title: Pediatric brain tumor 6  - FF

source_name: Pediatric brain tumor 6  - FF


title: Pediatric brain tumor 1  - FFPE Infinium

status: Public on Apr 01 2017

type: genomic

city: Gothenburg

first: Helena

last: Carén

address: Medicinaregatan 1F

country: Sweden

institute: Gothenburg University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchips using standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Raw methylation data was normalized using ssNoob-normalization with the R minfi package.  CpG-sites with detection p-value >0.01 were regarded as failed and were assigned as missing.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Pediatric brain tumor 1  - FFPE Infinium

label_protocol: 500 ng FF DNA, 1 µg REPLI-g restored FFPE DNA and 1 µg unrestored FFPE DNA (for restoration with the Infinium kit after bisulfite conversion) was used for bisulfite conversion with the EZ DNA methylation kit (D5001, Zymo Research, Orange, CA) according to the manufacturer’s instructions using the alternative incubation conditions recommended for the Illumina Infinium methylation arrays. Successful conversion was verified by control PCR reactions with a primer set specific for bisulfite converted DNA and a primer set for unconverted DNA.

extract_protocol: DNA from FF tumours was extracted with the DNeasy Blood & Tissue Kit (69504, Qiagen, Hilden, Germany) according to the manufacturer’s instructions with the addition of lysing the samples with the QIAGEN TissueLyser. FFPE samples (1-3 years old) were sectioned and DNA was isolated using QIAamp DNA FFPE Tissue Kit (56404, Qiagen) according to manufacturer’s recommendations except de-waxing steps with Xylene was repeated twice and the tissue was digested overnight. DNA concentration was determined with the Qubit® Fluorometer (Life technologies). The quality of the DNA extracted from FFPE samples was assessed in triplicates with the real-time PCR-based Illumina FFPE QC kit (WG-321-1001, Illumina, Inc., San Diego, CA) according to the provided protocol.

tag: tissue

value: brain tumor

tag: dna restoration

value: All of eluate 1 of the bisulfite converted unrestored FFPE DNA was used for restoration with the Infinium HD FFPE DNA Restore Kit (WG-321-1002, Illumina) using the Infinium HD FFPE Restore Protocol supplied by the manufacturer.


title: L211

city: Yokohama

first: Taishi

last: Nakamura

address: 3-9, Fukuura, Kanazawa-ku

department: Department of Neurosurgery

country: Japan

institute: Yokohama city university

description: * Tumor (clinical diagnosis) WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues, Fourth Edition

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: Genome Studio software was used.  Beta values were obtained after background correction and normalization to internal controls.

label: Cy3, Cy5

source_name: primary CNS lymphoma

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA samples were isolated using Phenol-chloroform extraction protocol.

tag: public id

tag: pcnsl/ metastatic dlbcl in cns

value: PCNSL

tag: gender

value: Female

tag: age

tag: ebv infection


title: EOC Primary 8

type: RNA

city: Boston

first: Ilya

last: Korsunsky

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

country: USA

institute: Brigham and Women's Hospital

description:
Primary Ovarian Tissue, Subject 8
microRNA

data_processing:
The raw data were processed using Bioconductor htqpcr package, and normalized using Delta-CT with RNU44 and U6, followed by quantile normalization. MicroRNAs absent in more than 25% of samples were discarded.
Data were processed using the OpenArray Real-Time qPCR Analysis software and exported for analysis using the Applied Biosystems DataAssist Software

label: FAMTP

molecule: total RNA

source_name: Ovarian Tissue

label_protocol: As per manufacturer instruction

extract_protocol: As per manufacturer instruction

tag: survival time (months)

tag: survival status

value: DECEASED

tag: tumor stage

value: IIIb


title: L032

value: Male


title: L075


title: L036


title: L109


title: L037


title: EOC Primary 6

description:
Primary Ovarian Tissue, Subject 6
microRNA

value: LIVING

value: IIc


title: L058


title: Benign 13

description:
Benign Ovarian Mass, Subject 13
microRNA

value: ALIVE


title: EOC Primary 5

description:
Primary Ovarian Tissue, Subject 5
microRNA


title: EOC Primary 4

description:
Primary Ovarian Tissue, Subject 4
microRNA


title: EOC Primary 2

description:
Primary Ovarian Tissue, Subject 2
microRNA


title: EOC Primary 3

description:
Primary Ovarian Tissue, Subject 3
microRNA

value: IIIc


title: Benign 12

description:
Benign Ovarian Mass, Subject 12
microRNA


title: EOC Primary 1

description:
Primary Ovarian Tissue, Subject 1
microRNA


title: Benign 10

description:
Benign Ovarian Mass, Subject 10
microRNA


title: Benign 8

description:
Benign Ovarian Mass, Subject 8
microRNA


title: Benign 9

description:
Benign Ovarian Mass, Subject 9
microRNA


title: Benign 11

description:
Benign Ovarian Mass, Subject 11
microRNA


title: Benign 6

description:
Benign Ovarian Mass, Subject 6
microRNA


title: Benign 5

description:
Benign Ovarian Mass, Subject 5
microRNA


title: Benign 7

description:
Benign Ovarian Mass, Subject 7
microRNA


title: Benign 3

description:
Benign Ovarian Mass, Subject 3
microRNA


title: Pediatric brain tumor 7  - FF

source_name: Pediatric brain tumor 2  - FF


title: Benign 2

description:
Benign Ovarian Mass, Subject 2
microRNA


title: Pediatric brain tumor 4  - FF

source_name: Pediatric brain tumor 4  - FF


title: Benign 4

description:
Benign Ovarian Mass, Subject 4
microRNA


title: 7336

city: Rotterdam

first: Askar

last: Obulkasim

state: Zuid Holland

address: Wytemaweg 80

department: Pediatric Oncology

country: Netherlands

institute: ErasmusMC - Sophia Children's Hospital

description: Test

data_processing: Raw Ct-values were analyzed, summarized and exported per plate using SDS 2.3 (Applied Biosystems). Baseline was manually set at 0.15 for all plates. All data mining and analyses were done in R 2.11.1.4 Per card type, Ct-values were imported (readCtData) into a qPCR-set using the package HTqPCR.5 The average cycle threshold (Ct) value was used to calculate microRNA expression levels relative to the expression level of the small reference RNAs (mean of (mean) Mamm-U6, RNU44 and RNU48) by use of the comparative cycle time (ΔCt) method. Non detected miRNAs were substituted by an artificial low level of expression of -25.

label: SYBR Green

source_name: AML blast cells

label_protocol: MicroRNA expression profiling was performed by Taqman® Array MicroRNA Cards v2.0 (Applied Biosystems, Foster City, CA, USA).

growth_protocol: Viably frozen diagnostic bone marrow or peripheral blood samples from a selection of 90 de novo pediatric AML cases were provided by the Dutch Childhood Oncology Group (DCOG), the AML ‘Berlin-Frankfurt-Münster’ Study Group (AML-BFM-SG), the Czech Pediatric Hematology Group (CPH), and the St. Louis Hospital in Paris, France.

extract_protocol: Total cellular RNA was isolated using Trizol reagent (Invitrogen, Breda, The Netherlands) as previously described (Van Vlierberghe P, van Grotel M, Beverloo HB, Lee C, Helgason T, Buijs-Gladdines J, et al. The cryptic chromosomal deletion del(11)(p12p13) as a new activation mechanism of LMO2 in pediatric T-cell acute lymphoblastic leukemia. Blood 2006;108:3520–9.).

tag: disease state

value: de novo pediatric AML

tag: genetic aberration

value: M

tag: age(yrs)


title: 7332

description: Test


title: 7338

description: Test

value: F


title: 7339

description: Test


title: L026


title: Pediatric brain tumor 1  - FF

source_name: Pediatric brain tumor 1  - FF


title: 7331

description: Test


title: L111


title: Benign 1

description:
Benign Ovarian Mass, Subject 1
microRNA


title: 7330

description: Test

value: MLL


title: 7327

description: Test


title: 7326

description: Test


title: 7325

description: Test


title: E3 2h-2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: gene expression 2h after E3 treatment

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

organism: Mus musculus

source_name: ovariectomized uterus, E3 treated for 2h, replicate #2

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: RNA was isolated using Trizol reagent (Thermo Scientific). RNA was further purified using Qiagen RNAeasy RNA clean-up protocol with DNAse treatment

treatment_protocol: Ovarectomized CD-1 mice were injected with vehicle (100 ul saline) , E2 (250 ng in 100 ul saline) or E3 (250 ng in 100 ul saline). Uterine tissue was collected after 2 hours or 24 hours, frozen in liquid nitrogen and crushed

value: uterus

tag: strain


title: Pediatric brain tumor 12  - FFPE_REPLI-g

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation450K Beadchips using standard Illumina protocol

source_name: Pediatric brain tumor 12  - FFPE_REPLI-g

value: 1µg FFPE DNA was used for REPLI-g restoration, Thirwell 2010.


