title: P-BC4-C-g107-pop-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2007-01-26 Scan Time : 10:02:59 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

value: ancestral hybrid strain

value: evolved hybrid strain


title: Hypoxia-HIF1A_Si6_b

status: Public on Feb 20 2017

type: RNA

city: Bethesda

first: Stacie

last: Loftus

address: 49 Convent Dr

country: USA

institute: National Human Genome Research Institute

hyb_protocol: Total RNA was reverse transcribed to obtain labeled cDNA. Labeled cDNA was hybridized to the chips. Chips were washed and stained using standard protocols for the Affymetrix Fluidics Station.

scan_protocol: Arrays were scanned using the Affymetrix Gene Chip Scanner 3000 and gene expression intensities were calculated using the Affymetrix GeneChip Command Console software (AGCC).

data_processing:
Raw probe intensities from the microarray hybridization were normalized and analyzed by implementing the robust multi-chip average (RMA) algorithm followed by log2 transformation using Partek Genomic Suite v6.6 software (Partek, Inc; St. Louis, MO).
Differentially expressed genes were identified by ANOVA using a false discovery rate adjusted p-value cutoff of 0.05 (Benjamini-Hochberg method).

label: biotin

molecule: total RNA

organism: Mus musculus

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

growth_protocol: According to guidelines from Bennett et al. 1987 (PMID 3102392), cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum (Gibco), 200 nM 12-O-tetradecanoylphorbol 13-acetate (Sigma-Aldrich, St Louis, MO, USA) and 200 pM cholera toxin (Sigma- Aldrich, St Louis, MO, USA) at 37°C.

extract_protocol: For RNA isolation, cells were lysed in Trizol reagent and RNA was isolated using RNAeasy Mini Kit (Qiagen) per manufacturer's instructions.

treatment_protocol: Normoxic - proliferative conditions were performed in an ambient oxygen-supplemented incubator with 10% CO2 at 37°C, providing ~21% oxygen. Hypoxia-treated cells were grown at 37°C in a hypoxic chamber supplied with 1% O2, 5% CO2, 94% N2 for 24 hrs.  For siHif1a KD cells si RNA's were transfected 24hr prior to Hypoxia treatment.

tag: strain

value: Cdkn2a tm1RDp/tm1RDp mice

tag: cell line

value: melan-Ink4a-Arf-1 (melan-a)

tag: cell type

value: immortalized melanocyte cell line


title: Normoxia_b

source_name: normoxia


title: Hypoxia-HIF1A_Si1_b


title: Hypoxia-HIF1A_SI6_c


title: Hypoxia_Ctrl_a


title: Hypoxia_NC_1a

source_name: hypoxia_negative control


title: Normoxia_a


title: Normoxia_c


title: Hypoxia-HIF1A_Si1_a


title: Hypoxia-HIF1A_Si6_a


title: 0GyTM/ reference male mouse11

status: Public on Feb 21 2017

type: genomic

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

country: Japan

institute: Institute for Environmental Science

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.

molecule: genomic DNA

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

tag: tissue

value: tail

source_name: reference male mouse11


title: Hypoxia_Ctrl_b


title: Hypoxia_NC_1b


title: Hypoxia-HIF1A_SI1_c


title: MN1~FLI1_M299 Replicate 1

city: Memphis

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

description:
Biological replicate 1 of 5: transduce human fusion gene MN1~FLI1
SJMMAMLM7011097_D1-MN1FLI1_M299

hyb_protocol: Hybridization was carried out in an Agilent oven at 65°C for 40 hours at 20 rpm; after hybridization, slides were washed sequentially according to manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1) with protocol CGH_105_Jan09 and LOWESS normalization.

source_name: non-leukemic  bone marrow

label_protocol: 1.5μg of genomic DNA was labeled using the Agilent ULS Labeling kit

growth_protocol: DNA was extracted from GFP+ leukemic bone marrow cells derived from wildtype or Ikzf1-altered mice

extract_protocol: Phenol-chloroform

tag: gender

value: mix male and female

value: bone morrow

source_name: transduce human fusion gene MN1~FLI1 mouse

value: female

tag: tranduced with

value: human fusion gene MN1~FLI1 mouse


title: Hypoxia_NC_1c


title: HOXB9_WG886 Replicate 1

description:
Biological replicate 1 of 2: transduce human gene HOXB9
SJMMAMLM7011102_D1-HOXB9_WG886

