibroblasts 6 hours following serum stimulation

source_name: skin fibroblast, patient 3, serum + 6h

value: skin fibroblast


title: cell10_not stim._90min_rep3

description: This sample is of the lymphoblastoid cell line 3696.10. It is the third of three technical replicates used in this experiment, each from separate cultures.

source_name: human lymphoblastoid cell line 3696.10 LMP2A:mCD69 not stimulated

value: primary human b cells infected with EBV mutant 3696

value: wtLMP2A knockout, LMP2A:mCD69 chimera introduced into BALF1 locus of EBV


title: pateint 4 oral mucosal fibroblasts 6h post serum treatment

source_name: oral mucosal fibroblast, patient 4, serum + 6h


title: AML sample #4

value: AML-MLD-sole

value: AML-NOS plus AML-MLD-sole


title: patient 6 skin fibroblasts 6h post serum treatment

source_name: skin fibroblast, patient 6, serum + 6h


title: 600_24_CSA_1

source_name: IMCD cultivated at 300 mosmol/kg challenged for 24h with 600 mosmol/kg + CSA rep.1


title: CB3 SDF, BIOLOGICAL REPLICATE 3

city: Hong Kong

first: Kathy

middle: YY

last: Chan

address: Rm84041, 6/F, Clinical Science Building, Prince of Wales Hospital, Shatin, N.T.

department: Paediatrics

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Gene expression data from cord blood CD34+ cells after SDF-1 stimulation.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C onAffymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (EukGE-Ws2v4).

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

data_processing:
GeneSpring data process settings: Threshold: 1
Logbase: 2
Technology: Affymetrix.GeneChip.HG-U133_Plus_2
Normalization: Median of all samples
Baseline Transformation: Median of all samples
FlagSettings:
Feature is not Uniform:A
Feature is a population outlier:A
Feature is Saturated:A
Feature is not positive and significant:A
Feature is not above background:A

label: BIOTIN

source_name: CORD BLOOD CD34+ CELLS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Two-Cycle cDNA Synthesis Kit and IVT labeling kit).

extract_protocol: RNA was prepared using the Trizol Reagent (Invitrogen, Carlsbad, CA) and Rneasy micro kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. The RNA quality and integrity were analyzed with Nanodrop ND 1000 spectrophotometer (Rockland, DE) and Bioanalyzer (Agilent, Cheshire, UK).

treatment_protocol: SDF-1 treatment for 4 hours at 100 ng/ mL.

value: CORD BLOOD CELLS

tag: agent


title: CB4 SDF, BIOLOGICAL REPLICATE 4


title: AML sample #2


title: AML sample #3

value: AML-NOS


title: 900_24_2

source_name: IMCD cultivated at 600 mosmol/kg challenged for 24h with 900 mosmol/kg rep.2

value: Renal inner medulla

value: challenged for 24h with 900 mosmol/kg


title: 900_24_1

source_name: IMCD cultivated at 600 mosmol/kg challenged for 24h with 900 mosmol/kg rep.1

value: collecting duct cells

value: 600 mosmol/kg


title: 600_24_CSA_3

source_name: IMCD cultivated at 300 mosmol/kg challenged for 24h with 600 mosmol/kg CSA rep.3


title: cell10_not stim._90min_rep1

description: This sample is of the lymphoblastoid cell line 3696.10. It is the first of three technical replicates used in this experiment, each from separate cultures.


title: pateint 3 oral mucosal fibroblasts 6h post serum treatment

source_name: oral mucosal fibroblast, patient 3, serum + 6h


title: 600_24_3

source_name: IMCD cultivated at 300 mosmol/kg challenged for 24h with 600 mosmol/kg rep.3

value: challenged for 24h with 600 mosmol/kg


title: cell10_not stim._90min_rep2

description: This sample is of the lymphoblastoid cell line 3696.10. It is the second of three technical replicates used in this experiment, each from separate cultures.


title: cell25_not stim._90min_rep1

source_name: human lymphoblastoid cell line 2525 BCR not stimulated

value: primary human b cells infected with EBV mutant 2525

value: wtLMP2A knockout


title: cell10_stimulated_90min_rep3

source_name: human lymphoblastoid cell line 3696.10 LMP2A:mCD69 stimulated for 90 min


title: patient 4 skin fibroblasts 6h post serum treatment

source_name: skin fibroblast, patient 4, serum + 6h

value: 6 hours


title: pateint 6 skin fibroblasts 0h post serum treatment

description: Gene expression data from human skin fibroblasts following serum starvation

source_name: skin fibroblast, patient 6, serum + 0h

value: 0 hours


title: CB2 SDF, BIOLOGICAL REPLICATE 2


title: CB1 SDF, BIOLOGICAL REPLICATE 1


title: ecsA mutant at time 6 hours vs WT at time 6 hours replicate 1

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description: Staphylococcus aureus WT versus ecsA mutant time 6h- Replicate 4/4

hyb_protocol: A mixture of RNA from WT and mutant strain was diluted in 50 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours in a dedicated hybridization oven

scan_protocol: 100% PMT using Agilent scanner

data_processing: Local background-subtracted signals were corrected for unequal dye incorporation or unequal load of labelled product. The algorithm consisted of a rank consistency filter and a curve fit using the default LOWESS (locally weighted linear regression) method.

label: cyanine 3

organism: Staphylococcus aureus

source_name: S. aureus ecsA mutant, 6 hours

label_protocol: Incorporation during reverse transcription

extract_protocol: Fixation followed by RNeasy purification

label: cyanine 5

source_name: S. aureus WT, 3 hours


title: cell10_stimulated_90min_rep1


title: pateint 5 skin fibroblasts 0h post serum treatment

source_name: skin fibroblast, patient 5, serum + 0h


title: CB3 CTRL, BIOLOGICAL REPLICATE 3

description: Gene expression data from cord blood CD34+ cells.

value: control


title: 600_24_1

source_name: IMCD cultivated at 300 mosmol/kg challenged for 24h with 600 mosmol/kg rep.1

value: 300 mosmol/kg


title: cell10_stimulated_90min_rep2

value: primary human b cells infected with EBV mutant 3696


title: CB4 CTRL, BIOLOGICAL REPLICATE 4


title: 600_1

source_name: IMCD cultivated at 600 mosmol/kg rep.1


title: 600_24_2

source_name: IMCD cultivated at 300 mosmol/kg challenged for 24h with 600 mosmol/kg rep.2


title: ecsA mutant at time 6 hours vs WT at time 6 hours replicate 2

description: Staphylococcus aureus WT versus ecsA mutant time 6h- Replicate 2/4


title: ecsA mutant at time 6 hours vs WT at time 6 hours replicate 4


title: CB2 CTRL, BIOLOGICAL REPLICATE 2


title: ecsA mutant at time 6 hours vs WT at time 6 hours replicate 3

description: Staphylococcus aureus WT versus ecsA mutant time 6h- Replicate 3/4


title: ecsA mutant at time 3 hours vs WT at time 3 hours replicate 3

description: Staphylococcus aureus WT versus ecsA mutant time 3h- Replicate 3/4

source_name: S. aureus ecsA mutant, 3 hours


title: ecsA mutant at time 3 hours vs WT at time 3 hours replicate 2

description: Staphylococcus aureus WT versus ecsA mutant time 3h- Replicate 2/4


title: 600_3

source_name: IMCD cultivated at 600 mosmol/kg rep.3


title: pateint 4 skin fibroblasts 0h post serum treatment

source_name: skin fibroblast, patient 4, serum + 0h

value: skin fibroblast


title: 600_2

source_name: IMCD cultivated at 600 mosmol/kg rep.2


title: pateint 3 skin fibroblasts 0h post serum treatment

source_name: skin fibroblast, patient 3, serum + 0h


title: 300_3

source_name: IMCD cultivated at 300 mosmol/kg rep.3


title: pateint 4 oral mucosal fibroblasts 0h post serum treatment

description: Gene expression data from human oral mucosal fibroblasts following serum starvation

source_name: oral mucosal fibroblast, patient 4, serum + 0h

value: oral mucosal fibroblast


title: pateint 3 oral mucosal fibroblasts 0h post serum treatment

source_name: oral mucosal fibroblast, patient 3, serum + 0h


title: SOD1 49-94

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

description: Gene expression data from human motor neurons

hyb_protocol: 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 2.0 Plus GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