title: E3 24h-1

description: gene expression 24h after E3 treatment

source_name: ovariectomized uterus, E3 treated for 24h, replicate #1


title: E3 2h-3

description: gene expression 2h after E3 treatment

source_name: ovariectomized uterus, E3 treated for 2h, replicate #3


title: EOC Primary 7

description:
Primary Ovarian Tissue, Subject 7
microRNA


title: 7198

description: Test


title: Pediatric brain tumor 9  - FF

source_name: Pediatric brain tumor 9  - FF

value: brain tumor


title: E3 24h-2

description: gene expression 24h after E3 treatment

source_name: ovariectomized uterus, E3 treated for 24h, replicate #2


title: E2 24h-3

description: gene expression 24h after E2 treatment

source_name: ovariectomized uterus, E2 treated for 24h, replicate #3


title: 7194

description: Test


title: E3 24h-3

description: gene expression 24h after E3 treatment

source_name: ovariectomized uterus, E3 treated for 24h, replicate #3


title: E3 2h-1

description: gene expression 2h after E3 treatment

source_name: ovariectomized uterus, E3 treated for 2h, replicate #1


title: Pediatric brain tumor 7  - FF

source_name: Pediatric brain tumor 8  - FF


title: 7190

description: Test


title: 7183

description: Test


title: Pediatric brain tumor 6  - FF

source_name: Pediatric brain tumor 6  - FF


title: Pediatric brain tumor 8  - FF


title: Pediatric brain tumor 11  - FFPE_REPLI-g

source_name: Pediatric brain tumor 11  - FFPE_REPLI-g


title: E2 24h-2

description: gene expression 24h after E2 treatment

source_name: ovariectomized uterus, E2 treated for 24h, replicate #2


title: Pediatric brain tumor 4  - FF


title: 7171

description: Test


title: 7180

description: Test


title: E2 2h-3

description: gene expression 2h after E2 treatment

source_name: ovariectomized uterus, E2 treated for 2h, replicate #3


title: 7153

description: Test


title: Pediatric brain tumor 5  - FF

source_name: Pediatric brain tumor 5  - FF


title: E2 24h-1

description: gene expression 24h after E2 treatment

source_name: ovariectomized uterus, E2 treated for 24h, replicate #1


title: V-3

description: gene expression after vehicle (saline) treatment

source_name: ovariectomized uterus, vehicle treated, replicate #3


title: 672

description: Test

source_name: AML blast cells


title: E2 2h-2

description: gene expression 2h after E2 treatment

source_name: ovariectomized uterus, E2 treated for 2h, replicate #2


title: 7152

description: Test


title: E2 2h-1

description: gene expression 2h after E2 treatment

source_name: ovariectomized uterus, E2 treated for 2h, replicate #1


title: 5644

description: Test


title: 5603

description: Test


title: V-1

source_name: ovariectomized uterus, vehicle treated, replicate #1


title: Pediatric brain tumor 3  - FF

source_name: Pediatric brain tumor 3  - FF


title: genomic DNA from blood sample 144

city: Chicago

first: Wei

last: Zhang

state: IL

address: 680 N. Lake Shore Drive, Suite 1400

institute: Northwestern University

description:
KS144
whole blood DNA samples from existing Chicago, IL cohorts

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: the M-values (log2 ratio of the intensities of modified probe versus unmodified probe) (30) of CpG probes that passed quality control based on detection p-value across at least 95% of samples were summarized and batch corrected using COMBAT

source_name: blood sample 144

extract_protocol: For each selected sample, 800ng DNA was submitted for bisulfite conversion (EZ-96 DNA Methylation Kit, Zymo Research). Approximately 150 ng of bisulfite-converted DNA from each sample was used for profiling DNA methylation levels using the Illumina Infinium HumanMethylation 450 BeadChip (450K array)

tag: male

tag: black

tag: ards

value: whole blood


title: genomic DNA from blood sample 142

description:
KS142
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 142

tag: tissue


title: Pediatric brain tumor 2  - FF

source_name: Pediatric brain tumor 2  - FF


title: EA1051_02

city: Bunkyo-ku

first: Takuma

last: Nakatsuka

state: Tokyo

department: Gastroenterology

institute: The University of Tokyo

description: Gene expression data from Pik3caTg;Kdm3aKO mice precancerous liver

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using GeneChip 3’IVT Express Kit User Manual.

data_processing: The data were analyzed using MAS5 Statistical Algorithm according to Affymetrix default analysis settings.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: The mice were maintained on a regular chow diet and autoclaved water provided ad libitum in a temperature controlled environment with 12 h light and dark cycles.

extract_protocol: Total RNA was extracted from mouse liver tissue using NucleoSpin® RNAII (Takara).

treatment_protocol: The hepatocyte-specific Pik3ca transgenic mice and the Kdm3a knockout mice.

tag: genotype/variation

value: liver


title: 5237

description: Test


title: EA1051_01

description: Gene expression data from Pik3caTg;Kdm3aWT mice precancerous liver


title: 5236

description: Test


title: WT [WT6]

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

description: Esophagus from WT mice

hyb_protocol: Hybridization was performed according to manufacturer specifications.

scan_protocol: Scanning was performed according to manufacturer specifications.

data_processing: Raw data from .CEL files was read into R using the oligo Bioconductor package and processed using the rma function with default settings.

label_protocol: Labeling was performed according to manufacturer specifications.

growth_protocol: All mice were housed under ACUC guidelines

extract_protocol: TRIzol reagent was used for total RNA extraction

treatment_protocol: Kinase-dead IKKa knockin mice (KA mice) were treated with amphotericin B for three months.

tag: background strain

value: Esophagus

tag: genotype

value: wild type

tag: treatment


title: Pediatric brain tumor 1  - FF

source_name: Pediatric brain tumor 1  - FF


title: genomic DNA from blood sample 137

description:
KS137
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 137

tag: age


title: genomic DNA from blood sample 143

description:
KS143
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 143


title: genomic DNA from blood sample 141

description:
KS141
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 141


title: WT [WT5]

description: Esophagus from WT mice


title: genomic DNA from blood sample 139

description:
KS139
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 139


title: genomic DNA from blood sample 136

description:
KS136
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 136


title: 5179

description: Test

tag: gender


title: 5178

description: Test


title: WT [WT7]

description: Esophagus from WT mice


title: V-2

source_name: ovariectomized uterus, vehicle treated, replicate #2


title: knockin (untreated) [KA9]

description: ESCC from untreated KA mouse

value: ESCC

value: Kinase-dead IKKa knockin


title: 5175

description: Test


title: genomic DNA from blood sample 135

description:
KS135
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 135


title: genomic DNA from blood sample 140

description:
KS140
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 140


title: 5173

description: Test

source_name: AML blast cells


title: genomic DNA from blood sample 132

description:
KS132
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 132


title: genomic DNA from blood sample 130

description:
KS130
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 130


title: genomic DNA from blood sample 134

description:
KS134
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 134


title: knockin (Amphotericin B treated) [57375-KAB6]

description: Esophagus from Amphotericin B treated KA mouse

value: amphotericin B


title: knockin (Amphotericin B treated) [57372-KAB6]


title: 5166

description: Test


title: 5183

description: Test


title: genomic DNA from blood sample 131

description:
KS131
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 131


title: 5165

description: Test


title: 5170

description: Test


title: 5164

description: Test


title: genomic DNA from blood sample 133

description:
KS133
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 133


title: 5157

description: Test


title: WT2

description: Wild Type CHUK, replicate 2

hyb_protocol: Hybridization was performed according to manufacturer instructions.

scan_protocol: Scanning was performed according to manufacturer instructions.

data_processing: The data were RMA normalized using the Bioconductor affy package (v.1.39.4).

source_name: CHUK wild type

label_protocol: Labeling was performed according to manufacturer instructions.

extract_protocol: Total RNAs were extracted using TRIzol reagent according to the manufacturer?s instruction.

treatment_protocol: Thymuses were minced in cold RPMI-1640 containing 5% FBS. Thymic stromal debris were digested with 0.25% Trypsin-EDTA, and thymic epithelial cells were isolated and further purified by CD45 depletion.

tag: strain background

value: 5-6 weeks

value: CHUK wild type

tag: cell type

value: thymic epithelial cells


title: WT3

description: Wild Type CHUK, replicate 3


title: 5156

description: Test

value: de novo pediatric AML


title: genomic DNA from blood sample 128

description:
KS128
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 128


title: genomic DNA from blood sample 127

description:
KS127
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 127


title: WT1

description: Wild Type CHUK, replicate 1


title: knockin (untreated) [KA1]

description: ESCC from untreated KA mouse


title: genomic DNA from blood sample 138

description:
KS138
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 138


title: 5153

description: Test


title: 5154

description: Test

value: M


title: KA1

description: Mutant CHUK, replicate 1

source_name: CHUK mutant

value: CHUK mutant


title: 5152

description: Test

value: F


title: KA3

description: Mutant CHUK, replicate 3


title: knockin (Amphotericin B treated) [56587-KAB6]


title: genomic DNA from blood sample 129

description:
KS129
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 129


title: KA2

description: Mutant CHUK, replicate 2


title: 5147

description: Test


title: genomic DNA from blood sample 124

description:
KS124
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 124


title: 5145

description: Test


title: 5146

description: Test


title: 5144

description: Test


title: genomic DNA from blood sample 125

description:
KS125
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 125


title: 5143

description: Test


title: Pediatric brain tumor 10  - FFPE_REPLI-g

source_name: Pediatric brain tumor 10  - FFPE_REPLI-g

tag: dna restoration


title: genomic DNA from blood sample 126

description:
KS126
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 126


title: 5126

description: Test

tag: disease state


title: 5127

description: Test

tag: genetic aberration


title: 5120

description: Test

tag: age(yrs)


title: genomic DNA from blood sample 123

description:
KS123
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 123


title: genomic DNA from blood sample 120

description:
KS120
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 120


title: 5064

description: Test

source_name: AML blast cells


title: 5115

description: Test

value: MLL


title: genomic DNA from blood sample 119

description:
KS119
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 119


title: 5063

description: Test


title: genomic DNA from blood sample 118

description:
KS118
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 118


title: genomic DNA from blood sample 122

description:
KS122
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 122


title: 5148

description: Test


title: 5061

description: Test


title: 5036

description: Test


title: genomic DNA from blood sample 121

description:
KS121
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 121


title: 5062

description: Test


title: genomic DNA from blood sample 113

description:
KS113
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 113


title: 5033

description: Test


title: genomic DNA from blood sample 117

description:
KS117
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 117


title: 5023

description: Test


title: 5032

description: Test


title: genomic DNA from blood sample 114

description:
KS114
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 114


title: genomic DNA from blood sample 115

description:
KS115
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 115


title: genomic DNA from blood sample 112

description:
KS112
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 112


title: 5017

description: Test


title: 5013

description: Test


title: 5005

description: Test


title: 4936

description: Test


title: TH-MYCN_Tumor sphere replicate 7

city: Nagoya

first: Shoma

last: Tsubota

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Molecular Biology

institute: Nagoya University Graduate School of Medicine

description: Biological replicate 7 of 8. Primary spheres derived from the tumor tissue of TH-MYCN (hemizygote) mouse.