value: male

source_name: transduce human gene HOXB9 to mouse

value: human gene HOXB9


title: FLI1_WG972

description:
transduce human gene FLI1
SJMMAMLM7011106_D1-FLI1_WG972

source_name: transduce human gene FLI1 to mouse

value: human gene FLI1


title: MN1~FLI1_WG922 Replicate 4

description:
Biological replicate 4 of 5: transduce human fusion gene MN1~FLI1
SJMMAMLM7011100_D1-MN1FLI1_WG922


title: HOXB9_WG932 Replicate 2

description:
Biological replicate 2 of 2: transduce human gene HOXB9
SJMMAMLM7011103_D1-HOXB9_WG932


title: MN1~FLI1_WG890 Replicate 2

description:
Biological replicate 2 of 5: transduce human fusion gene MN1~FLI1
SJMMAMLM7011098_D1-MN1FLI1_WG890


title: MN1~FLI1_M298 Replicate 3

description:
Biological replicate 3 of 5: transduce human fusion gene MN1~FLI1
SJMMAMLM7011099_D1-MN1FLI1_M298


title: WT564-2

city: New York

first: Emily

last: Hsu

state: NY

address: 1130 St. Nicholas Ave.

department: ICG

institute: Columbia University

description: Gene expression data

hyb_protocol: The RNA was converted to cRNA probes, which were hybridized to Affymetrix 133A following the protocol of the manufacturer.

data_processing: After scanning, mRNA expression values were determined using Affymetrix GeneChip software version 5.0. Expression values for each probe set were first filtered for a minimal level of variation (1.5-fold variation from the experiment mean in at least six tumors) and for reliability (Affymetrix presence calls in at least five tumors). Genes that passed these criteria were subjected to nonsupervised clustering using the five-cluster K-means algorithm. For supervised analysis we labeled the cases as WT1 wild type or WT1-mutant. Starting with the probe sets that passed the initial criteria of variability and reliability, we asked for the genes that differed in their expression most strongly between these two groups of tumors, using the nonparametric Mann-Whitney U-test. Identical lists of the genes with the strongest differential expression were obtained when the genes were ranked using parametric tests. We used GeneSpring (Silicon Genetics, Redwood City, CA) for data analysis and for creating dendrograms.

label: Cy3, Cy6

organism: Homo sapiens

source_name: Class 2 human Wilms tumor

extract_protocol: Total RNA was prepared using Trizol reagent.

tag: genotype

value: Class 3


title: GATA2~HOXA9_WG909 Replicate 5

description:
Biological replicate 5 of 5: transduce human fusion gene GATA2~HOXA9
SJMMAMLM7011096_D1-GATA2HOXA9_WG909

source_name: transduce human fusion gene GATA2~HOXA9 mouse

value: human fusion gene GATA2~HOXA9 mouse


title: GATA2~HOXA9_M272 Replicate 3

description:
Biological replicate 3 of 5: transduce human fusion gene GATA2~HOXA9
SJMMAMLM7011094_D1-GATA2HOXA9_M272


title: WT3825

description: Gene expression data

scan_protocol: The RNA was converted to cRNA probes, which were hybridized to Affymetrix 133A following the protocol of the manufacturer.

label: Cy3, Cy5

value: Class 2


title: GATA2~HOXA9_WG874 Replicate 4

description:
Biological replicate 4 of 5: transduce human fusion gene GATA2~HOXA9
SJMMAMLM7011095_D1-GATA2HOXA9_WG874


title: Non-Tobacco_User_replicate_40

city: Winston-Salem

first: Gaddamanugu

middle: L

last: Prasad

state: NC

institute: RAI Services Company

hyb_protocol: Following fragmentation, cRNA was hybridized using SeqWright SOP LAB.58.15 according to Affymetrix protocols.  GeneChips were washed and stained in the Affymetrix Fluidics Station F450.

scan_protocol: The raw image was acquired by scanning the arrays using Affymetrix 7G Plus Scanner as per SeqWright SOPs LAB.58.16 and Multiple files were generated and exported by Affymetrix’s software Command console and Expression Console as per SeqWright SOP LAB.58.17.

data_processing: The Affymetrix .CEL files were imported and analyzed using Partek’s Genomics Suite software. All data were normalized using the Robust Multi-array Analysis expression statistical analysis (RMA).