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

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

extract_protocol: PicoPure RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions

treatment_protocol:
10 um cervical spinal cord frozen sections were fixed, washed and stained with toluidine blue. They were then washed and dehydrated through graded ethanol concentrations (70%, 90%, 100%) and xylene.
From each individual 500 motor neurons (MN) were isolated using a PixCell II laser-capture microdissection system (Arcturus Bioscience)

value: cervical spinal cord

value: motor neuron

tag: disease status

value: SOD1 mutant individual


title: pateint 6 oral mucosal fibroblasts 0h post serum treatment

source_name: oral mucosal fibroblast, patient 6, serum + 0h


title: CB1 CTRL, BIOLOGICAL REPLICATE 1

source_name: CORD BLOOD CD34+ CELLS

value: CORD BLOOD CELLS


title: 300_2

description: Rat primary cultured inner medullary collecting duct cells

source_name: IMCD cultivated at 300 mosmol/kg rep.2

value: Renal inner medulla


title: iPSC 3.12_Definitive Endoderm Induced_biological rep 3

status: Public on Dec 25 2010

city: Cincinnati

first: James

middle: M

last: Wells

address: 3333 Burnet Ave.

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression profile for Definitive Endoderm induced by 3 day Activin A treatment

hyb_protocol: 2.5 micrograms of labeled cDNA in 80 microliters of hybridization cocktail was hybridized to the GeneChip Human Gene 1.0 ST Array for 18 hours at 45 degrees Celsius.  GeneChips were washed and stained with R-Phycoerythrin Streptavidin (Molecular Probes) and goat-Anti-Streptavidin biotinylated antibody (Vector Laboratories) using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0007.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G and analyzed with Affymetrix Genechip Operating Software.

data_processing: Data was processed by creating an Affymetrix Exon Expression experiment with advanced analysis workflow In GeneSpring GX 10.0.2.  The Probe Summarization algorithm was RMA16 with a core transcript level and a baseline transformation set to the median of all samples.

source_name: Human induced pluripotent stem cells (iPSC) post 3 day DE induction protocol

label_protocol: The Affymetrix Whole Transcript Sense Target Labeling Assay (Affymetrix) is used to create biotin-labeled sense-strand cDNA targets for hybridization to the Gene 1.0 ST Arrays.  Starting material is 100-300 nanograms of total RNA.

growth_protocol: Undifferentiated stem cells were maintained in feeder free conditions using hES qualified matrigel (BD Biosciences) and mTeSR media (Stemcell Technologies).

extract_protocol: Total RNA was extracted with TRIzol Reagent according to Invitrogen's product instruction.

treatment_protocol: To induce Definitive Endoderm (DE) differentiation, stem cell cultures were treated for three days as follows: D1- 100 ng/ml Recombinant Human Activin A (R&D Systems), 25ng/ml recombinant human Wnt3a (R&D Systems) and 0% dFBS (Fisher/Hyclone); D2-100ng/ml Activin A, 0.2% dFBS; D3- 100ng/ml Activin A, 2%dFCS.  Basal media for treatment is RPMI + L-glut + Non-Essential Amino Acids (Invitrogen).

tag: biological source

value: NHSK - Normal Human Dermal Keratinocyte

tag: source

value: Generated at Cincinnati Children's Hospital Pluripotent Stem Cell Facility


title: pateint 5 oral mucosal fibroblasts 0h post serum treatment

source_name: oral mucosal fibroblast, patient 5, serum + 0h


title: ecsA mutant at time 3 hours vs WT at time 3 hours replicate 1

description: Staphylococcus aureus WT versus ecsA mutant time 3h- Replicate 1/4

source_name: S. aureus WT, 3 hours


title: 300_1

source_name: IMCD cultivated at 300 mosmol/kg rep.1

value: collecting duct cells


title: SOD1 37-04


title: iPSC 3.6_Definitive Endoderm Induced_biological rep 2


title: iPSC 3.6_Definitive Endoderm Induced_biological rep 1


title: iPSC 3.6_Definitive Endoderm Induced_biological rep 3


title: iPSC 3.5_Definitive Endoderm Induced_biological rep 1


title: H9_Definitive Endoderm Induced_biological rep 2

source_name: Human embryonic stem cells (H9) post 3 day DE induction protocol

value: WA09 -  from blastocyst

value: WiCell


title: iPSC 3.12_Undifferentiated_biological rep 2

description: Gene expression profile for pluripotent stem cells

source_name: Undifferentiated human induced pluripotent stem cells (iPSC)


title: iPSC 3.12_Undifferentiated_biological rep 1


title: iPSC 3.5_Definitive Endoderm Induced_biological rep 2


title: H9_Definitive Endoderm Induced_biological rep 3


title: iPSC 3.12_Definitive Endoderm Induced_biological rep 1


title: iPSC 3.12_Undifferentiated_biological rep 3


title: iPSC 3.12_Definitive Endoderm Induced_biological rep 2


title: H9_Definitive Endoderm Induced_biological rep 1


title: iPSC 3.6_Undifferentiated_biological rep 3


title: SOD1 34-92


title: iPSC 3.5_Undifferentiated_biological rep 2


title: relative expression ratio of  egg to the first larva

status: Public on Dec 22 2010

city: Nanyang

first: Yunchao

last: Kan

state: Henan

address: Wolong road 1638

country: China

institute: China-UK-NYNU-RRes Joint Libratory of insect biology

description: Analysis used larva1 RNA as control sample for comparison to the sample of egg

hyb_protocol: Labelled cDNA hybridized using the BioMixer™ Ⅱ system (Capitalbio). Slides placed in shaking water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1 % SDS), 1x SSC, 0.2x SSC and 0.1x SSC, each at 37 °C for 5 min prior to drying and scanning.

scan_protocol: Arrays scanned using an LuxScan-10K/A scanner (Capitalbio)

data_processing: Data analysis was carried out using Imagene version Genepix5.1 software. For each slide, spots flagged bad by Genepix were removed from the latter analysis step. Only those genes expressed at least two independent replications were kept for further analysis. Any intensity which was zero or negative after background subtraction was set equal to half the minimum of the positive corrected intensities for that array. Normalization of two channels of each array was done using global LOWESS method with R language. The vsn method was performed for normalization between arrays. R language was used.

organism: Bombyx mori

source_name: RNA from diapaused eggs

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using YM30 column (Millipore) before hybridization.

growth_protocol: Bombyx mori strain Dazao P50 were raised in 25 ℃ with light/dark 14/10h, 70% relative humidity after egg hatching.

extract_protocol: Total RNA was extracted using Trizol reagent following manufacturer's instructions

value: Dazao P50

tag: developmental stage

value: egg

source_name: RNA from the first instar larva

value: larva, first instar


title: iPSC 3.6_Undifferentiated_biological rep 1


title: relative expression ratio of  pupa to the fifth larva

description: Analysis used larva5 RNA as control sample for comparison to the sample of pupa

source_name: RNA from the first day of pupation

value: pupa

source_name: RNA from the fifth instar larva

value: larva, fifth instar


title: relative expression level of pupa

description: Analysis used larva RNA as control sample for comparison to the samples of egg, pupa and adult.