hyb_protocol: Agilent protocol

scan_protocol: Slides were scanned on an Agilent G600D Micoroarray Scanner System.

data_processing:
Scanned signals were analyzed using Agilent Genomic Workbench (7.0.4.0) software. Normalized log2 ratio (Cy5/Cy3) was calcurated using Preprocessing function in the software with default settings.
Normalized log2 ratio (Cy5/Cy3)

source_name: TH-MYCN derived tumor spheres

label_protocol: 500 ng of DNA was digested, labeled, purified, and hybridized to the SurePrint G3 Mouse CGH Microarray 4x180K (G4839A, Agilent Technologies) according to the manufacturers instructions (Agilent Technologies).

extract_protocol: Genomic DNAs from spheres and tissue samples were isolated using AllPrep DNA/RNA/miRNA Universal Kit (80224, QIAGEN).

value: TH-MYCN (hemizygote)

tag: strain

value: 10- to 15-week-old

value: Tumor tissue

source_name: TH-MYCN spleen

value: spleen


title: genomic DNA from blood sample 116

description:
KS116
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 116

tag: male

value: whole blood


title: 4905

description: Test


title: TH-MYCN_Tumor sphere replicate 6

description: Biological replicate 6 of 8. Primary spheres derived from the tumor tissue of TH-MYCN (hemizygote) mouse.


title: genomic DNA from blood sample 109

description:
KS109
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 109

tag: black


title: genomic DNA from blood sample 106

description:
KS106
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 106

tag: ards


title: 4806

description: Test


title: genomic DNA from blood sample 103

description:
KS103
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 103

tag: tissue


title: genomic DNA from blood sample 110

description:
KS110
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 110


title: genomic DNA from blood sample 111

description:
KS111
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 111


title: TH-MYCN_Tumor sphere replicate 5

description: Biological replicate 5 of 8. Primary spheres derived from the tumor tissue of TH-MYCN (hemizygote) mouse.


title: genomic DNA from blood sample 107

description:
KS107
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 107


title: 4770

description: Test

source_name: AML blast cells


title: genomic DNA from blood sample 102

description:
KS102
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 102


title: TH-MYCN_Tumor sphere replicate 8

description: Biological replicate 8 of 8. Primary spheres derived from the tumor tissue of TH-MYCN (hemizygote) mouse.


title: 4769

description: Test


title: genomic DNA from blood sample 100

description:
KS100
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 100


title: TH-MYCN_Tumor sphere replicate 4

description: Biological replicate 4 of 8. Primary spheres derived from the tumor tissue of TH-MYCN (hemizygote) mouse.


title: TH-MYCN_Tumor sphere replicate 3

description: Biological replicate 3 of 8. Primary spheres derived from the tumor tissue of TH-MYCN (hemizygote) mouse.


title: genomic DNA from blood sample 101

description:
KS101
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 101


title: TH-MYCN_Tumor sphere replicate 2

description: Biological replicate 2 of 8. Primary spheres derived from the tumor tissue of TH-MYCN (hemizygote) mouse.


title: 4747

description: Test


title: TH-MYCN_Tumor sphere replicate 1

description: Biological replicate 1 of 8. Primary spheres derived from the tumor tissue of TH-MYCN (hemizygote) mouse.


title: 4746

description: Test


title: 4745

description: Test


title: TH-MYCN_3w sphere replicate 8

description: Biological replicate 8 of 8. Spheres, passaged two times, derived from the superior mesenteric ganglion of 3-week-old TH-MYCN (hemizygote) mouse.

source_name: TH-MYCN derived 3w spheres

value: Superior mesenteric ganglion


title: 4742

description: Test


title: TH-MYCN_3w sphere replicate 7

description: Biological replicate 7 of 8. Spheres, passaged two times, derived from the superior mesenteric ganglion of 3-week-old TH-MYCN (hemizygote) mouse.


title: genomic DNA from blood sample 97

description:
KS097
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 97


title: genomic DNA from blood sample 105

description:
KS105
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 105


title: 4740

description: Test


title: genomic DNA from blood sample 108

description:
KS108
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 108


title: genomic DNA from blood sample 93

description:
KS093
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 93


title: TH-MYCN_3w sphere replicate 6

description: Biological replicate 6 of 8. Spheres, passaged two times, derived from the superior mesenteric ganglion of 3-week-old TH-MYCN (hemizygote) mouse.

source_name: TH-MYCN spleen


title: genomic DNA from blood sample 96

description:
KS096
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 96


title: 4736

description: Test


title: TH-MYCN_3w sphere replicate 5

description: Biological replicate 5 of 8. Spheres, passaged two times, derived from the superior mesenteric ganglion of 3-week-old TH-MYCN (hemizygote) mouse.


title: 4735

description: Test


title: genomic DNA from blood sample 94

description:
KS094
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 94


title: genomic DNA from blood sample 95

description:
KS095
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 95


title: genomic DNA from blood sample 98

description:
KS098
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 98


title: TH-MYCN_3w sphere replicate 4

description: Biological replicate 4 of 8. Spheres, passaged two times, derived from the superior mesenteric ganglion of 3-week-old TH-MYCN (hemizygote) mouse.


title: TH-MYCN_3w sphere replicate 3

description: Biological replicate 3 of 8. Spheres, passaged two times, derived from the superior mesenteric ganglion of 3-week-old TH-MYCN (hemizygote) mouse.


title: 4734

description: Test


title: 4731

description: Test


title: TH-MYCN_3w sphere replicate 1

description: Biological replicate 1 of 8. Spheres, passaged two times, derived from the superior mesenteric ganglion of 3-week-old TH-MYCN (hemizygote) mouse.


title: genomic DNA from blood sample 91

description:
KS091
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 91


title: genomic DNA from blood sample 87

description:
KS087
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 87


title: TH-MYCN_3w sphere replicate 2

description: Biological replicate 2 of 8. Spheres, passaged two times, derived from the superior mesenteric ganglion of 3-week-old TH-MYCN (hemizygote) mouse.


title: genomic DNA from blood sample 92

description:
KS092
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 92


title: genomic DNA from blood sample 99

description:
KS099
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 99


title: 4730

description: Test

source_name: AML blast cells


title: TH-MYCN_E13.5 sphere replicate 6

description: Biological replicate 6 of 6. Spheres, passaged two times, derived from the superior mesenteric ganglion of E13.5 TH-MYCN (hemizygote) mouse.

source_name: TH-MYCN derived E13.5 spheres

value: embyonic day 13.5

source_name: TH-MYCN head

value: whole head


title: genomic DNA from blood sample 88

description:
KS088
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 88


title: 4720

description: Test


title: genomic DNA from blood sample 90

description:
KS090
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 90


title: 4729

description: Test


title: genomic DNA from blood sample 89

description:
KS089
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 89


title: TH-MYCN_E13.5 sphere replicate 3

description: Biological replicate 3 of 6. Spheres, passaged three times, derived from the superior mesenteric ganglion of E13.5 TH-MYCN (hemizygote) mouse.


title: 4717

description: Test


title: 4714

description: Test


title: genomic DNA from blood sample 85

description:
KS085
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 85


title: TH-MYCN_E13.5 sphere replicate 1

description: Biological replicate 1 of 6. Spheres, passaged three times, derived from the superior mesenteric ganglion of E13.5 TH-MYCN (hemizygote) mouse.


title: TH-MYCN_E13.5 sphere replicate 5

description: Biological replicate 5 of 6. Spheres, passaged four times, derived from the superior mesenteric ganglion of E13.5 TH-MYCN (hemizygote) mouse.


title: genomic DNA from blood sample 81

description:
KS081
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 81


title: genomic DNA from blood sample 104

description:
KS104
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 104


title: 4712

description: Test


title: TH-MYCN_E13.5 sphere replicate 4

description: Biological replicate 4 of 6. Spheres, passaged two times, derived from the superior mesenteric ganglion of E13.5 TH-MYCN (hemizygote) mouse.


title: 4710

description: Test


title: LymphNode_Dog10_Resistant_rep3

city: Bunko-ku

first: Hirotaka

last: Tomiyasu

department: Department of Veterinary Internal Medicine

institute: the University of Tokyo

description:
SAMPLE 060
Gene expression of lymphoma tissue sample of Dog 10 at resistant phase

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >20.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 1x Agilent Fragmentation buffer and 2x Agilent Gene Expression Blocking Agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent Canine oligo DNA microarray ver.2 (4×44K) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed with Gene Expression Wash Buffer Kit, then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner G2505C using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 021193_D_F_20080808) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Canis lupus familiaris

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies) and One-Color RNA Spike-In Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was isolated from tumor cell samples using RNeasy Mini Kit or AllPrep DNA/RNA Mini Kit (QIAGEN) following the manufacturer's recommendations. The protocol includes an on-column DNase digestion.  RNA quantity and qualtiy were assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and RNA integrity numbers were confirmed as above 9.0.

treatment_protocol: Tumor cell samples derived from peripheral lymph nodes were obtained from 6 dogs with lymphoma at both drug-sensitive and drug-resistant phases by fine needle aspiration. The samples had been stored in RNA later (Qiagen, Hilden, Germany) at -20C until batch analysis.