label_protocol: One hundred ng of total RNA from each sample was used for double-stranded cDNA synthesis,using Affymetrix 3' IVT Express kit.

growth_protocol: PBMCs were isolated from the fresh blood collected from subjects by standard density gradient centrifugation by using Isolymph (CTL Scientific  Supply Corp., Deer Park, NY).

extract_protocol: The total RNA was isolated from frozen cell lysate using the Qiagen RNeasy Plus Mini kit (Qiagen Cat. No. 74134) as per SeqWright SOP LAB.50.16.

treatment_protocol: The three cohorts in this study were Cigarette Smokers (Smk), Moist snuff consumers (MSC) and Non-tobacco consumers (NTC).

tag: subject status

value: generally healthy

tag: age

tag: sample group

value: Peripheral blood mononuclear cells (PBMCs)


title: NIPBL~HOXB9_WG879 Replicate 2

description:
Biological replicate 2 of 5: transduce human fusion gene NIPBL~HOXB9
SJMMAMLM7011088_D1-NIPBLHOXB9_WG879

source_name: transduce human fusion gene NIPBL~HOXB9 mouse

value: human fusion gene NIPBL~HOXB9 mouse


title: TB3494

description: Gene expression data

label_protocol: The RNA was converted to cRNA probes, which were hybridized to Affymetrix 133A following the protocol of the manufacturer.


title: WT899A

description: Gene expression data

source_name: Class 1 human Wilms tumor

value: Class 1


title: MN1_WG936 Replicate 5

description:
Biological replicate 5 of 5: transduce human gene MN1
SJMMAMLM7011086_D1-MN1_WG936

source_name: transduce human gene MN1 to mouse

value: human gene MN1


title: MN1~FLI1_M297 Replicate 5

description:
Biological replicate 5 of 5: transduce human fusion gene MN1~FLI1
SJMMAMLM7011101_D1-MN1FLI1_M297


title: NIPBL~HOXB9_WG912 Replicate 4

description:
Biological replicate 4 of 5: transduce human fusion gene NIPBL~HOXB9
SJMMAMLM7011090_D1-NIPBLHOXB9_WG912


title: GATA2~HOXA9_WG808 Replicate 1

description:
Biological replicate 1 of 5: transduce human fusion gene GATA2~HOXA9
SJMMAMLM7011092_D1-GATA2HOXA9_WG808


title: MN1_WG937 Replicate 2

description:
Biological replicate 2 of 5: transduce human gene MN1
SJMMAMLM7011083_D1-MN1_WG937


title: NIPBL~HOXB9_WG911 Replicate 3

description:
Biological replicate 3 of 5: transduce human fusion gene NIPBL~HOXB9
SJMMAMLM7011089_D1-NIPBLHOXB9_WG911


title: MN1_WG955 Replicate 3

description:
Biological replicate 3 of 5: transduce human gene MN1
SJMMAMLM7011084_D1-MN1_WG955


title: WT3497

description: Gene expression data


title: WT3498

description: Gene expression data


title: MN1_WG934 Replicate 1

description:
Biological replicate 1 of 5: transduce human gene MN1
SJMMAMLM7011082_D1-MN1_WG934


title: Rptor-null Tfr, biological rep1

city: Chongqing

first: Lifan

last: Xu

address: 30 Gaotanyan Street

department: Institute of Immunology, PLA

country: China

institute: Third Military Medical University

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: Follicular regulatory T cells_CD4-Cre-Rptorfl/fl mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: All mouse experiments were performed in accordance with the guidelines of the Institutional Animal Care and Use Committees of the Third Military Medical University.

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

treatment_protocol: To isolate Tfr cells, total lymphocytes from WT and Rptor-/- mice at day 8 post OVA immunization were subjected to lineage depletion. The Lin- cells were then surface-stained with CD4, CD44, GITR,CD25 and CXCR5, followed by sorting with a FACSAriaII cell sorter at the core facility center of Third Military Medical University.Sorted cells were then lysed with TRIzol LS reagent.