source_name: mixed RNA from the first day to the ninth day of pupation

source_name: mixed RNA from the first to the fifth instar larva

value: larva


title: iPSC 3.5_Undifferentiated_biological rep 1


title: relative expression level of egg

source_name: mixed RNA from diapaused and non-diapaused eggs


title: H9_Undifferentiated_biological rep 3

source_name: Undifferentiated/pluripotent human embryonic stem cells (H9)


title: H9_Undifferentiated_biological rep 2


title: H9_Undifferentiated_biological rep 1


title: relative expression level of adult

source_name: mixed RNA from male and female moths

value: adult


title: AB_90_10_2

status: Public on Dec 01 2010

type: genomic

city: Chicago

first: Pan

last: Du

state: IL

address: 676 N ST Clair St, 1200#

institute: Northwestern University

description: A methylation titration sample series for the evaluation of preprocessing algorithm

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: Array data processing were performed on Illumina GenomeStudio software.

molecule: genomic DNA

source_name: Mix of Sample A and B in the rato of 90:10

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

value: mixture

tag: gender


title: Liver Mouse11_Sample02

status: Public on Oct 01 2010

city: Bar Harbor

first: Peter

middle: Thomas

last: Vedell

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: We analyzed intensities of 45,905 probes with unique sequences and annotated by Illumina as probes for genomic regions corresponding to protein-coding genes.

hyb_protocol: 1.5µg biotin-labeled cRNA was then hybridized onto Mouse-6 Expression BeadChips (Illumina, San Diego CA) for 16 hours at 55°C.  Post-hybridization staining and washing were performed according to manufacturer’s protocols (Illumina).

scan_protocol: Illumina Sentrix ® Mouse-6 v1.1 BeadChips were scanned using Illumina’s BeadStation 500 scanner.

data_processing:
Images were checked for grid alignment and then quantified using the BeadStudio software.  Control summary graphs generated by BeadStudio were used as quality assurance tools for hybridization, washing stringency, and background.  Integrity of the arrays was investigated using the BeadStudio array images and also using bead level image plots generated using the R/beadarray package.  Mean pixel intensities by bead type, were created using BeadStudio v3.1 and processed within the R/beadarray package (Dunning et al. 2006).
The raw data conains the log base 2 transformed intensities.  A two-step procedure was used for normalization.  Quantile normalization (Bolstad et al. 2003) was applied within each tissue type.  Then, a correction for batch effects was applied separately for each gene performed using an MM-regression estimator described in Yohai (1987) and computed using the R/robustbase software package (Rousseeuw et al. 2009).  The normalized data is also on a log base 2 scale.

organism: Mus musculus

source_name: Liver Mouse11_Sample02

label_protocol: Illumina Sentrix ® Mouse-6 v1.1 BeadChip processing.  For each sample, an in-vitro transcription (IVT) reaction was carried out incorporating biotinylated nucleotides according to the manufacturer’s protocol for Illumina® Totalprep RNA amplification kit (Ambion).

growth_protocol: We obtained twelve C57BL/6J male mice from The Jackson Laboratory. Six pairs of littermates were pair-housed from weaning and put on a 5k52 diet (standard chow containing 6% fat).

extract_protocol: Inguinal fat pad, heart, liver, and both kidneys were extracted, perfused with RNase-free DEPC-treated PBS, cut into pieces not exceeding 0.5 cm in any dimension, and placed in 15 ml conical tubes.  The pieces were divided into 2 aliquots and stored in RNAlater (Ambion, Austin TX).  Each kidney aliquot consisted of one complete kidney.  Tissues were homogenized in TRIzolTM (Invitrogen, Carlsbad, CA).  Total RNA was isolated by standard TRIzolTM  methods according to the manufacturer’s protocols, and quality was assessed using an Agilent 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Santa Clara, CA).  The RNA was then treated with DNase1 (Qiagen, Valencia, Ca.) according to the manufacturer’s methods.    Total RNA was then reverse transcribed followed by second strand cDNA synthesis.

treatment_protocol: At 10 weeks, body weight was recorded and the mice were euthanized by cervical dislocation. Dissection procedures were started  at 11:00 a.m. after a 4-hour fasting period and were completed within a one-hour time window.

tag: tissue type

value: Liver

value: male

tag: body weight (g)

tag: age (days)


title: AB_90_10_1

tag: tissue


title: A2

source_name: B-Lymphocyte sample from a male donor 100:0

value: B-Lymphocyte


title: B1

source_name: colon cancer sample from a female donor 0:100

value: colon cancer

value: female


title: AB_75_25

source_name: Mix of Sample A and B in the rato of 75:25


title: DU145 Non-invasive (Top)Sample 11

status: Public on Dec 04 2010

city: Frederick

first: Lesley

middle: A

last: Mathews

state: MD

address: 1050 Boyles Street Bldg 560 Rm 21-81

department: Laboratory of Cancer Prevention

institute: National Cancer Institute

description: Input versus methyl collector: MethylCollector (Active Motif, Carlsbard, CA) assay was used to isolate methylated and non-methylated fractions of DNA.  The kit utilizes histidine-tagged MeBP2 (methyl-binding protein 2) and magnetic bead separation

hyb_protocol: Samples were applied to Agilent’s 2x244K Human Promoter Tiling Arrays for 40 hours at 65ºC and washed for 5 minutes in wash buffer 1 and then 5 minutes in wash buffer 2.

scan_protocol: The arrays were scanned using a Gene Pix 4000B scanner (Molecular Devices, Sunnyvale, CA) with GenePix Pro software version 6.1 and extracted using Agilent’s Feature Extraction software version 9.5.3.1.

data_processing:
The data was annotated using Agilent’s ChIP Analytics software version 4.0. Normalization was carried out using a blank subtraction model and statistical stringency (p-value) between 0.01-0.05 was applied using a Whitehead Per-Array Neighbourhood Analysis. This analysis allowed for the determination of differentially methylated genes between non-invasive and invasive cells.
Methylated probes appear in the array with a value of 1 in the ISINBOUND Region and un-methylated probes array with a value of 0. Using FileMaker Pro Software (version 9) the full text files were imported and the find option was used in order to query probes that were methylated in the Non-Invasive cells and non-methylated in the Invasive cells.

source_name: Prostate Cancer Cell Line

label_protocol: The isolated methylated and non-methylated DNA from each sample (as little as 5 ng) was then amplified in a series of PCR reactions following the mammalian ChIP on ChIP protocol from Agilent. The input DNA was labeled with Cy3-dUTP and the methylated DNA with Cy5-dUTP.

extract_protocol: For the isolation of DNA from both non-invasive and invasive cells the DNeasy kit from Qiagen (Valencia, CA) was used and parallel invasion chambers were setup. For non-invading cells, the bottom of the membrane was scrubbed with a cotton swab and cells on top were trypsinized and harvested in 200 µL of PBS followed by the direct addition of lysis buffer or stored at -80ºC. For bottom ‘invading cells’ the top of the membrane was scrubbed with a cotton swab and the membrane was removed and placed directly into lysis buffer or stored at -80ºC until needed.  MethylCollector (Active Motif, Carlsbard, CA) assay was used to isolate methylated and non-methylated fractions of DNA.  The kit utilizes histidine-tagged MeBP2 (methyl-binding protein 2) and magnetic bead separation.