tag: breed

value: Mix

tag: animal id

tag: Sex

value: Castrated male

value: lymph node

value: canine B-cell lymphoma

tag: cell phase

value: drug-resistant phase


title: genomic DNA from blood sample 86

description:
KS086
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 86

tag: age


title: 4728

description: Test

value: de novo pediatric AML

tag: gender

value: M


title: LymphNode_Dog10_Resistant_rep2

description:
SAMPLE 059
Gene expression of lymphoma tissue sample of Dog 10 at resistant phase


title: genomic DNA from blood sample 80

description:
KS080
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 80


title: genomic DNA from blood sample 79

description:
KS079
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 79


title: genomic DNA from blood sample 82

description:
KS082
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 82


title: genomic DNA from blood sample 78

description:
KS078
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 78


title: genomic DNA from blood sample 77

description:
KS077
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 77


title: 4708

description: Test

value: F


title: genomic DNA from blood sample 84

description:
KS084
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 84


title: LymphNode_Dog10_Resistant_rep1

description:
SAMPLE 058
Gene expression of lymphoma tissue sample of Dog 10 at resistant phase


title: 4718

description: Test


title: genomic DNA from blood sample 76

description:
KS076
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 76


title: 4704

description: Test

source_name: AML blast cells


title: 4703

description: Test


title: 4713

description: Test

value: MLL


title: 4700

description: Test


title: 4706

description: Test


title: genomic DNA from blood sample 74

description:
KS074
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 74


title: LymphNode_Dog10_Sensitive_rep3

description:
SAMPLE 057
Gene expression of lymphoma tissue sample of Dog 10 at sensitive phase

value: drug-sensitive phase


title: genomic DNA from blood sample 83

description:
KS083
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 83


title: LymphNode_Dog10_Sensitive_rep1

description:
SAMPLE 055
Gene expression of lymphoma tissue sample of Dog 10 at sensitive phase


title: LymphNode_Dog10_Sensitive_rep2

description:
SAMPLE 056
Gene expression of lymphoma tissue sample of Dog 10 at sensitive phase


title: 4698

description: Test


title: genomic DNA from blood sample 73

description:
KS073
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 73


title: 4567

description: Test


title: 4601

description: Test


title: LymphNode_Dog9_Resistant_rep3

description:
SAMPLE 054
Gene expression of lymphoma tissue sample of Dog 9 at resistant phase


title: LymphNode_Dog9_Resistant_rep2

description:
SAMPLE 053
Gene expression of lymphoma tissue sample of Dog 9 at resistant phase


title: 4561

description: Test


title: LymphNode_Dog9_Sensitive_rep3

description:
SAMPLE 051
Gene expression of lymphoma tissue sample of Dog 9 at sensitive phase


title: genomic DNA from blood sample 72

description:
KS072
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 72


title: LymphNode_Dog9_Resistant_rep1

description:
SAMPLE 052
Gene expression of lymphoma tissue sample of Dog 9 at resistant phase


title: 4555

description: Test


title: 4554

description: Test

value: other


title: genomic DNA from blood sample 70

description:
KS070
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 70


title: genomic DNA from blood sample 69

description:
KS069
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 69


title: LymphNode_Dog9_Sensitive_rep1

description:
SAMPLE 049
Gene expression of lymphoma tissue sample of Dog 9 at sensitive phase


title: LymphNode_Dog9_Sensitive_rep2

description:
SAMPLE 050
Gene expression of lymphoma tissue sample of Dog 9 at sensitive phase


title: TH-MYCN_E13.5 sphere replicate 2

description: Biological replicate 2 of 6. Spheres, passaged two times, derived from the superior mesenteric ganglion of E13.5 TH-MYCN (hemizygote) mouse.

source_name: TH-MYCN derived E13.5 spheres

tag: genotype

value: TH-MYCN (hemizygote)

source_name: TH-MYCN head


title: genomic DNA from blood sample 68

description:
KS068
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 68


title: genomic DNA from blood sample 71

description:
KS071
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 71


title: LymphNode_Dog8_Resistant_rep3

description:
SAMPLE 048
Gene expression of lymphoma tissue sample of Dog 8 at resistant phase

value: Jack Russell terrier

value: Spayed female

tag: cell type


title: 4533

description: Test


title: LymphNode_Dog8_Resistant_rep2

description:
SAMPLE 047
Gene expression of lymphoma tissue sample of Dog 8 at resistant phase


title: 4530

description: Test


title: genomic DNA from blood sample 65

description:
KS065
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 65

value: whole blood


title: 4531

description: Test


title: 4525

description: Test


title: genomic DNA from blood sample 67

description:
KS067
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 67


title: genomic DNA from blood sample 63

description:
KS063
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 63


title: 4536

description: Test


title: genomic DNA from blood sample 64

description:
KS064
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 64


title: genomic DNA from blood sample 75

description:
KS075
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 75


title: LymphNode_Dog8_Sensitive_rep3

description:
SAMPLE 045
Gene expression of lymphoma tissue sample of Dog 8 at sensitive phase


title: LymphNode_Dog8_Sensitive_rep2

description:
SAMPLE 044
Gene expression of lymphoma tissue sample of Dog 8 at sensitive phase


title: genomic DNA from blood sample 62

description:
KS062
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 62


title: 4508

description: Test

source_name: AML blast cells


title: LymphNode_Dog8_Resistant_rep1

description:
SAMPLE 046
Gene expression of lymphoma tissue sample of Dog 8 at resistant phase


title: 4501

description: Test


title: genomic DNA from blood sample 60

description:
KS060
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 60


title: 4451

description: Test


title: 4500

description: Test


title: LymphNode_Dog8_Sensitive_rep1

description:
SAMPLE 043
Gene expression of lymphoma tissue sample of Dog 8 at sensitive phase


title: genomic DNA from blood sample 66

description:
KS066
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 66


title: LymphNode_Dog7_Resistant_rep3

description:
SAMPLE 042
Gene expression of lymphoma tissue sample of Dog 7 at resistant phase

value: Welch Corgi Pembroke


title: 4450

description: Test


title: LymphNode_Dog7_Resistant_rep1

description:
SAMPLE 040
Gene expression of lymphoma tissue sample of Dog 7 at resistant phase


title: LymphNode_Dog7_Resistant_rep2

description:
SAMPLE 041
Gene expression of lymphoma tissue sample of Dog 7 at resistant phase


title: 4448

description: Test


title: 4445

description: Test


title: LymphNode_Dog7_Sensitive_rep2

description:
SAMPLE 038
Gene expression of lymphoma tissue sample of Dog 7 at sensitive phase


title: LymphNode_Dog7_Sensitive_rep3

description:
SAMPLE 039
Gene expression of lymphoma tissue sample of Dog 7 at sensitive phase


title: 4432

description: Test


title: genomic DNA from blood sample 59

description:
KS059
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 59


title: LymphNode_Dog7_Sensitive_rep1

description:
SAMPLE 037
Gene expression of lymphoma tissue sample of Dog 7 at sensitive phase


title: LymphNode_Dog6_Resistant_rep2

description:
SAMPLE 035
Gene expression of lymphoma tissue sample of Dog 6 at resistant phase

value: Miniature Dachshund


title: LymphNode_Dog6_Resistant_rep3

description:
SAMPLE 036
Gene expression of lymphoma tissue sample of Dog 6 at resistant phase


title: genomic DNA from blood sample 61

description:
KS061
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 61


title: genomic DNA from blood sample 55

description:
KS055
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 55


title: 4431

description: Test


title: 4444

description: Test


title: LymphNode_Dog6_Resistant_rep1

description:
SAMPLE 034
Gene expression of lymphoma tissue sample of Dog 6 at resistant phase


title: 4420

description: Test


title: genomic DNA from blood sample 54

description:
KS054
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 54


title: genomic DNA from blood sample 56

description:
KS056
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 56


title: LymphNode_Dog6_Sensitive_rep2

description:
SAMPLE 032
Gene expression of lymphoma tissue sample of Dog 6 at sensitive phase


title: genomic DNA from blood sample 57

description:
KS057
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 57


title: LymphNode_Dog6_Sensitive_rep1

description:
SAMPLE 031
Gene expression of lymphoma tissue sample of Dog 6 at sensitive phase


title: LymphNode_Dog5_Resistant_rep3

description:
SAMPLE 030
Gene expression of lymphoma tissue sample of Dog 5 at resistant phase

value: Shih Tzu

value: Female


title: genomic DNA from blood sample 52

description:
KS052
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 52


title: 4418

description: Test


title: LymphNode_Dog5_Resistant_rep2

description:
SAMPLE 029
Gene expression of lymphoma tissue sample of Dog 5 at resistant phase

value: lymph node


title: genomic DNA from blood sample 51

description:
KS051
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 51


title: 4409

description: Test


title: LymphNode_Dog5_Sensitive_rep3

description:
SAMPLE 027
Gene expression of lymphoma tissue sample of Dog 5 at sensitive phase

value: canine B-cell lymphoma


title: genomic DNA from blood sample 50

description:
KS050
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 50


title: 4425

description: Test


title: 4408

description: Test


title: 4403

description: Test


title: genomic DNA from blood sample 49

description:
KS049
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 49


title: genomic DNA from blood sample 53

description:
KS053
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 53


title: genomic DNA from blood sample 47

description:
KS047
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 47


title: genomic DNA from blood sample 45

description:
KS045
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 45


title: LymphNode_Dog6_Sensitive_rep3

description:
SAMPLE 033
Gene expression of lymphoma tissue sample of Dog 6 at sensitive phase

value: Castrated male


title: LymphNode_Dog5_Resistant_rep1

description:
SAMPLE 028
Gene expression of lymphoma tissue sample of Dog 5 at resistant phase

value: drug-resistant phase


title: LymphNode_Dog5_Sensitive_rep1

description:
SAMPLE 025
Gene expression of lymphoma tissue sample of Dog 5 at sensitive phase


title: genomic DNA from blood sample 46

description:
KS046
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 46


title: 4396

description: Test

source_name: AML blast cells

value: de novo pediatric AML


title: genomic DNA from blood sample 43

description:
KS043
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 43


title: 4416

description: Test

value: M


title: genomic DNA from blood sample 58

description:
KS058
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 58


title: 4391

description: Test

value: F


title: 4394

description: Test


title: genomic DNA from blood sample 44

description:
KS044
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 44


title: 4382

description: Test

value: MLL


title: genomic DNA from blood sample 41

description:
KS041
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 41


title: genomic DNA from blood sample 39

description:
KS039
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 39


title: 4372

description: Test


title: genomic DNA from blood sample 48

description:
KS048
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 48


title: 4370

description: Test


title: genomic DNA from blood sample 40

description:
KS040
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 40


title: 4217

description: Test


title: genomic DNA from blood sample 42

description:
KS042
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 42


title: 4216

description: Test


title: 4127

description: Test


title: genomic DNA from blood sample 38

description:
KS038
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 38


title: genomic DNA from blood sample 37

description:
KS037
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 37


title: 4092

description: Test


title: 4102

description: Test


title: 4096

description: Test


title: 4412

description: Test


title: 4090

description: Test


title: 4087

description: Test


title: 4079

description: Test


title: 3496

description: Test


title: 3494

description: Test


title: genomic DNA from blood sample 36

description:
KS036
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 36


title: LymphNode_Dog5_Sensitive_rep2

description:
SAMPLE 026
Gene expression of lymphoma tissue sample of Dog 5 at sensitive phase

value: drug-sensitive phase


title: 3492

description: Test


title: genomic DNA from blood sample 35

description:
KS035
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 35


title: 4084

description: Test


title: FA-2

city: Tempe

first: Ben

last: Readhead

state: AZ

address: 797 E. Tyler Street

institute: ASU-Banner Neurodegenerative Disease Research Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: We used the R software package, Limma, and the neqc function to perform background subtraction using the negative control probes, and quantile normalization using both positive and negative control probes.