tag: strain background

tag: genotype/variation

value: Rptor-/-

value: spleen

value: Follicular regulatory T cells


title: NIPBL~HOXB9_WG914 Replicate 5

description:
Biological replicate 5 of 5: transduce human fusion gene NIPBL~HOXB9
SJMMAMLM7011091_D1-NIPBLHOXB9_WG914

value: mix male and female

value: bone morrow


title: Hypoxia_Ctrl_c

value: Cdkn2a tm1RDp/tm1RDp mice

value: melan-Ink4a-Arf-1 (melan-a)

value: immortalized melanocyte cell line


title: Rptor-null Tfr, biological rep2


title: WT4729

description: Gene expression data


title: NIPBL~HOXB9_285 Replicate 1

description:
Biological replicate 1 of 5: transduce human fusion gene NIPBL~HOXB9
SJMMAMLM7011087_D1-NIPBLHOXB9_285

value: female


title: WT931

description: Gene expression data


title: WT Tfr

source_name: Follicular regulatory T cells_wild type mouse

value: wild type


title: MN1_WG938  Replicate 4

description:
Biological replicate 4 of 5: transduce human gene MN1
SJMMAMLM7011085_D1-MN1_WG938


title: WT3663

description: Gene expression data


title: WT3820

description: Gene expression data


title: OT-I Central memory T cells

city: Boston

first: Youdong

last: Pan

state: MA

address: 77 Avenue Louis Pasteur

department: Dermatology

institute: Harvard Medical School

description:
Gene expression data
102_2215B

hyb_protocol: Following fragmentation, 4.1 ug of cDNA were hybridized for 16 hr at 45 C on GeneChip Mouse 2.0 ST Array in an Affymetrix GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G running Affymetrix Gene Command Console ver 3.2.

data_processing: The data were analyzed with using Affymetrix Expression Console ver 1.3.0.187 using Analysis algorithm RMA.

source_name: OT-I central memory T cells were sorted from spleen of mice 30 days post infected with VACV-Ova

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 33.5 ng total RNA using amplification kit Nugen Ovation Pico WTA, Lot # 1408175A, followed by labeling 5 ug cDNA using kit Encore Biotin Module, Lot # 1409115-A.

growth_protocol: OT-I naïve WT or Fabp4/5 dKO T cells were sorted from naïve OT-I Thy1.1+ Rag1-/- mice and adoptively transferred into cognate recipient mice one day before infection

extract_protocol: RNA was extracted with an RNeasy Micro kit (74004; Qiagen). RNA quality and quantity was assessed with a Bioanalyzer 2100 (Agilent).

treatment_protocol: Mice was infected with 2 × 10^6 p.f.u. of VACV-Ova by skin scarification

tag: infection

value: VACV-Ova

tag: time

value: 30 days post VACV-Ova infection

value: OT-I central memory T cells


title: WT2071

description: Gene expression data


title: D-CC8-A-g160-pop-DNA

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

hyb_protocol: reference URL : http://dunham.gs.washington.edu/MDhomemadeDNA.pdf

scan_protocol: Pixel Size : 5 Scan Date : 2006-12-29 Scan Time : 15:00:19 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.1.0.10
Datafile type : GenePix Results 3
Image Origin : 0, 0

organism: Saccharomyces cerevisiae

extract_protocol:
Extracted molecule : Genomic DNA
Extraction method : Hoffman-Winston prep http://dunham.gs.washington.edu/UWyeastDNAprep.pdf

value: ancestral S. cerevisiae strain

value: evolved S. cerevisiae strain


title: TB3822

description: Gene expression data

value: Class 1


title: WT_ESC_Sample3

city: Seoul

first: DONG-MYUNG

last: SHIN

address: Pungnap-2 dong, Songpa-gu

department: Department of Biomedical Sciences

country: South Korea

institute: University of Ulsan College of Medicine

description: Gene expression data from Sirt1 wild-type ESCs

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip 3’ Mouse Genome 430 2.0 array (Affymetrix),according to manufacture mannual (GeneChip 3'IVT Expression Kit User Mannual, Affymetrix)

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 1.0 (Affymetrix)

data_processing: The CEL files for 6 cell samples (3 samples for each genotype ESC) were imported into Partek software Version 6.5 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization. A one-way ANOVA was set up for the different cell types with contrasts comparing Sirt1+/+ versus Sirt1-/- ESCs.

label: Biotin

source_name: Sirt1-wild-type ESC

label_protocol: 100 ng of total RNA isolated from Sirt1+/+ or Sirt1-/- ESCs were converted to cDNA, followed by biotin-labeled using GeneChip 3’ in vitro transcription (IVT) kit

growth_protocol: Wild-type and Sirt1 deficient murine R1 ESCs were grown in DMEM-high glucose medium supplemented with 2 mM L-glutamine, 20 mM HEPES, MEM non-essential amino-acid, penicillin/streptomycin solution, 0.1 mM beta-mercaptoethanol, 15% heat-inactivated FBS, and 100 IU/ml ESGRO/LIF.