tag: phenotype

value: Non-invasive

tag: sample type

value: Non-methylated Genomic DNA

tag: cell line

value: Methylated Genomic DNA


title: Liver Mouse12_Sample02

source_name: Liver Mouse12_Sample02

tag: strain


title: DU145 Invasive (Bottom)Sample 6

value: Invasive


title: B2


title: LNCaP Non-invasive (Top)Sample 3

value: LNCaP


title: DU145 Invasive (Bottom)Sample 12


title: AB_50_50

source_name: Mix of Sample A and B in the rato of 50:50


title: ecsA mutant at time 3 hours vs WT at time 3 hours replicate 4

source_name: S. aureus ecsA mutant, 3 hours

source_name: S. aureus WT, 3 hours


title: LNCaP Invasive (Bottom)Sample 4


title: DU145 Non-invasive (Top)Sample 5


title: PCSC1 Invasive (Bottom)Sample 14

source_name: Primary Prostate Cancer Cell Line


title: Liver Mouse10_Sample02

source_name: Liver Mouse10_Sample02


title: PCSC2 Invasive (Bottom)Sample 16


title: A1


title: PCSC1 Non-invasive (Top)Sample 13


title: LNCaP Invasive (Bottom)Sample 2


title: PCSC2 Non-invasive (Top)Sample 9


title: PCSC1 Non-invasive (Top)Sample 7


title: PCSC1 Invasive (Bottom)Sample 8


title: LNCaP Non-invasive (Top)Sample 1


title: iPSC 3.6_Undifferentiated_biological rep 2

source_name: Undifferentiated human induced pluripotent stem cells (iPSC)

value: NHSK - Normal Human Dermal Keratinocyte

value: Generated at Cincinnati Children's Hospital Pluripotent Stem Cell Facility


title: Liver Mouse07_Sample02

source_name: Liver Mouse07_Sample02


title: iPSC 3.5_Definitive Endoderm Induced_biological rep 3

source_name: Human induced pluripotent stem cells (iPSC) post 3 day DE induction protocol


title: Liver Mouse08_Sample01

source_name: Liver Mouse08_Sample01


title: Liver Mouse09_Sample02

source_name: Liver Mouse09_Sample02


title: Liver Mouse07_Sample01

source_name: Liver Mouse07_Sample01


title: Liver Mouse10_Sample01

source_name: Liver Mouse10_Sample01


title: Liver Mouse06_Sample02

source_name: Liver Mouse06_Sample02


title: Liver Mouse12_Sample01

source_name: Liver Mouse12_Sample01


title: Liver Mouse09_Sample01

source_name: Liver Mouse09_Sample01


title: PCSC2 Non-invasive (Top)Sample 15


title: Liver Mouse06_Sample01

source_name: Liver Mouse06_Sample01


title: Liver Mouse05_Sample02

source_name: Liver Mouse05_Sample02


title: Liver Mouse04_Sample02

source_name: Liver Mouse04_Sample02


title: Liver Mouse08_Sample02

source_name: Liver Mouse08_Sample02


title: Liver Mouse04_Sample01

source_name: Liver Mouse04_Sample01


title: Liver Mouse02_Sample02

source_name: Liver Mouse02_Sample02


title: Liver Mouse01_Sample02

source_name: Liver Mouse01_Sample02


title: Liver Mouse05_Sample01

source_name: Liver Mouse05_Sample01


title: Liver Mouse11_Sample01

source_name: Liver Mouse11_Sample01


title: Liver Mouse02_Sample01

source_name: Liver Mouse02_Sample01


title: Liver Mouse03_Sample02

source_name: Liver Mouse03_Sample02


title: PCSC2 Invasive (Bottom)Sample 10

source_name: Primary Prostate Cancer Cell Line


title: melanoma progressing 3

status: Public on Sep 11 2010

city: Granada

first: Rafael

last: Carretero

address: Avenida del Hospicio

country: Spain

institute: Universidad de Granada

description: metastasis non responding after M-VAX immunotherapy 3

hyb_protocol: 6 ug of labeled, fragmented cRNA per sample was applied to microarrays in Kreatech's Hybridization buffer, and hybridized for 16 h at 42C. After hybridization, slides were washed three four times with wash solutions containg gradually decreased concentrations of SSC (1x-0x)

scan_protocol: Scanned on an Agilent DNA Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.3).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used for feature extraction.

source_name: melanoma, progressing

label_protocol: 0.5 µg of total RNA was primed with 0.25 ug oligo dT-T7 primer (5’ AAA CGA CGG CCA GTG AAT TGT AAT ACG ACT CAC TAT AGG CGC T(15) 3’) at 70°C for 3 min, then reverse transcribed at 42°C for 90 min in the presence of 200 U SuperScript II RTase (Invitrogen), and 1 mM dNTP. Second strand synthesis was done with the 5’ primer switch method using 0.25 ug Ts/SMARTII primers (5’ AAG CAG TGG TAA CAA CGC AGA GTA CGC GGG 3’) for priming at 65°C for 1 min, and subsequent primer extension at 75°C for 30 min using the Advantage cDNA Polymerase Mix (Clontech) and 0.2mM dNTP. Double stranded cDNA subjected to in vitro transcription at 42°C for 6h using Megascript T7 kit (Ambion). After two rounds of linear amplification, cRNA was chemically labeled using ULS Cy3/Cy5 Fluorescent Labeling Kit (Kreatech), and fragmented by Fragmentation Reagents kit (Ambion).

extract_protocol: Total RNA extracted using Qiagen's RNEasy Mini kit following manufacturer's instructions

value: melanoma

tag: treatment protocol

value: M-VAX

tag: preservation

value: cryopreservation

tag: patient

source_name: Total RNA from pooled PBMC

value: Blood

tag: reference

value: Total RNA from pooled PBMC


title: Control 2

status: Public on Sep 25 2010

city: La Jolla

first: Tae Hyuk

last: Kang

state: CA

address: 9500 Gilman Drive # 0634

department: Pediatrics

institute: University of California, San Diego

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised by loess normalization method (31. Sásik, R., Woelk, C. H., and Corbeil, J. (2004) J. Mol. Endocrinol. 33, 1-9) in BeadStudio.

source_name: Control human fibroblast

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Cell were grown to approcomately 90% confluence in Dulbecco's modified Eagle medium (DMEM) high-glucose medium supplemented with 10% (v/v) fetal bovine serum, 1% (v/v) penicillin/streptomycin (Invitrogen, Carlsbad, CA) and 0.2% (v/v) nomocin (Invivogen, San Diego, CA) in 5% CO2 atmosphere.

extract_protocol: Total RNAs from HPRT knockdown and control cells were purified by Rneasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instruction. The pooled total RNAs of HPRT knockdown and control sample were obtained from the independently triplicated cultures.

treatment_protocol: HPRT knockdown cells were infected by retrovirus with shRNA against HPRT and control cells were infected by retrovirus with shRNA against luciferase.

value: adult skin


title: Knockdown 1

source_name: HPRT knockdown human fibroblast


title: T-cells_CD4_centralmemory

status: Public on Dec 31 2009

city: rome

first: Graziella

last: Curtale

address: viale regina elena 324

country: Italy

institute: "Sapienza" University of Rome

description: MicroRNA expression data from purified human central memory CD4+ T lymphocytes

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies)

scan_protocol: Axon GenePix 4000B Microarray Scanner

data_processing: Data were analyzed with R. Signal values from each array were background subtracted (array background value was set as quantified by the service provider), quantile-normalized between the 7 intra-array replicates and the signal value for each miRNA summarized as the average of repeating spots. Processed miRNA intensity values were normalized between-array by quantile normalization.

source_name: peripheral blood

label_protocol: Lc Sciences proprietary labeling method which utilizes an affinity tag for signal amplification after miRNA hybridization to the chip

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

tag: cell type

value: CD4+ lymphocytes

tag: t cell status

value: central memory


title: T-cells_CD8_naive

description: MicroRNA expression data from purified human naive CD8+ T lymphocytes

value: CD8+ lymphocytes

value: naive


title: T-cells_CD4_naive

description: MicroRNA expression data from purified human naive CD4+ T lymphocytes


title: Knockdown 3


title: MRC5_iPS2_IH

status: Public on Sep 30 2010

city: Boston

first: Hu

last: Li

state: MA

address: 3 Blackfan Circle

institute: Wyss Institute

description: Gene expression data obtained from MRC5 iPS

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

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

data_processing: RMA (Bioconductor Affy Package)

source_name: viral derived iPS

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

growth_protocol: For feeder-free culture of iPSCs, the plate was coated with 0.3mg/ml Matrigel (BD-Bioscience, San Jose, CA) and mTeSR (StemCell Technologies, Vancouver, Canada) was used according to the manufacturer’s instruction.