label: Biotin

source_name: HaCat Cells

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

growth_protocol: HaCat cells grown in DMEM supplemented with 10 % Fetal Bovine Serum and 1 X Pen/Strep

extract_protocol: RNA was extracted using EZNA Total RNA Kit I exactly according to the manufacturer's instructions (Omega Bio-tek). The RNA quality and concentration was analyzed using Nanodrop.

treatment_protocol: One day prior to the experiment, cells were either pre-treated with 1 μM Rapamycin for 6 h followed by 1 μM of FA for additional 24 h (IB4 and IB8) or were treated with 1 μM of FA alone for 24 h (IB2 and IB6). Control cells used for comparison were either treated with DMSO (vehicle control. IB1 and IB5) or 1 μM of Rapamycin (IB3 and IB7).

tag: treatment

value: FA


title: genomic DNA from blood sample 31

description:
KS031
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 31


title: 3471

description: Test

tag: disease state


title: Rapamycin-2

value: Rapamycin


title: 3470

description: Test

tag: genetic aberration


title: Control-2

value: Untreated


title: genomic DNA from blood sample 32

description:
KS032
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 32

value: whole blood


title: FA.Rapamycin-1

value: FA+Rapamycin


title: genomic DNA from blood sample 34

description:
KS034
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 34


title: FA.Rapamycin-2


title: genomic DNA from blood sample 33

description:
KS033
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 33


title: Rapamycin-1


title: genomic DNA from blood sample 29

description:
KS029
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 29


title: genomic DNA from blood sample 26

description:
KS026
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 26


title: 3454

description: Test

source_name: AML blast cells

tag: age(yrs)


title: genomic DNA from blood sample 30

description:
KS030
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 30


title: genomic DNA from blood sample 27

description:
KS027
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 27


title: genomic DNA from blood sample 28

description:
KS028
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 28


title: 3451

description: Test


title: 3450

description: Test


title: FA-1


title: 3447

description: Test


title: genomic DNA from blood sample 24

description:
KS024
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 24


title: 3446

description: Test


title: genomic DNA from blood sample 23

description:
KS023
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 23


title: genomic DNA from blood sample 20

description:
KS020
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 20


title: 3443

description: Test


title: genomic DNA from blood sample 18

description:
KS018
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 18


title: KIND1 P159 D12

city: Mumbai

first: Deepa

last: Bhartiya

state: Maharashtra

address: Opposite Ramesh Bhavan, Jehangir Merwanji Street, Parel East

department: Stem Cell Biology

country: India

institute: National Institute for Research in Reproductive Health

description:
KIP159 D12
NKX2.5+ MESP1+

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing:
Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)
R 3.1.2 (www.r-project.org)

source_name: embryonic stem cell line

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

growth_protocol: KIND1 hES cell line is is a feeder-free monolayer human embryonic stem cell line. It is grown in Stempro hES SFM medium containing 8ng/ml of bFGF. The bFGF medium containing medium is chnged every day with a fresh medium.

extract_protocol: For microarray RNA was extracted by standard trizol method as per manufacturer's instructions. Briefly, hES cells were dislodged from culture plates and collected in 1ml of trizol reagent. Following 10-15 mins of cells in trizol, chloroform was added to the trzol containing cells. the suspension was vigorously shaken and incubated at RT for 2-5 mins. the clear aqueous layer seen post centrifugation at 12000g at 4 degree celsius was separated carefully into fresh tube. Chilled iso propanol was added and centrifuged at 12000g at 4 degree celsius. the tube was then stored at -80 degree celsius for overnight. next day isopropnol supernatent was separated from the cells by centrifugation and ice cold 75% ethanol was added to the pellet and centrifuged for 7 mins at 7500g at 4 degree celsius. following one more wash with 75% ethanol, the pellet was dried at room temperature. the dried pellet (not over dried) was dissolved in 0.1% DEPC water and this RNA sample was quantitated spectrophotometrically before submiiting for microarray studies.

treatment_protocol: For this study, the KIND1 ES cells were subjected to directed differentiation for obtaining cardiomyocytes as reported by our lab earlier (Pawing et al. 2013). The cells obtained at days days 12 and were harvested and subjected to microarray analysis along with day 0 undifferentiated cells.

tag: cell line

value: hES cell line KIND1

tag: passage no.

tag: protocol

value: cardiac directed differentiation protocol

tag: time

value: day 12

value: cardiovascular progenitors


title: genomic DNA from blood sample 22

description:
KS022
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 22

tag: male

tag: black

tag: ards

tag: tissue


title: genomic DNA from blood sample 21

description:
KS021
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 21


title: genomic DNA from blood sample 17

description:
KS017
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 17


title: 3442

description: Test


title: genomic DNA from blood sample 19

description:
KS019
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 19


title: KIND1 P151 D20

description:
KIP151 D20
CTNT+ alpha MHC+

value: day 20

value: beating cardiomyocytes


title: KIND1 P159 D20

description:
KIP159 D20
CTNT+ alpha MHC+


title: 3439

description: Test


title: genomic DNA from blood sample 14

description:
KS014
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 14


title: KIND1 P151 D12

description:
KIP151 D12
NKX2.5+ MESP1+


title: KIND1 P152 D0

description:
KIP152 D0
OCT4+ NANOG+ SOX2+

value: control

value: day 0

value: pluripotent hES cells


title: 3436

description: Test

value: de novo pediatric AML

value: F


title: genomic DNA from blood sample 15

description:
KS015
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 15


title: Control-1

source_name: HaCat Cells


title: 3435

description: Test

value: MLL

value: M


title: genomic DNA from blood sample 25

description:
KS025
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 25


title: genomic DNA from blood sample 16

description:
KS016
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 16


title: 3420

description: Test

source_name: AML blast cells


title: Patient 3 - Biopsy with Imiquimod and IFNgamma - Day 22 - repeat 2 - mAdbID:120033

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

description: mAdb experiment ID: 120033

hyb_protocol: Affymetrix Hybridization Protocol Other: Fragmented single-stranded sense DNA were hybridized to the Human GeneChip 1.0 ST array and stained on a Genechip Fluidics Station 450 (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

scan_protocol: Scanning Protocol Other: Arrays were scanned on a GeneChip Scanner 3000-7G (Affymetrix).

data_processing:
Data Processing Protocol
Calculation Method: Data were analyzed using Expression Console and Transcriptome Analysis Console Software. After Robust Multichip Average normalization, differentially expressed genes were identified by paired test with a significance cut off p <= 0.05 and fold change (linear) of < -2 or > 2 (Affymetrix).

label_protocol:
Affymetrix Labeling Protocol
Other: RNA was amplified using the Ambion WT expression kit (Life Technologies, Carlsbad, CA). Fragmented single-stranded sense DNA were terminally labeled with biotin according to the manufacturer's protocol.

extract_protocol:
Sample Extraction Protocol
Other: Cells from melanoma metastasis were lysed directly in QIAzol Lysis Reagent (Qiagen, Hilden, Germany) and RNA was extracted according to the manufacturer's protocol.

treatment_protocol:
Treatment type: small molecule
Agent: Imiquimod, IFNgamma
Treatment time: day 22
In-vivo treatment: Biopsies (incisional, core or excisional biopsies) of cutaneous or subcutaneous metastatic melanoma were obtained on day 22 (after 3 weeks of imiquimod treatment, and 1 week after the third vaccine).

value: skin

value: metastatic melanoma

tag: day


title: Patient 3 - Biopsy with Imiquimod and IFNgamma - Day 43 - repeat 2 - mAdbID:120035

description: mAdb experiment ID: 120035

treatment_protocol:
Treatment type: small molecule
Agent: Imiquimod, IFNgamma
Treatment time: day 43
In-vivo treatment: Biopsies (incisional, core or excisional biopsies) of cutaneous or subcutaneous metastatic melanoma were obtained on day 43 (after 6 weeks of imiquimod, and 1 week after the 4th vaccine).


title: Patient 3 - Biopsy with Imiquimod and IFNgamma - Day 43 - repeat 1 - mAdbID:120034

description: mAdb experiment ID: 120034


title: genomic DNA from blood sample 13

description:
KS013
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 13

tag: age

value: whole blood


title: 3418

description: Test

tag: gender


title: 3415

description: Test


title: Patient 3 - Pre-treatment Biopsy - Day 1 - mAdbID:120031

description: mAdb experiment ID: 120031

source_name: Pre-treatment Biopsy - Day 1

treatment_protocol:
Treatment time: day 1
In-vivo treatment: Biopsies (incisional, excisional, or core biopsies, and fine needle aspiration biopsies) of cutaneous metastatic melanoma were obtained on day 1 (baseline, no treatment).