extract_protocol: Total RNA from Sirt1+/+ or Sirt1-/- ESCs was isolated using the RNeasy Mini Kit (Qiagen Inc) including treatment of DNase I (Qiagen Inc).

treatment_protocol: Both ESC cells were maintained under 0.1% gelatin coated tissue culture dish


title: KO_ESC_Sample1

description: Gene expression data from Sirt1 knock-out ESCs

source_name: Sirt1-knock-out ESC


title: KO_ESC_Sample3


title: KO_ESC_Sample2


title: Abdominal_Sham_3

city: Kraków

first: Mateusz

last: Siedliński

address: Skarbowa 1

country: Poland

institute: Jagiellonian University Medical College

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were processed in R (v.3.0.2; packages lumi, limma). Data processing included variance stabilization and data normalization using robust spline normalization method implemented in the lumi package. Normalization was performed for each of the 3 tissue types separately.

source_name: abdominal aorta of normotensive mice (2 weeks infusion of Sham buffer)

label_protocol: Illumina® TotalPrep™ RNA Amplification Kit (Ambion, USA)

growth_protocol: SPF animal facility

extract_protocol: Two tissues of the same type and treatment status were pooled and RNA was isolated from such pools using RNeasy Microarray Tissue Mini Kit with Dnase I treatment (Qiagen, USA). Quality control was performed with Tapestation 2200 instrument (Agilent, USA).

treatment_protocol: Twelve-week old mice underwent either sham or Ang II (490 ng/min/kg s.c.) treatment for 14 days, via a surgically implanted osmotic minipump (Alzet Model 2002, Alzet Corporation, CA, USA). Sham treatment involved infusion of the vehicle for angiotensin II.

tag: sample type

value: male, 12 weeks of age, SPF animal facility

value: abdominal aorta


title: Abdominal_Sham_2


title: Abdominal_Sham_1


title: WT_ESC_Sample2


title: Abdominal_ANGII_2

source_name: abdominal aorta of hypertensive mice (2 weeks infusion of AngII at 490 ng/kg/min. rate)


title: Abdominal_ANGII_3


title: Mesenteric_Sham_5

source_name: 2nd and 3rd order branches of superior mesenteric artery of normotensive mice (2 weeks infusion of Sham buffer)


title: Mesenteric_Sham_4

value: 2nd and 3rd order branches of superior mesenteric artery


title: Thoracic_Sham_2

source_name: thoracic aorta of normotensive mice (2 weeks infusion of Sham buffer)

value: thoracic aorta


title: Thoracic_ANGII_3

source_name: thoracic aorta of hypertensive mice (2 weeks infusion of AngII at 490 ng/kg/min. rate)


title: Thoracic_ANGII_2


title: Thoracic_ANGII_1


title: WT_ESC_Sample1


title: Thoracic_Sham_3


title: Mesenteric_Sham_2


title: Abdominal_ANGII_1


title: Mesenteric_ANGII_6

source_name: 2nd and 3rd order branches of superior mesenteric artery of hypertensive mice (2 weeks infusion of AngII at 490 ng/kg/min. rate)


title: Mesenteric_ANGII_2


title: Mesenteric_ANGII_1


title: GATA2~HOXA9_M278 Replicate 2

description:
Biological replicate 2 of 5: transduce human fusion gene GATA2~HOXA9
SJMMAMLM7011093_D1-GATA2HOXA9_M278

source_name: non-leukemic  bone marrow

value: mix male and female

value: human fusion gene GATA2~HOXA9 mouse


title: Mesenteric_Sham_3


title: Mesenteric_Sham_1


title: Mesenteric_ANGII_3


title: Mesenteric_ANGII_5


title: 125 ADI sarcoma - resection

city: Rotterdam

first: Erik

last: Wiemer

address: Wytemaweg 80

department: Medical Oncology

country: Netherlands

institute: Erasmus University Medical Center

description: sarcoma - resection

data_processing: The expression of a specific miRNA in a sample was normalized to the median CT of all detectable miRNAs in that sample (ΔCT = CT miR-X – median CT all miRNAs in a sample). The normalized expression (ΔCT) was subsequently used to calculate the relative expression values (2^-ΔCT) for each specific miRNA. The normalized miRNA expression data were median centered to acquire relative expression values that were eventually used for clustering analyses (average linkage was used with uncentered correlation as similarity metric). The Mann-Whitney U test was used to identify significant miRNAs, miRNAs with a p<0.05 were considered significant.