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

value: iPS cells derived from MRC5 fibroblast

tag: reprogramming protocol

value: viral derived iPS


title: Control 3


title: Control 1


title: T-cells_CD8_centralmemory

description: MicroRNA expression data from purified human central memory CD8+ T lymphocytes


title: melanoma progressing 1

description: metastasis non responding after M-VAX immunotherapy 1


title: melanoma regressing 2

description: metastasis responding after M-VAX immunotherapy 2

source_name: melanoma, regressing


title: NC-MSC EF rep2

status: Public on Jun 15 2010

city: Ann Arbor

first: Elizabeth

middle: R

last: Lawlor

state: MI

address: 1600 Huron Parkway, NCRC Bldg 520

institute: University of Michigan

description: hESC-derived neural crest-MSC isolated 5 days after lentiviral transduction with EWS-FLI1 vector

hyb_protocol: hybridization to HuEx1.0 microarrays was carried out following the manufacturer’s instructions

data_processing:
Signal intensities from core probesets were quantile normalized by robust multichip averaging and transcript expression levels median summarized using Partek Genomics Suite software (Partek, St. Louis, MO).
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: hNC-MSC with EWS-FLI1

label_protocol: Samples were prepared in the CHLA genome core using the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix, Santa Clara)

extract_protocol: Qiagen miRNA easy

value: NC-MSC


title: Liver Mouse01_Sample01

source_name: Liver Mouse01_Sample01

value: Liver

value: male


title: Liver Mouse03_Sample01

source_name: Liver Mouse03_Sample01


title: NC-MSC EF rep3

scan_protocol: hybridization to HuEx1.0 microarrays was carried out following the manufacturer’s instructions


title: NC-MSC EF rep1


title: Knockdown 2


title: melanoma regressing 1

description: metastasis responding after M-VAX immunotherapy 1


title: two day heated 1

status: Public on Oct 31 2009

city: San Francisco

first: Michael

last: DeSalvo

department: Department of Anesthesia

institute: UC San Francisco

hyb_protocol: Dye-coupled cDNAs were cleaned (MinElute), and a Cy3-reference cDNA and a Cy5-control/stress a cDNA were mixed together in a hybridization buffer containing 0.25% SDS, 25mM HEPES, and 3x SSC. The hybridization mixtures were boiled for 2min at 99oC then allowed to cool at room temperature for 5min. The cooled hybridization mixtures were pipetted under an mSeries Lifterslip (Erie Scientific), and hybridization took place in custom-fabricated hybridization chambers overnight at 63oC. Microarrays were washed twice in 0.6x SSC and 0.01% SDS followed by a rinse in 0.06x SSC and dried via centrifugation.

scan_protocol: All microarrays were scanned using an Axon 4000B scanner (Molecular Devices) where care was taken to balance photomultiplier tube (PMT) settings.

data_processing: Gridding was performed using GenePix Pro 6.0. TIGR Express Converter was used to convert GenePix results files into .mev files for input into TIGR MIDAS 2.19 (Saeed, Sharov et al. 2003). Data for a particular spot was discarded according to the stringent one bad channel policy. Additional data were discarded if spots had been flagged during gridding in GenePix, and if the intensity in either channel was less than 30,000. After filtering, background-subtracted median intensity values were LOWESS normalized, and in-slide duplicates were averaged. Both PMT balancing and LOWESS normalization equalize for differing amounts of host RNA input (a potential issue when processing tissue where symbiont densities can vary). We employed a reference design where all control and heat-stressed samples were compared to a pooled reference aRNA sample composed of aRNA from the four t0C fragments. Since all RNA samples were compared to the reference sample, direct comparisons of gene expression across all time points and conditions can be performed. Genes were included in statistical analyses only if there were data for three out of four replicates for t0C, t0H, 1dC, and 1dH, and two out of three replicates for 2dC and 2dH. This left 1,697 genes for statistical analyses of gene expression (additional matrix file included in this submission). Missing values were imputed using PAMR (Tibshirani, Hastie et al. 2002). The ratio between the fluorescence intensity of the two channels was then used as input for BAGEL (Bayesian Analysis of Gene Expression Levels) (Townsend and Hartl 2002). The filtered lowess-normalized Cy5/Cy3 ratios (included in the Ratio column) were used as input for BAGEL. BAGEL computes an estimated mean and 95% credible interval of the relative level of expression of each gene in each treatment and time point (i.e. t0C, t0H, 1dC, 1dH, 2dC, and 2dH). We used the conservative gene-by-gene criterion of non-overlapping 95% credible intervals to regard a gene as significantly differentially expressed. Genes significant at 1day satisfied the following conditions: t0C=t0H, 1dH≠t0C, 1dH≠t0H, 1dH≠1dC. Genes significant at 2days satisfied the following conditions: t0C=t0H, 2dH≠t0C, 2dH≠t0H, and 2dH≠2dC. Genes significantly different at both days were the overlap between the previous two tests. Genes significantly different between 1dH and 2dH had to be among those genes significant on both days and also satisfy the additional test 1dH≠2dH. Clustering of genes differentially expressed at both 1d and 2d were performed in TIGR TMEV 4.0 (Saeed, Sharov et al. 2003) using hierarchical clustering according to Euclidean distance and average linkage.

molecule: polyA RNA

organism: Acropora palmata

label_protocol: One microgram of total RNA was amplified using the MessageAmp II aRNA kit (Ambion), and 3μg of aRNA per sample were primed with 10μg random nonamer for 10min at 70oC. Reverse transcription (RT) lasted for 2hr at 50oC using a master mix containing a 4:1 ratio of aminoallyl-dUTP to TTP. Following RT, single-stranded RNA was hydrolyzed by incubating the RT reactions in 10μL 0.5M EDTA and 10μL 1M NaOH for 15min at 65oC. After hydrolysis, RT reactions were cleaned using MinElute Reaction Cleanup columns (Qiagen). Cy3 and Cy5 dyes (GE Healthcare) were dissolved in 18μL DMSO, and the coupling reactions lasted for 1hr at room temperature in the dark (the reference was labeled with Cy3 while the control and heat-stressed samples were labeled with Cy5.

extract_protocol: Total RNA from all frozen coral fragments was isolated using Qiazol lysis reagent (QIAGEN). Live tissue was chiseled off each coral fragment and homogenized using a pre-chilled mortar and pestle. Frozen coral powder was transferred directly to Qiazol. Three chloroform extractions were performed, followed by isopropanol precipitation and three washes in 70% ethanol. RNA pellets were re-dissolved in nuclease-free water and cleaned further with RNeasy Mini columns (QIAGEN). RNA quantity and integrity were assessed with a NanoDrop ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.

treatment_protocol: After an acclimation period of four days at the natural temperature of the seawater system (mean temperature = 30.29±0.07oC), a fragment from each control and experimental aquaria was sampled (t0C and t0H). After time zero sampling, the heaters in each of the experimental aquaria were turned on. The temperatures of the experimental aquaria increased to ca. 32oC over three hours. The mean temperature of the control aquaria during the entire experiment was 29.74±0.03oC, and the mean temperature of the heated aquaria was 32.72±0.32oC. Control and experimental fragments were sampled again one day (1dC and 1dH) and two days (2dC and 2dH) after turning on the heaters. Heated fragments from one of the colonies (col3) showed extreme bleaching after one day of thermal stress. The remaining fragment of col3 was removed at this time to avoid fouling of the water due to death. Thus, there are four replicates for t0C, t0H, 1dC, and 1dH, and three replicates for 2dC and 2dH. All samples were taken at night. Fragments were frozen in liquid nitrogen.