title: 3434

description: Test


title: Patient 2 - Biopsy with Imiquimod and IFNgamma - Day 22 - repeat 2 - mAdbID:120030

description: mAdb experiment ID: 120030


title: genomic DNA from blood sample 11

description:
KS011
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 11


title: 3414

description: Test


title: Patient 3 - Biopsy with Imiquimod and IFNgamma - Day 22 - repeat 1 - mAdbID:120032

description: mAdb experiment ID: 120032


title: genomic DNA from blood sample 10

description:
KS010
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 10


title: genomic DNA from blood sample 12

description:
KS012
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 12


title: RPON_STAT_BR1

city: Dublin

first: Shane

last: Dillon

address: Kevin Street

department: School of Biological Sciences

country: Ireland

institute: Dublin Institute of Technology

description: biological replicate 1

hyb_protocol: Cy3 labeled ChIP DNA and Cy5 labeled control genomic DNAs were co-precipitated using standard sodium acetate/ethanol procedures and resuspended in hybridization buffer (Oxford Gene Technologies), and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridiized for 24 hours at 55oC in an Agilent hybiridization oven at 5 rpm. After hybridization, slides were washed according to instructions provided by Oxford Gene Technologies

scan_protocol: The microarray slides were scanned using an Agilent G2505C scanner. Cy3 and Cy5 images were acquired at 5 micron resolution. Scanned images were analyzed using Feature extraction software (Agilent).

data_processing: Median normalization of background subtracted Cy3/Cy5 ratios

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: ChIP DNA from SL1344 cells

label_protocol: Fluorescent labeling of DNA samples were carried out using the BioPrime Random Labeling kit (Invitrogen) as follows: 60 ul of 2.5 x random primer solution, x* ul DNA, and (70.5-x) ul sterile water were heated at 100oC for 10 minutes, snap chilled on ice and following were then added – 15 ul dNTP mix (1mM dCTP, 2mM dGTP, dTTP, dATP), 1.5 ul 1 mM Cy3/Cy5 labeled dCTP (GE healthcare) and 3 ul Klenow fragment (40 U/ ul). *[20 ul of ChIP DNA and 300 ng of Input DNA were fluorescently labeled with Cy3 d-CTP and Cy5-dCTP respectively]. The Labeling reactions wereas carried out at 37 oC overnight and 15 ml of stop buffer added to terminate the reaction. Labeled DNAs were purified using G-50 columns (GE-healthcare), according to manufacturers instructions.

growth_protocol: SL1344 cells were inoculated 1:100 into 25 ml fresh Lennox Broth (LB) and grown at 37degrees celsius in a shaking waterbath until OD600 2.0

extract_protocol: 25 ml of culture were harvested and re-suspended in 50 ml of PBS.  DNA-protein interactions were cross-linked by adding formaldehyde to a final concentration of 1% for 30 minutes. Glycine was then added to a final concentration of 0.125M to stop the cross-linking. The cells were pelleted, re-suspended in 0.6 ml of lysis buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA, 1% SDS, Roche protease inhibitor cocktail). 1.4 ml of IP dilution buffer (20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.01% SDS, Roche protease inhibitor cocktail) was added and the chromatin was sonicated on ice in a 5ml tube to reduce the DNA length to an average size of approximately 500 bp using the Sanyo/MES Soniprep sonicator (8 bursts at an amplitude 10 microns for 30 seconds, with 1 minute cooling between bursts). 1.0 ml of IP dilution buffer was added to the chromatin, which was then pre-cleared by adding 50 ul of normal rabbit IgG for 1 hour at 4°C on a rotating wheel. 100 ul of homogeneous Protein G-agarose suspension was added to the pre-cleared chromatin and the samples were incubated for 3 hours at 4°C on a rotating wheel. The samples were centrifuged at 7500 rpm for 2 minutes at 4°C to pellet the protein G-agarose beads and the supernatant was used to set up various immunoprecipitation conditions in 2 ml microfuge tubes. An aliquot of 200 ul of chromatin was stored at -20°C to be used as input DNA. Experimental ChIP conditions – 1350 ul chromatin + 10 μl of mouse monoclonal antibodies from Neoclone (RNA polymerase RpoB (W0001), RpoD (W0004), RpoH (WP006), RpoE (WP007), RpoN (W0005). The samples were incubated at 4°C overnight on a rotating wheel. 50 μl of homogeneous protein G-agarose suspension was added to each sample and the samples were incubated at 4°C for at least 3 hours on a rotating wheel. The samples were centrifuged at 7,500 rpm for 2 minutes at 4°C to pellet the protein G-agarose beads. The supernatant was removed and the protein G-agarose beads were washed twice with 750 ul of cold IP wash buffer 1 (20 mM Tris-HCl pH 8.1, 50 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), once with 750 ul of cold IP wash buffer 2 (10 mM Tris-HCl pH 8.1, 250 mM LiCl, 1 mM EDTA, 1% NP-40, 1% deoxycholic acid) and twice with 750 ul of cold TE pH 8.0. DNA-protein-antibody complexes were eluted from the protein G-agarose beads by twice washing the beads with 225 ul of IP elution buffer (100 mM NaHCO3, 1% SDS) and both eluates were combined. 0.2 ul of RNase A (10 mg/ml) and NaCl (to a final concentration of 0.3 M) were added to each of the IP test and input samples and incubated at 65ºC for 6 hours to reverse the cross-links. 9 ul of Proteinase K (10 mg/ml) was then added to each sample and incubated at 45ºC for at least 3 hours. DNA was purified and recovered by performing a standard phenol-chloroform extraction, followed by ethanol precipitation with 5 ug of glycogen and 5 ug of yeast tRNA. The DNA pellets of the IP samples were re-suspended in 50 ul of sterile filtered water and 100 ul for the Input DNA samples

tag: strain

tag: antibody

value: RPON

tag: Stage

value: stationary

source_name: Input DNA from SL1344

value: none, Input DNA


title: 3411

description: Test

tag: disease state


title: RPOH_STAT_BR2

description: biological replicate 2

value: RPOH


title: genomic DNA from blood sample 9

description:
KS009
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 9


title: Patient 2 - Pre-treatment Biopsy - Day 1 - mAdbID:120028

description: mAdb experiment ID: 120028


title: KIND1 P151 D0

description:
KIP151 D0
OCT4+ NANOG+ SOX2+

source_name: embryonic stem cell line

value: hES cell line KIND1

tag: cell type


title: genomic DNA from blood sample 7

description:
KS007
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 7


title: RPON_STAT_BR2

description: biological replicate 2


title: RPOH_STAT_BR1

description: biological replicate 1


title: genomic DNA from blood sample 6

description:
KS006
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 6


title: 3398

description: Test

tag: genetic aberration

tag: age(yrs)


title: 3399

description: Test


title: 3400

description: Test


title: 3410

description: Test


title: genomic DNA from blood sample 8

description:
KS008
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 8


title: Patient 1 - Biopsy with Imiquimod and IFNgamma - Day 43 - mAdbID:120027

description: mAdb experiment ID: 120027


title: RPOE_STAT_BR2

description: biological replicate 2

value: RPOE


title: 325

description: Test


title: Patient 1 - Pre-treatment Biopsy - Day 1 - mAdbID:120025

description: mAdb experiment ID: 120025


title: genomic DNA from blood sample 5

description:
KS005
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 5


title: genomic DNA from blood sample 4

description:
KS004
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 4


title: 3433

description: Test


title: Patient 1 - Biopsy with Imiquimod and IFNgamma - Day 22 - mAdbID:120026

description: mAdb experiment ID: 120026


title: 3186

description: Test


title: RPOD_STAT_BR1

description: biological replicate 1

value: RPOD


title: TAZ-KD LEC, biological rep2

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

description: Gene expression data from TAZ-KD human intestinal LEC

hyb_protocol: Affymetrix Human Gene 1.0 ST arrays (Affymetrix, Santa Clara , CA, USA) were hybridized with 2.7μg of biotinylated target, at  45°C for 17 hours washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix).

data_processing: The data was corrected for batch effect with the COMBAT method, which adjusts for known batches using an empirical Bayes framework , and was normalized using Robust Multichip Average (method Bioconductor package  affy, R version 3.0.1).

source_name: Human intestinal lymphatic endothelial cells isolated from jejunum

label_protocol: For each sample, 100ng of total RNA were amplified using the WT sense strand Target Labelling kit (Affymetrix, Cat.no. 900223); 5.5μg of the resulting sense cDNA was fragmented by UDG (uracil DNA glycosylase) and APE 1 (apurinic/apyrimidic endonuclease 1) and biotin-labelled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip® WT Terminal labelling kit (Affymetrix Cat.no. 900671, Santa Clara, USA).

growth_protocol: Human intestinal lymphatic endothelial cells were isolated from jejunum as described (Norrmen et al, 2010, Blood). Cells were grown on plates coated with 0.5 µg/cm2 fibronectin (Roche) in EBM-2 complete medium (Lonza).

extract_protocol: Cells were collected 48h post-transfection with a 30-min trypsin treatment at 37°C, followed by trypsin inactivation by diluting 7x in complete medium. Cells were lysed in RLT buffer (Qiagen) and total RNA was extracted using the Qiagen RNeasy Micro Kit.

treatment_protocol: Cells were seeded at 30’000 cells/cm2 and transfected 18 hours later with 33 nM siRNA using Lipofectamine RNAiMAX (Invitrogen). A SMARTpool (ThermoScientific, ref.L-016083-00) comprising 4 different siRNAs, or a single independent siRNA (GGAUUCGAAUGCGCCAAGA, Ambion) were used to knockdown TAZ. AllStars Negative Control siRNA (Qiagen) was used as a control.  Cells were collected 6 hours post-transfection by trypsin-treatment, and seeded at confluency (50’000 cells/cm2) on chamber slides pre-coated with 3 µg/cm2 fibronectin.

value: intestinal lymphatic endothelial cells

tag: treatment

value: TAZ knockdown


title: RPOD_STAT_BR2

description: biological replicate 2


title: RPOE_STAT_BR1

description: biological replicate 1


title: TAZ-KD LEC, biological rep1


title: genomic DNA from blood sample 3

description:
KS003
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 3


title: 3165

description: Test

source_name: AML blast cells


title: RPON_EXP_BR1

description: biological replicate 1

growth_protocol: SL1344 cells were inoculated 1:100 into 25 ml fresh Lennox Broth (LB) and grown at 37degrees celsius in a shaking waterbath until OD600 0.2

value: exponential


title: RPON_EXP_BR2

description: biological replicate 2


title: control LEC, biological rep1

description: Gene expression data from control human intestinal LEC

value: control


title: 1732

description: Test

value: de novo pediatric AML


title: 1886

description: Test


title: 1583

description: Test

value: MLL


title: RPOH_EXP_BR2

description: biological replicate 2


title: 1311

description: Test

value: M


title: 2771

description: Test

value: F


title: control LEC, biological rep2


title: RPOH_EXP_BR1

description: biological replicate 1


title: RPOE_EXP_BR2

description: biological replicate 2


title: Patient 2 - Biopsy with Imiquimod and IFNgamma - Day 22 - repeat 1 - mAdbID:120029

description: mAdb experiment ID: 120029

value: skin

value: metastatic melanoma


title: CaP8 cell with stable PKCe expression, biological rep 2

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

hyb_protocol: Hybridization was done over Affymetrix GeneChip Mouse Gene 1.0 ST Array according to the standard protocols at the University of Pennsylvania Microarray Facility.