label: FAM

source_name: Adipocytic sarcoma

label_protocol: MiRNA expression was determined using TaqMan® Low Density Array (TLDA) Human MicroRNA Cards v3.0 (Applied Biosystems) capable of detecting 756 distinct human miRNAs (annotation miRBase release 14). In brief:  two separate pools of cDNA were prepared from total RNA in a megaplex reverse transcription reaction  using Megaplex™ RT Primers Human Pools v3.0 and a TaqMan® microRNA Reverse Transcription kit (Applied Biosystems) as recommended by the manufacturer. The cDNA was subjected to a preamplification protocol using Megaplex™ PreAmp Primers Human Pools v3.0 (Applied Biosystems) together with the TaqMan® Universal PCR Master Mix No AmpErase® UNG (Applied Biosystems) according to the manufacturer’s protocol. The product of the preamplification was added to human microRNA A and B cards using TaqMan® Universal PCR Master Mix No AmpErase® UNG. The TLDA cards were analyzed using a 7900HT Fast Real-Time PCR system (Applied Biosystems).

extract_protocol: Total RNA was isolated from two 20 μm FFPE tumor sections using the RecoverAll™ Total Nucleic Acid Isolation kit (Ambion/Life Technologies) according to the recommendations of the manufacturer. RNA  quality and quantity were checked using a Nanodrop-1000 (Nanodrop Technologies).

treatment_protocol: From 65 patients, involved in the EORTC 62052 phase II clinical study (Schöffski, P. et al. (2011) Lancet Oncol 12, 1045-1052), and consenting to the translational research, archived formalin fixed paraffin embedded (FFPE) tumor tissue was collected from either the primary tumor or a metastatic lesion. The series included 21 leiomyosarcomas, 14 adipocytic sarcomas, 9 synovial sarcomas and 21 other sarcoma histotypes (see Supplemental Table S1 for a further specification of the latter group). The tumor samples were collected prior to starting the eribulin treatment and the diagnosis was confirmed by a reference pathologist. Before RNA isolation all tissue sections were examined to estimate the tumor cell percentage. In case of samples with <70% of tumor content a macrodissection was used to collect material. All patients participating in EORTC 62052 had advanced or metastatic STS of high or intermediate grade and were treated with eribulin mesylate at a starting dose of 1.4 mg/m2 administered as a 2 – 5 min intravenous infusion on days 1 and 8 of a 21-day cycle. The treatment was continued until disease progression or drug intolerance. A response to eribulin treatment was defined as either stable disease, partial or complete response at 12 weeks following start of treatment; the PFS rate at 12 weeks was the primary endpoint of the trial. For 12 patients no response data were available as they were not eligible (n=7) or not evaluable (n=5).

value: Adipocytic sarcoma

tag: response to eribulin

value: responder


title: 128 OTH sarcoma - resection

description: sarcoma - resection

source_name: Undifferentiated sarcoma NOS

value: Other sarcoma subtype

value: non-responder


title: 118 ADI sarcoma - resection

description: sarcoma - resection

value: not eligible/evaluable


title: kchip2 shRNA3

city: Columbus

first: Thomas

last: Hund

state: OH

address: 473 W 12th Ave

institute: Ohio State University

description: mRNA expression data (log2 scale) from isolated neonatal rat ventricular myocytes

hyb_protocol: The labeled RNA were hybridized for 16 hr at 48C on GeneChip miRNA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with ExpressionConsole version 1.4.1.46 using the Affymetrix  Gene Level - SST-RMA analysis with default settings and global scaling as normalization method to identify the log2 probe intensity values.

organism: Rattus norvegicus

source_name: isolated ventricular myocytes from neonatal rats (1-2 days old) that were treated with KChIP2 siRNA

label_protocol: Biotinylated RNA were prepared according to Affymetrix FlashTag Biotin HSR RNA Labeling Kit from 1 ug total RNA

growth_protocol: Rat neonatal ventricular myocytes were isolated 1-2 days after birth. Briefly, hearts were minced in HBSS, and tissue fragments were digested overnight with trypsin at 4 °C. Trypsinized fragments were treated repeatedly for short periods of time with collagenase at 37 °C followed by trituration. Dissociated cells were pre-plated for 2 hrs at 37 °C in DMEM supplemented with 5% fetal bovine serum (FBS) and penicillin/streptomycin. NRVMs were collected and replated with 1.5 x 10^6 cells per 35 mm dish in DMEM/5% FBS/penicillin/streptomycin with 0.1 mM bromodeoxyuridine (BrdU) to suppress fibroblast growth and maintained at 37 °C, 5% CO2. These conditions were maintained for 24-36 hrs,  after which control or KChIP2 shRNA was delivered by adenovirus. Cells were left an additional 48 hrs before collection.