tag: sample

value: Pool of RNAs from all time zero control samples

source_name: two day heated 1

value: Fragment from colony 1

tag: time

value: 2 days

tag: treatment

value: heated aquarium


title: MEF1-HS+LPS

status: Public on Dec 21 2009

city: Ube

first: Akira

last: Nakai

state: Yamaguchi Prefecture

address: Minami-Kogushi 1-1-1

department: Graduate School of Medicine

institute: Yamaguchi University

description: Gene expression data from cells treated with LPS for 4 hours after the pretreatment of heat shock at 42˚C for 1 hour

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45˚C on GeneChip Mouse Genome 430 2.0 Array (Affymetrix). Arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Softwere version 1.4 (GCOS1.4, Affymetrix) 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: Mouse embryo fibroblasts #1

label_protocol: Biotinylated cRNA were prepared from 1 μg total RNA with a One-Cycle cDNA Synthesis Kit and 3'-Amplification Reagents for IVT Labeling (Affymetrix).

growth_protocol: Cells were maintained at 37˚C in 5% CO2 in Dulbecco’s modified eagle medium (DMEM) containing 10% fetal bovine serum.

extract_protocol: Total RNA was prepared using RNeasy Mini (Qiagen).

treatment_protocol: Cells were maintained at 37˚C (Control), treated with lipopolysaccharide (LPS, E. coli 0127:B8, Sigma, 1 μg/ml) for 4 hours, or treated with LPS for 4 hours after the pretreatment of heat shock at 42˚C for 1 hour.

value: ICR

value: Embryo

tag: developmental stage

value: Embryonic day 15.5

tag: stress

value: heat shock at 42˚C for 1 hour

tag: agent

value: LPS for 4 hours after HS pretreatment


title: MEF2-HS+LPS

source_name: Mouse embryo fibroblasts #2

tag: tissue


title: two day heated 2

source_name: two day heated 2

value: Fragment from colony 2


title: two day heated 4

source_name: two day heated 4

value: Fragment from colony 4


title: time zero heated 2

source_name: time zero heated 2

value: time zero


title: two day control 4

source_name: two day control 4

value: control aquarium


title: time zero heated 3

source_name: time zero heated 3

value: Fragment from colony 3


title: one day heated 2

source_name: one day heated 2

value: 1 day


title: one day heated 4

source_name: one day heated 4


title: time zero heated 1

source_name: time zero heated 1


title: one day control 1

source_name: one day control 1


title: one day control 4

source_name: one day control 4


title: one day control 3

source_name: one day control 3


title: one day control 2

source_name: one day control 2


title: one day heated 1

source_name: one day heated 1


title: time zero control 2

source_name: time zero control 2


title: time zero heated 4

source_name: time zero heated 4


title: time zero control 3

source_name: time zero control 3


title: one day heated 3

source_name: one day heated 3


title: two day control 1

source_name: two day control 1


title: two day control 2

source_name: two day control 2


title: time zero control 4

source_name: time zero control 4


title: time zero control 1

source_name: time zero control 1


title: melanoma progressing 2

description: metastasis non responding after M-VAX immunotherapy 2

source_name: melanoma, progressing

value: melanoma

value: M-VAX

value: cryopreservation

source_name: Total RNA from pooled PBMC

value: Blood

value: Total RNA from pooled PBMC


title: Normal Ovary, 2237

status: Public on Oct 17 2009

last: Birrer

address: 70 Blossom Street

department: Medicine

institute: MGH

description:
Gene expression data from normal ovary.
HOSE2237

hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).

scan_protocol: Arrays were scanned using the laser confocal GeneChip Scanner 3000 (Affymetrix).

data_processing:
Low-level analysis included array normalization and estimation of expression level using an invariant set of probe sets to adjust the overall signal level of the arrays to the same level. Next, a model-based PM-only approach established gene expression levels using dChip software.    A modified “semi-supervised” method was applied in two stages: (1) supervised dimension reduction by fitting a univariate Cox model that included a jackknifing step to each gene, so only those genes with a consistently large Cox score were included in the signature. Among 200, 100, or 300 probe sets, 200 yielded an optimally sized predictor; (2) In stage 2, the dimensions of the data set were reduced from 200 to 5 by PC analysis. The number of PCs was set at 5 capturing 90% of the expression data. 4 or 6 PCs were investigated to see whether this parameter affected the results. A prediction model was then built using multivariate Cox regression, where independent variables included the first 5 PCs and debulking status.
Standard leave-one-out validation evaluated the prediction model reserving one sample for testing, and using the remaining 52 patients to establish the prediction model following the method described above. The reserved patient had no contribution to the prediction model yielding 53 separate predicted hazards. Patients were equally divided into low and high-risk groups according to whether their hazard was less or greater than the sample median and were compared by Kaplan Meier analysis with a non-parametric log-rank test.

source_name: normal ovarian surface epithelium (OSE)

label_protocol: Two rounds of amplification were completed according to standard Affymetrix Two-Cycle Amplification protocol using 25ng of total RNA.

extract_protocol: RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen Inc., Valencia, CA).

treatment_protocol: All specimens were subjected to laser-based microdissection and analyzed as pure, microdissected epithelial cell populations.

value: ovarian surface epithelium (OSE)