scan_protocol: Affymetrix Gene ChIP Scanner.

data_processing: The Robust Multichip Average algorithm was employed for background adjustment, quantile normalization and probe set values summarization. QC and normalization procedures in R/Bioconductor were carried out using the Simpleaffy package.

source_name: prostate epithelial cells

label_protocol: Total RNA was reversed transcribed to cDNA (GeneChip® Whole Transcript cDNA Synthesis and Amplification Kit, Affymetrix; Santa Clara, CA), fragmented and end labeled (GeneChip® WT Terminal Labelling Kit, Affymetrix) for further hybridization.

growth_protocol: Murine P8 and CaP8 prostate epithelial cells were kindly provided by Dr. Hong Wu (UCLA) and grown as described (Jiao et al., 2007; PMID:17616663)

extract_protocol: Total RNA for each sample were obtained using the miRNeasy kit (Qiagen; Valencia, CA). RNA quality was analyzed using Agilent Bioanalyzer Nano assay.

treatment_protocol: For the generation of stable cell lines, P2, P8, CaP2 and CaP8 cells were transduced with either PKCe or control (LacZ) lentivirus and subsequently were subjected to blasticidin selection for 10 days. Blasticidin-resistant P2-PKCe, P8-PKCe, CaP2-PKCe and CaP8-PKCe clones were isolated and screened for PKCe expression by Western blot.

tag: cell line


title: RPOD_EXP_BR2

description: biological replicate 2


title: genomic DNA from blood sample 2

description:
KS002
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 2

value: whole blood


title: CaP8 cell with stable PKCe expression, biological rep 3


title: P8 cell with stable PKCe expression, biological rep 3


title: CaP8 cell with stable PKCe expression, biological rep 1


title: RPOD_EXP_BR1

description: biological replicate 1


title: CaP8 parental cells, biological rep 2

description: CaP8 parental cells, biological rep 2


title: P8 cell with stable PKCe expression, biological rep 2


title: RNAP_STAT_BR1

description: biological replicate 1

value: RNAP

value: stationary


title: RNAP_STAT_BR2

description: biological replicate 2

value: none, Input DNA


title: CaP8 parental cells, biological rep 1

description: CaP8 parental cells, biological rep 1


title: RPOE_EXP_BR1

description: biological replicate 1


title: RNAP_EXP_BR2

description: biological replicate 2


title: P8 parental cells, biological rep 1

description: P8 parental cells, biological rep 1


title: P8 parental cells, biological rep 3

description: P8 parental cells, biological rep 3


title: monocyte-derived macrophage_Gal-3BP 2

city: Eggenfelden

first: Christian

middle: Albert

last: Gleissner

address: Simonsöder Allee 20

department: Cardiology

country: Germany

institute: Rottal-Inn Kliniken KU

description: SAMPLE 4

hyb_protocol: Hybridization is performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed once in High Temp Wash buffer (Illumina Inc.) at 55°C and then twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes (in between washed with ethanol at room temperature). After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals are developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays are dried and scanned.

scan_protocol: Microarray scanning was done using an iScan array scanner. Data extraction was done for all beads individually, and outliers are removed when > 2.5 MAD (median absolute deviation). All remaining data points are used for the calculation of the mean average signal for a given probe, and standard deviation for each probe was calculated.

data_processing: The analysis is done with R on the bead-level data which you can find in the raw data produced by the scanner. All analyses are done using the following mechanisms: 1) outlier removal (see below). 2) average values over beads are means (not median). 3) statistical tests are t-tests over all beads (e.g for one probeID over all beads of all samples of a group) in original scale (not log2 scale).    Calculation of GeneView data: The calculations are also done on the set of beads which belong to a given Gene Symbol (annotation column Symbol).       Outlier removal on bead level: Outliers are removed by taking only beads with an expression value > 20 before using the 2.5 MADs rule. The ProbeIDs expression value is than the mean of the remaining beads.    The remaining bead level lists of different length for each sample are randomly filled with NAs (NA=not available) and build the bead level matrix on which quantile normalization is performed.    MAD rule: mad = median absolute deviation, x = one bead level expression value of some specific probeID, Than: outliers are those x where abs((x-median)/mad) > 2.5    The analysis is done with R on the bead-level data which you can find in the raw data produced by the scanner. All analyses are done using the following mechanisms: 1) outlier removal (see below). 2) average values over beads are means (not median). 3) statistical tests are t-tests over all beads (e.g for one probeID over all beads of all samples of a group) in original scale (not log2 scale).    Calculation of GeneView data: The calculations are also done on the set of beads which belong to a given Gene Symbol (annotation column Symbol).       Outlier removal on bead level: Outliers are removed by taking only beads with an expression value > 20 before using the 2.5 MADs rule. The ProbeIDs expression value is than the mean of the remaining beads.    The remaining bead level lists of different length for each sample are randomly filled with NAs (NA=not available) and build the bead level matrix on which quantile normalization is performed.    MAD rule: mad = median absolute deviation, x = one bead level expression value of some specific probeID, Than: outliers are those x where abs((x-median)/mad) > 2.5    The analysis is done with R on the bead-level data which you can find in the raw data produced by the scanner. All analyses are done using the following mechanisms: 1) outlier removal (see below). 2) average values over beads are means (not median). 3) statistical tests are t-tests over all beads (e.g for one probeID over all beads of all samples of a group) in original scale (not log2 scale).    Calculation of GeneView data: The calculations are also done on the set of beads which belong to a given Gene Symbol (annotation column Symbol).       Outlier removal on bead level: Outliers are removed by taking only beads with an expression value > 20 before using the 2.5 MADs rule. The ProbeIDs expression value is than the mean of the remaining beads.    The remaining bead level lists of different length for each sample are randomly filled with NAs (NA=not available) and build the bead level matrix on which quantile normalization is performed.    MAD rule: mad = median absolute deviation, x = one bead level expression value of some specific probeID, Than: outliers are those x where abs((x-median)/mad) > 2.5

source_name: monocyte-derived macrophage_Gal-3BP

label_protocol: The laboratory work was done in the Genomics and Proteomics Core Facility at the German Cancer Research Center, Heidelberg, Germany (DKFZ). Biotin-labeled cRNA samples for hybridization on Illumina Human Sentrix-8 BeadChip arrays (Illumina, Inc.) were prepared according to Illumina's recommended sample labeling procedure based on the modified Eberwine protocol (Eberwine et al., 1992). In brief, 100 ng total RNA was used for complementary DNA (cDNA) synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA according to the Illumina® Total Prep™ RNA Amplification Kit (Life Technologies).  Biotin-16-UTP was purchased from Roche Applied Science, Penzberg, Germany. The cRNA was column purified according to TotalPrep RNA Amplification Kit, and eluted in 60 µl of water. Quality of cRNA was controlled using the RNA Nano Chip Assay on an Agilent 2100 Bioanalyzer and spectrophotometrically quantified (NanoDrop).

growth_protocol: Monocyte-derived macrophages were generated in serum-free media with MCSF as described previously (Cho HJ, Shashkin P, Gleissner CA, Dunson D, Jain N, Lee JK, et al. Induction of dendritic cell-like phenotype in macrophages during foam cell formation. Physiol Genomics. 2007;29:149-60; Gleissner CA, Shaked I, Little KM, Ley K. CXC chemokine ligand 4 induces a unique transcriptome in monocyte-derived macrophages. Journal of immunology. 2010;184:4810-8; Gleissner CA, Shaked I, Erbel C, Bockler D, Katus HA, Ley K. CXCL4 downregulates the atheroprotective hemoglobin receptor CD163 in human macrophages. Circ Res. 2010;106:203-11.)

extract_protocol: mRNA was isolated from cultured macrophages using the RNeasy Mini kit (Qiagen, Hilden, Germany).

treatment_protocol: Human monocyte-derived macrophages were treated with recombinant Gal-3BP (5 μg/mL) or control buffer for 48 hours.

value: Monocyte-derived macrophage

tag: treated with

value: recombinant Gal-3BP (5 μg/mL) for 48 hours.


title: P8 parental cells, biological rep 2

description: P8 parental cells, biological rep 2


title: CaP8 parental cells, biological rep 3

description: CaP8 parental cells, biological rep 3


title: P8 cell with stable PKCe expression, biological rep 1


title: RNAP_EXP_BR1

description: biological replicate 1


title: M2

city: Barcelona

first: Bruno

last: Campos

address: jordi girona, 18, 18

department: Environmental Chemistry

country: Spain

institute: IDAEA-CSIC

description: SAMPLE 20

hyb_protocol: according to manufacturer protocols Low input Quick Amp lebelling

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1-v1_91 and Grid:066414_D_F_20140506)to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Daphnia magna

source_name: MALE 1

growth_protocol: daphnias were cultured and grown according to Barata and Baird, 200

extract_protocol: Total RNA was extracted using Trizol according to Soetaert et al. 2007

treatment_protocol: no treatment was performed,

value: 16 days

tag: Sex

value: male

value: all body


title: monocyte-derived macrophage_Control 1

description: SAMPLE 1

source_name: monocyte-derived macrophage_Control

value: control buffer for 48 hours.