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

treatment_protocol: Knockdown of KChIP2 was conducted by transducing with a viral shRRNA for KChIP2, or a non-targeting shRNA control. Media was changed with fresh DMEM/5% FBS/penicillin/sptreptomycin after 24 hrs and then cultured for an additional 24 hrs before collection for total RNA.

value: isolated cardiac ventricular myocytes

value: Sprague Dawley

value: neonatal (1-2 days old)


title: kchip2 shRNA2


title: 90 ADI sarcoma - resection

description: sarcoma - resection


title: 97 SYN sarcoma - resection

description: sarcoma - resection

source_name: Synovial sarcoma

value: Synovial sarcoma


title: 94 ADI sarcoma - resection

description: sarcoma - resection


title: 96 LMS sarcoma - resection

description: sarcoma - resection

source_name: Leiomyosarcoma

value: Leiomyosarcoma


title: 98 SYN sarcoma - resection

description: sarcoma - resection


title: control3

source_name: isolated ventricular myocytes from neonatal rats (1-2 days old) that were treated with control siRNA


title: control2


title: kchip2 shRNA1


title: control1


title: Mesenteric_ANGII_4


title: Thoracic_Sham_1


title: 111 ADI sarcoma - resection

description: sarcoma - resection


title: 103 ADI sarcoma - resection

description: sarcoma - resection


title: 113 ADI sarcoma - resection

description: sarcoma - resection


title: 85 LMS sarcoma - resection

description: sarcoma - resection


title: 115 ADI sarcoma - resection

description: sarcoma - resection


title: 82 OTH sarcoma - resection

description: sarcoma - resection


title: 84 SYN sarcoma - resection

description: sarcoma - resection


title: 78 OTH sarcoma - resection

description: sarcoma - resection

source_name: Epithelioid sarcoma


title: 77 OTH sarcoma - resection

description: sarcoma - resection

source_name: Sclerosing epithelioid fibrosarcoma


title: 73 LMS sarcoma - resection

description: sarcoma - resection


title: 72 LMS sarcoma - resection

description: sarcoma - resection


title: 68 LMS sarcoma - resection

description: sarcoma - resection


title: 63 SYN sarcoma - resection

description: sarcoma - resection


title: 76 LMS sarcoma - resection

description: sarcoma - resection


title: 61 LMS sarcoma - resection

description: sarcoma - resection


title: 65 SYN sarcoma - resection

description: sarcoma - resection


title: 56 LMS sarcoma - resection

description: sarcoma - resection


title: 59 ADI sarcoma - resection

description: sarcoma - resection


title: 52 SYN sarcoma - resection

description: sarcoma - resection


title: 55 OTH sarcoma - resection

description: sarcoma - resection


title: 53 OTH sarcoma - resection

description: sarcoma - resection

source_name: Gastrointestinal stromal tumor


title: 51 SYN sarcoma - resection

description: sarcoma - resection


title: hippocampal T4

city: Beijing

first: changwei

last: wei

address: 8 Gongren Tiyuchang Nanlu, Chaoyang District

department: Department of Anesthesiology

institute: Beijing Chao-Yang Hospital, Capital Medical University

description: mouse_POCD 4

hyb_protocol: The labled RNA were hybridized for 16 hr at 48C on Affymetrix miRNA Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with miRNA QCTool using Affymetrix default analysis settings and quantile as normalization method.