title: Normal Ovary, 2230

description:
Gene expression data from normal ovary.
HOSE2230


title: Normal Ovary, 2225

description:
Gene expression data from normal ovary.
HOSE2225


title: Normal Ovary, 2061

description:
Gene expression data from normal ovary.
HOSE2061


title: Normal Ovary, 2064

description:
Gene expression data from normal ovary.
HOSE2064


title: Normal Ovary, 2234

description:
Gene expression data from normal ovary.
HOSE2234


title: Normal Ovary, 2226

description:
Gene expression data from normal ovary.
HOSE2226


title: Ovarian Tumor, 631

description:
Gene expression data from tumor.
631

source_name: papillary serous ovarian adenocarcinoma

value: papillary serous ovarian adenocarcinoma

tag: tumor stage

value: late

tag: tumor grade

value: high

tag: surv data


title: Ovarian Tumor, 461

description:
Gene expression data from tumor.
461


title: Ovarian Tumor, 778

description:
Gene expression data from tumor.
778


title: Normal Ovary, 2085

description:
Gene expression data from normal ovary.
HOSE2085


title: Ovarian Tumor, 1109

description:
Gene expression data from tumor.
1109


title: Ovarian Tumor, 1214

description:
Gene expression data from tumor.
1214


title: Normal Ovary, 2008

description:
Gene expression data from normal ovary.
HOSE2008


title: Ovarian Tumor, 692

description:
Gene expression data from tumor.
692


title: Ovarian Tumor, 358

description:
Gene expression data from tumor.
358


title: Normal Ovary, 2228

description:
Gene expression data from normal ovary.
HOSE2228


title: Ovarian Tumor, 394

description:
Gene expression data from tumor.
394


title: Ovarian Tumor, 794

description:
Gene expression data from tumor.
794


title: Ovarian Tumor, 786

description:
Gene expression data from tumor.
786


title: Ovarian Tumor, 970

description:
Gene expression data from tumor.
970


title: Ovarian Tumor, 345

description:
Gene expression data from tumor.
345


title: Ovarian Tumor, 477

description:
Gene expression data from tumor.
477


title: Ovarian Tumor, 486

description:
Gene expression data from tumor.
486


title: Ovarian Tumor, 715

description:
Gene expression data from tumor.
715


title: Ovarian Tumor, 1993

description:
Gene expression data from tumor.
1993


title: Ovarian Tumor, 694

description:
Gene expression data from tumor.
694


title: Ovarian Tumor, 656

description:
Gene expression data from tumor.
656


title: Ovarian Tumor, 744

description:
Gene expression data from tumor.
744


title: Ovarian Tumor, 396

description:
Gene expression data from tumor.
396


title: Ovarian Tumor, 321

description:
Gene expression data from tumor.
321


title: Ovarian Tumor, 934

description:
Gene expression data from tumor.
934


title: Ovarian Tumor, 1231

description:
Gene expression data from tumor.
1231


title: Ovarian Tumor, 367

description:
Gene expression data from tumor.
367


title: Ovarian Tumor, 312

description:
Gene expression data from tumor.
312


title: Ovarian Tumor, 1660

description:
Gene expression data from tumor.
1660


title: Ovarian Tumor, 380

description:
Gene expression data from tumor.
380


title: Ovarian Tumor, 800

description:
Gene expression data from tumor.
800


title: Ovarian Tumor, 377

description:
Gene expression data from tumor.
377


title: Ovarian Tumor, 324

description:
Gene expression data from tumor.
324


title: Ovarian Tumor, 1562

description:
Gene expression data from tumor.
1562


title: P98 UK normal prostate

status: Public on May 15 2010

city: London

first: Xueying

last: Mao

address: Charterhouse Square

institute: Queen Mary

description: Hybridized to human SNP 6.0 array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: CEL files and CHP files generated by Affymetrix Genechip Operating Software. Very weakly hybridized SNPs were filtered by the same software. The signal intensity data from SNP array were analyzed by in-house software- GOLF and commerical software-Partek.

source_name: UK normal prostate

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Fresh frozen samples were digested by Proteinase K  and RNaseA. DNA was extracted from these samples using phenol/chroloform.

value: Normal prostate


title: Ovarian Tumor, 443

description:
Gene expression data from tumor.
443


title: Ovarian Tumor, 780

description:
Gene expression data from tumor.
780


title: Ovarian Tumor, 872

description:
Gene expression data from tumor.
872


title: Ovarian Tumor, 714

description:
Gene expression data from tumor.
714


title: Ovarian Tumor, 702

description:
Gene expression data from tumor.
702


title: Ovarian Tumor, 799

description:
Gene expression data from tumor.
799


title: Ovarian Tumor, 467

description:
Gene expression data from tumor.
467


title: Ovarian Tumor, 662

description:
Gene expression data from tumor.
662


title: Ovarian Tumor, 410

description:
Gene expression data from tumor.
410


title: Ovarian Tumor, 765

description:
Gene expression data from tumor.
765


title: Ovarian Tumor, 412

description:
Gene expression data from tumor.
412


title: Ovarian Tumor, 434

description:
Gene expression data from tumor.
434


title: Ovarian Tumor, 389

description:
Gene expression data from tumor.
389


title: Ovarian Tumor, 629

description:
Gene expression data from tumor.
629


title: P68 UK normal prostate

description: Hybridized to human SNP 6.0 array


title: Ovarian Tumor, 388

description:
Gene expression data from tumor.
388


title: Ovarian Tumor, 402

description:
Gene expression data from tumor.
402


title: Ovarian Tumor, 386

description:
Gene expression data from tumor.
386


title: Ovarian Tumor, 317

description:
Gene expression data from tumor.
317


title: Ovarian Tumor, 332

description:
Gene expression data from tumor.
332


title: Ovarian Tumor, 718

description:
Gene expression data from tumor.
718


title: Ovarian Tumor, 351

description:
Gene expression data from tumor.
351


title: Leaves from well watered cotton

status: Public on Sep 25 2009

city: Las Cruces

first: Laura

last: Rodriguez-Uribe

state: NM

address: 945 College Dr. Skeen Hall RM 127

department: Plant and environmental Sciences

institute: New Mexico State University

description: Gene expression profiling in drought tolerant Acala 1517-99 cotton (Gossypium hirsutum L.) under reduced irrigation field conditions

hyb_protocol: After fragmentation of the cRNA, the Cotton GeneChips were hybridized with 15 μg of cRNA for 16hr at 45oC. After hybridization, the arrays were washed and stained using a Fluidics Station 450 (Affymetrix).

scan_protocol: The cotton GeneChips were scanned with the GCS 3000 7G high-resolution confocal laser scanner (Affymetrix).

data_processing:
The scanned images were analyzed using programs resident in GeneChip Operating System v1.4 (GCOS; Affymetrix). Fold changes in expression (e.g., > 2-fold), the Microarray Suite (MAS) 5.0 probe set detection p-values, and/or p-values (e.g., < 0.05) from standard statistical tests (e.g., independent t-test, Welch's t-test, Wilcoxon's rank sum test, ANOVA, etc.) were used to identify genes with significant changes in expression.
Differentially expressed genes are listed in the 'GSE18253_differentially_expressed.txt' file, which is linked to the Series GSE18253 record as a supplementary file.

organism: Gossypium hirsutum

label_protocol: Biotinylated cRNA probes were prepared according to standard protocols from Affymetrix with 5.0 μg total RNA.

growth_protocol: Seeds from Upland cotton (Gossypium hirsutum L.) Acala 1517-99 were planted in the Leyendecker Plant Science Research Center, Las Cruces, NM, USA on May 7, 2008. Furrow irrigation was applied on May 8, 2008, for seedling emergence. The field tests were strip plots of 8 rows divided into three paired side-by-side plots of 40 ft (ca. 120 plants per row) long each (4 rows for normal irrigation and 4 rows for drought stress).

extract_protocol: Total RNA was extracted from leaf tissues using the modified hot borate method (Wilkins and Smart, 1996).

treatment_protocol: For the normal irrigation (well watered) treatment, plants were irrigated on June 17, 2008. For the drought stressed treatment, no furrow irrigation was applied. Plants in drought stressed plots showed reduced growth as measured by fresh weight and plant height 9 days after withholding water on June 26, 2008. Leaf tissues from the third topmost leaf (8 plants per replicate) were harvested from three field plots as biological replicates for RNA isolation.

tag: genotype

value: third topmost leaf;

tag: age

value: 9 weeks;

tag: condition

value: well watered.


title: Leaves from drought-stressed cotton

hyb_protocol: After fragmentation of the cRNA, the cotton GeneChips were hybridized with 15 μg of cRNA for 16hr at 45oC. After hybridization, the arrays were washed and stained using a Fluidics Station 450 (Affymetrix).

source_name: Gene expression profiling in drought tolerant Acala 1517-99 cotton (Gossypium hirsutum L.) under reduced irrigation field conditions

value: drought stress.


title: Xba_JA.1978

status: Public on May 05 2009

city: San Diego

first: Jack

last: Yu

address: 3210 Merryfield Row

institute: Veridex, LLC

description: Gene copy data from breast cancer

hyb_protocol: Biotinylated genomic DNA fragments were hybridized for 17 hr at 48C on Affy Human Mapping 100K Array sets.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip scanner

data_processing: The data were analyzed with Affy GTYPE and CCNT 3.0 software to generate copy numbers for the probes.

source_name: human breast cancer, time: 69, status: 0

label_protocol: Biotinylated genomic DNA were prepared according to the standard Affymetrix protocol

extract_protocol: QIAamp DNA mini kit according to the manufacturer

tag: differentiation

value: poor

tag: er

value: Neg

tag: menopause

value: pre

tag: pr

tag: survival time (months)

tag: status (0=no relapse, 1=relapse)


title: Xba_JA.2007

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 91, status: 0

value: post


title: Xba_JA.1060

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 71, status: 0


title: Xba_JA.632

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 61, status: 0


title: Breast tumor biopsy_DMBA_07SE117

status: Public on Jun 01 2009

first: Sergio

last: Granados

address: Avenida del Conocimiento

institute: University of Granada

description: Affymetrix standard protocols

hyb_protocol: Affymetrix GeneChip Hybridization standard protocol

scan_protocol: Affymetrix GeneChip scan standard protocol

data_processing: Data were pre-processed by RMA method, filtered, and normalized using the GeneSpring GX v7.3.1 software (Agilent). Each trucut biopsy sample (basal moment) was normalized versus itself at the moment of the sacrifice (final moment) (Paired samples comparison). Compared data from experimental conditions are normalized versus array's base line mean considered for each case. This would be in the second line of the comparison (e.g. A vs B. Is normalized A and B respecting B). Thus, differentially expressed genes are presented as Fold Change values (Final vs Basal), for each breast tumor.