title: genomic DNA from blood sample 1

description:
KS001
whole blood DNA samples from existing Chicago, IL cohorts

source_name: blood sample 1

tag: male

tag: black


title: F33

description: SAMPLE 18

scan_protocol: according to manufacturer protocols Low input Quick Amp lebelling

source_name: FEMALE 3

value: 18 days

value: female

tag: tissue


title: monocyte-derived macrophage_Control 2

description: SAMPLE 2


title: monocyte-derived macrophage_Gal-3BP 1

description: SAMPLE 3


title: F32

description: SAMPLE 17

label_protocol: according to manufacturer protocols Low input Quick Amp lebelling


title: F31

description: SAMPLE 16


title: F23

description: SAMPLE 15

source_name: FEMALE 2


title: M1

description: SAMPLE 19


title: gcn5.100GLN_3

city: Neuherberg, Germany

last: Sieber

address: Ingolstädter Landstraße 1

department: Institute of Bioinformatics and Systems Biology

institute: Helmholtz Zentrum München

description: This sample is of Fusarium fujikuroi delta-gcn5 mutant grown in 60 mM Gln (100%) ICI medium. It is the third of three biological replicates for this condition in this experiment.

hyb_protocol: Hybridization of microarrays was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning of microarrays was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.

data_processing: Preprocessing steps including background correction, normalization and summarization of probe intensities were performed in employing the oligo R package (Carvalho 2010) and its implementation of the RMA algorithm (Irizarry et al., 2003)

organism: Fusarium fujikuroi IMI 58289

source_name: Fusarium fujikuroi, delta-gcn5 knock-out mutant, mycelium, growth medium: 60 mM Gln (100%), 3 days

label_protocol: Labeling was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.

growth_protocol: Strains were grown for 2.5 days in Darken medium and subsequently an aliquot of 500 µL was transferred to liquid ICI medium with either 6 mM or 60 mM glutamine and grown for additional three days on a rotary shaker (180 rpm) at 28 °C in darkness.

extract_protocol: Total RNA was extracted using the TRI Reagent (Sigma-Aldrich, Steinheim, Germany)with a final clean-up using the NucleoSpin® RNA Clean-up Kit (Macherey Nagel, Düren, Germany) and DNA was removed using DNAse I (Roche Diagnostics GmbH, Mannheim, Germany). RNA quality and concentration was measured with an Bioanalyzer (Agilent Technologies Deutschland, Böblingen, Germany).

treatment_protocol: Mycelium was harvested after 72h, directly frozen with liquid nitrogen and lyophilized prior to RNA extraction.

tag: genotype/variation


title: gcn5.100GLN_2

description: This sample is of Fusarium fujikuroi delta-gcn5 mutant grown in 60 mM Gln (100%) ICI medium. It is the second of three biological replicates for this condition in this experiment.


title: gcn5.100GLN_1

description: This sample is of Fusarium fujikuroi delta-gcn5 mutant grown in 60 mM Gln (100%) ICI medium. It is the first of three biological replicates for this condition in this experiment.


title: F22

description: SAMPLE 14

tag: age


title: Panc-1ER_10nM beta-estradiol (E2)_24hrs

city: Aichi

first: Shingo

last: Inaguma

address: Nagakute

department: Department of Pathology and Promoting Center for Clinical Research

institute: Aichi Medical University School of Medicine

description: Panc-1ER E2 treatment

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x GEx Hybridization buffer HI-RPM (Agilent) was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays 4x44k (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then rinsed with Acetonitrile for cleaning up and drying.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (protocol GE1-v5_91_0806 and Grid: 014850_D_20060725) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Panc-1ER, 10nM beta-estradiol (E2), 24hrs

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were maintained in DMEM containing 10% of activated-charcoal treated FBS.

extract_protocol: QIAGEN RNeasy mini kit was used.

treatment_protocol: 10 nM of beta-estradiol (E2) was added to the medium.

value: Panc-1ER (derived from pancreatic cancer cell line Panc-1)

tag: agent

tag: time

value: 24 hrs


title: Panc-1GLI1ER_10nM beta-estradiol (E2)_24hrs

description: Panc-1GLI1ER E2 treatment

source_name: Panc-1GLI1ER, 10nM beta-estradiol (E2), 24hrs.

value: Panc-1GLI1ER (derived from pancreatic cancer cell line Panc-1)


title: gcn5.10GLN_2

description: This sample is of Fusarium fujikuroi delta-gcn5 mutant grown in 6 mM Gln (10%) ICI medium. It is the second of three biological replicates for this condition in this experiment.

source_name: Fusarium fujikuroi, delta-gcn5 knock-out mutant, mycelium, growth medium: 6 mM Gln (10%), 3 days


title: PC3ER_10nM beta-estradiol (E2)_3hrs

description: PC3ER E2 treatment

source_name: PC3ER, 10nM beta-estradiol (E2), 3hrs

value: PC3ER (derived from prostate cancer cell line PC3)

value: 3 hrs


title: F21

description: SAMPLE 13


title: gcn5.10GLN_1

description: This sample is of Fusarium fujikuroi delta-gcn5 mutant grown in 6 mM Gln (10%) ICI medium. It is the first of three biological replicates for this condition in this experiment.


title: wt.100GLN_3

description: This sample is of Fusarium fujikuroi wild-type IMI58289 grown in 60 mM Gln (100%) ICI medium. It is the third of three biological replicates for this condition in this experiment.

source_name: Fusarium fujikuroi, wild-type IMI58289, mycelium, growth medium: 60 mM Gln (100%), 3 days

value: Wild-type


title: PC3ER_0hrs (control)

description: PC3ER control

source_name: PC3ER, 0hrs

value: control

value: 0 hrs


title: PC3GLI1ER_10nM beta-estradiol (E2)_24hrs

description: PC3GLI1ER E2 treatment

source_name: PC3GLI1ER, 10nM beta-estradiol (E2), 24hrs.

value: PC3GLI1ER (derived from prostate cancer cell line PC3)


title: PC3GLI1ER_10nM beta-estradiol (E2)_3hrs

description: PC3GLI1ER E2 treatment

source_name: PC3GLI1ER, 10nM beta-estradiol (E2), 3hrs.


title: wt.100GLN_1

description: This sample is of Fusarium fujikuroi wild-type IMI58289 grown in 60 mM Gln (100%) ICI medium. It is the first of three biological replicates for this condition in this experiment.


title: wt.100GLN_2

description: This sample is of Fusarium fujikuroi wild-type IMI58289 grown in 60 mM Gln (100%) ICI medium. It is the second of three biological replicates for this condition in this experiment.


title: PC3ER_10nM beta-estradiol (E2)_24hrs

description: PC3ER E2 treatment

source_name: PC3ER, 10nM beta-estradiol (E2), 24hrs


title: PC3GLI1ER_0hrs (control)

description: PC3GLI1ER control

source_name: PC3GLI1ER, 0hrs


title: wt.10GLN_2

description: This sample is of Fusarium fujikuroi wild-type IMI58289 grown in 6 mM Gln (10%) ICI medium. It is the second of three biological replicates for this condition in this experiment.

source_name: Fusarium fujikuroi, wild-type IMI58289, mycelium, growth medium: 6 mM Gln (10%), 3 days


title: F13

description: SAMPLE 12

source_name: FEMALE 1

value: 15 days


title: wt.10GLN_1

description: This sample is of Fusarium fujikuroi wild-type IMI58289 grown in 6 mM Gln (10%) ICI medium. It is the first of three biological replicates for this condition in this experiment.


title: F11

description: SAMPLE 10


title: wt.10GLN_3

description: This sample is of Fusarium fujikuroi wild-type IMI58289 grown in 6 mM Gln (10%) ICI medium. It is the third of three biological replicates for this condition in this experiment.


title: E33

description: SAMPLE 6

source_name: EGGS 3

value: 60h embryo development


title: JUV2

description: SAMPLE 8

source_name: JUV

value: 4 days


title: JUV1

description: SAMPLE 7


title: E32

description: SAMPLE 5


title: JUV3

description: SAMPLE 9


title: F12

description: SAMPLE 11


title: gcn5.10GLN_3

description: This sample is of Fusarium fujikuroi delta-gcn5 mutant grown in 6 mM Gln (10%) ICI medium. It is the third of three biological replicates for this condition in this experiment.


title: E11

description: SAMPLE 1

source_name: EGGS 1

value: <12h embryo development


title: E31

description: SAMPLE 4

value: all body


title: E13

description: SAMPLE 3


title: E12

description: SAMPLE 2


title: reference male mouse1/ 0GyG6

status: Public on Nov 17 2016

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

institute: Institute for Environmental Science

description: 0GyG6 Cy3

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8.

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing:
Agilent Genomic Workbench Software (v 7.0.) was used and performed FuzzyZero correction. Agilent Feature Extraction Software (version 10.7.1.1) also performed the following normalization.
The log ratio i is the measure of differential expression between the red and green channels for every probe i: LogRatio = Log2 (ProcessedSignalr/ProcessedSignalg) where ProcessedSignalr and ProcessedSignalg are signals post dye normalization and post surrogate processing in the red and green channels, respectively. The dye-normalized signal is calculated by multiplying the background-subtracted signal by the dye normalization factor: DyeNormSignal = (BGSubSignal/MultDetrendSignal) x DNF DNF: LinearDyeNormFactor The linear dye normalization method assumes that dye bias is not intensity-dependent and therefore takes a global approach to dye normalization. A linear dye normalization factor is computed per channel by setting the geometric mean of signal intensity of the normalization features equal to 1000.

source_name: reference male mouse1

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

tag: strain/background

tag: gender

value: male

value: tail

tag: sample type

value: reference

tag: generation

value: progeny


title: 0GyG5/ reference male mouse1

description: 0GyG5 Cy5

label_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8.


title: reference male mouse1/ 0GyG5

description: 0GyG5 Cy3


title: 0GyG1/ reference male mouse1

description: 0GyG1 Cy5


title: 0GyG2/ reference male mouse1

description: 0GyG2 Cy5


title: 0GyG4/ reference male mouse1

description: 0GyG4 Cy5


title: reference male mouse1/ 0GyG2

description: 0GyG2 Cy3


title: 0GyGF/ reference male mouse1

description: 0GyGF Cy5

value: female

value: parent