source_name: Breast tumor biopsy, DMBA, basal moment

label_protocol: Affymetrix's One-cycle target labeling (IVT Labeling kit from Affymetrix)

extract_protocol: Total RNA was extracted using a RNeasy Mini Kit from Qiagen, and later homogenized with QIAshredder (Quiagen) columns. Quality and quantity was assessed by agarose electrophoresis and spectrophotometric analysis (Absorbance 260/280 nm)

treatment_protocol: RNA was preserved using RNAlater (Quiagen) for 24h and frozen at -80ºC until RNA extraction.

tag: strain

value: Sprague-Dawley

tag: gender

value: female

value: 12 weeks

value: Breast tumor. Trucut Biopsy of breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene. Such biopsy was taken when tumor had 2cm3 volume.

tag: biopsy dimensions

tag: treatment

tag: sample

value: 37I1 (basal)


title: Xba_JA.2001

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 4, status: 1


title: Xba_JA.1563

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 103, status: 0


title: Xba_JA.245

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 22, status: 1


title: Xba_JA.120

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 96, status: 0

value: moderate


title: Ovarian Tumor, 349

description:
Gene expression data from tumor.
349

tag: tissue

value: papillary serous ovarian adenocarcinoma

tag: tumor stage

value: late


title: Xba_JA.248

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 29, status: 1


title: Xba_JA.243

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 10, status: 1


title: Xba_JA.2025

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 83, status: 0


title: Xba_JA.2038

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 102, status: 0


title: Xba_JA.1455

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 64, status: 0


title: Xba_JA.1222

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 7, status: 1


title: Xba_JA.941

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 87, status: 0


title: Xba_JA.1966

description: Gene copy data from breast cancer


title: Xba_JA.1967

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 80, status: 0


title: Xba_JA.282

description: Gene copy data from breast cancer


title: Xba_JA.746

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 123, status: 0


title: Xba_JA.1069

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 24, status: 1


title: Xba_JA.1938

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 90, status: 0


title: Xba_JA.1650

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 88, status: 0


title: Xba_JA.1501

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 74, status: 0


title: Xba_JA.1487

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 71, status: 0


title: Xba_JA.1524

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 68, status: 0


title: Xba_JA.1482

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 86, status: 0


title: Xba_JA.872

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 69, status: 1


title: Xba_JA.1568

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 115, status: 0


title: Xba_JA.1939

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 152, status: 0


title: Xba_JA.1593

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 127, status: 0


title: Xba_JA.1535

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 42, status: 1


title: Xba_JA.1821

description: Gene copy data from breast cancer


title: Xba_JA.076

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 136, status: 0


title: Xba_JA.1828

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 103, status: 0


title: Xba_JA.401

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 12, status: 1


title: Xba_JA.1571

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 76, status: 0


title: Xba_JA.1858

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 89, status: 0


title: Xba_JA.1853

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 63, status: 0


title: Xba_112

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 17, status: 1


title: Xba_216

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 13, status: 1


title: Xba_98

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 14, status: 1


title: Xba_JA.1412

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 128, status: 0


title: Xba_621

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 80, status: 0

value: good


title: Xba_100

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 39, status: 1


title: Xba_107

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 94, status: 0


title: Xba_111

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 98, status: 0


title: Xba_20

description: Gene copy data from breast cancer

value: Pos


title: Xba_61

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 11, status: 1


title: Xba_29

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 25, status: 1


title: Xba_37

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 7, status: 1


title: Xba_93

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 48, status: 1


title: Xba_118

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 95, status: 0


title: Xba_14

description: Gene copy data from breast cancer


title: Xba_121

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 23, status: 1


title: Xba_713

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 156, status: 0


title: Xba_862

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 87, status: 0


title: Xba_94

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 109, status: 0


title: Xba_3

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 101, status: 0


title: Xba_846

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 84, status: 0


title: Xba_JA.812

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 117, status: 0


title: Xba_90

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 108, status: 0


title: Xba_780

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 124, status: 0


title: Xba_782

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 148, status: 0


title: Xba_853

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 88, status: 0


title: Xba_806

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 85, status: 0


title: Xba_864

description: Gene copy data from breast cancer


title: Xba_879

description: Gene copy data from breast cancer


title: Xba_855

description: Gene copy data from breast cancer


title: Xba_833

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 97, status: 0


title: Xba_844

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 114, status: 0


title: Xba_839

description: Gene copy data from breast cancer


title: Xba_805

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 103, status: 0


title: Xba_637

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 54, status: 0


title: Xba_710

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 50, status: 0


title: Xba_777

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 153, status: 0


title: Xba_813

description: Gene copy data from breast cancer


title: Xba_894

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 123, status: 0


title: Xba_774

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 120, status: 0


title: Xba_857

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 98, status: 0


title: Xba_633

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 76, status: 0


title: Xba_287

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 79, status: 0


title: Xba_293

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 56, status: 0


title: Xba_275

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 105, status: 0


title: Xba_261

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 18, status: 1


title: Xba_215

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 6, status: 1


title: Xba_263

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 32, status: 1


title: Xba_268

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 82, status: 0


title: Xba_260

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 29, status: 1


title: Xba_255

description: Gene copy data from breast cancer


title: Xba_259

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 14, status: 1


title: Xba_267

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 59, status: 0


title: Xba_78

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 152, status: 0


title: Xba_136

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 25, status: 1


title: Xba_84

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 114, status: 0


title: Xba_65

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 9, status: 1


title: Xba_71

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 12, status: 1


title: Xba_74

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 90, status: 0


title: Xba_79

description: Gene copy data from breast cancer


title: Xba_64

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 134, status: 0


title: Xba_55

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 11, status: 1


title: Xba_38

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 133, status: 0


title: Xba_8

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 37, status: 1

value: Tx


title: Xba_7

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 106, status: 0


title: Xba_264

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 33, status: 1


title: Xba_265

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 66, status: 0


title: Xba_113

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 101, status: 0


title: Xba_707

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 98, status: 0


title: Xba_609

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 79, status: 0


title: Xba_647

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 105, status: 0


title: Xba_6

description: Gene copy data from breast cancer


title: Xba_204

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 24, status: 1


title: Xba_236

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 16, status: 1


title: Xba_292

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 58, status: 0


title: Xba_88

description: Gene copy data from breast cancer


title: Xba_728

description: Gene copy data from breast cancer


title: Xba_96

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 30, status: 1


title: Xba_233

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 5, status: 1


title: Xba_68

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 112, status: 0


title: Xba_737

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 123, status: 0


title: Xba_103

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 97, status: 0


title: Xba_213

description: Gene copy data from breast cancer


title: Xba_115

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 15, status: 1


title: Xba_54

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 144, status: 0


title: Xba_50

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 125, status: 0


title: Xba_48

description: Gene copy data from breast cancer


title: Xba_56

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 153, status: 0


title: Xba_106

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 40, status: 1


title: Xba_41

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 25, status: 1


title: Xba_104

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 11, status: 1


title: Xba_114

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 86, status: 0


title: Xba_139

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 111, status: 0


title: Xba_122

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 104, status: 0


title: Xba_32

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 84, status: 0


title: Xba_18

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 34, status: 1


title: Xba_108

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 28, status: 1


title: Xba_28

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 155, status: 0


title: Xba_105

description: Gene copy data from breast cancer

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