source_name: POCD hippocampal tissue

label_protocol: Briefly microfuge the 15μl of tailed RNA and place on ice; Add 4μl 5X FlashTag Ligation Mix Biotin; Add 2μl of T4 DNA Ligase (Vial 6). Mix gently (do not vortex) and microfuge; Incubate at room temperature for 30 minutes; Stop the reaction by adding 2.5μl Stop Solution; Mix and microfuge the 23.5μl of ligated sample. Remove 2μl of the biotin-labeled sample and proceed to the ELOSA QC Assay (Appendix A). It is acceptable to store the 2μl of biotin-labeled sample on ice for up to 6 hours, or at -20°C for up to 2 weeks, and run the ELOSA QC Assay at a convenient time. The remaining 21.5μl biotin-labeled sample may be stored on ice for up to 6 hours, or at -20°C for up to 2 weeks, prior to hybridization on Affymetrix GeneChip miRNA Arrays.

growth_protocol: The animals used in this study were C57BL/6 mice purchased from Beijing Vital River Laboratory Animal Technology Co., Ltd. (Beijing, China). The mice were male, aged 12–14 months, and weighed 25–35 g. The room temperature and humidity were controlled at 25°C and 55%, respectively. All mice were acclimated to the environment for 1 week prior to the initiation of the study.

extract_protocol: Total RNA was extracted from the POCD and control group hippocampal tissues using TRIzol (Invitrogen, Carlsbad, CA, USA) according to manufacturer’s instructions. Subsequently, total RNA was assessed by electrophoresis on a denaturing agarose gel and quantified by NanoDrop spectrophotometer (NanoDrop, USA).

treatment_protocol: Mice from the POCD group were experienced tibia fracture surgery, mice from the control group did not receive any prior treatment or surgery.

value: male

value: 12-14 months

value: Postoperative cognitive dysfunction (POCD)

value: bilateral hippocampal tissue


title: 49 OTH sarcoma - resection

description: sarcoma - resection


title: hippocampal T5

description: mouse_POCD 5


title: 50 SYN sarcoma - resection

description: sarcoma - resection


title: hippocampal C4

description: mouse_control 4

source_name: Control hippocampal tissue

value: control


title: hippocampal T3

description: mouse_POCD 3


title: hippocampal C2

description: mouse_control 2


title: hippocampal T2

description: mouse_POCD 2


title: WT3531

description: Gene expression data

source_name: Class 1 human Wilms tumor

value: Class 1


title: hippocampal T1

description: mouse_POCD 1


title: hippocampal C5

description: mouse_control 5


title: hippocampal C6

description: mouse_control 6


title: 45 LMS sarcoma - resection

description: sarcoma - resection


title: NRVM KChIP2 siRNA treated

description: miRNA expression data (log2 scale) from isolated neonatal rat ventricular myocytes

data_processing: The data were analyzed with ExpressionConsole version 1.4.1.46 using the Affymetrix  MicroRNA Arrays - RMA+DABG-Rat_only analysis with default settings and global scaling as normalization method to identify the log2 probe intensity values.

growth_protocol: Rat neonatal ventricular myocytes were isolated 1-2 days after birth. Briefly, hearts were minced in HBSS, and tissue fragments were digested overnight with trypsin at 4 °C. Trypsinized fragments were treated repeatedly for short periods of time with collagenase at 37 °C followed by trituration. Dissociated cells were pre-plated for 2 hrs at 37 °C in DMEM supplemented with 5% fetal bovine serum (FBS) and penicillin/streptomycin. NRVMs were collected and replated with 1.5 x 10^6 cells per 35 mm dish in DMEM/5% FBS/penicillin/streptomycin with 0.1 mM bromodeoxyuridine (BrdU) to suppress fibroblast growth and maintained at 37 °C, 5% CO2. These conditions were maintained for 24-36 hrs,  after which control or KChIP2 siRNA was delivered. Cells were left an additional 72 hrs before collection.

treatment_protocol: Knockdown of KChIP2 was conducted by transfecting with siRNA for KChIP2 (Ambion, Cat#: 4390771, ID: s132782), or a scrambled siRNA control (Ambion, Cat#: 4390843). 180 pmol of siRNA was transfected using 15 μL of Lipofectamine 2000 reagent according to the manufacturer’s instructions. Following the transfection period, media was changed to DMEM/5% FBS/penicillin/streptomycin. Cells were cultured for 72 hrs total before collection for total RNA, with a media change once after 48 hrs of culture.


title: 44 LMS sarcoma - resection

description: sarcoma - resection


title: hippocampal C3

description: mouse_control 3


title: 42 OTH sarcoma - resection

description: sarcoma - resection

source_name: Undifferentiated pleomorphic sarcoma (pleomorphic MFH)


title: 41 LMS sarcoma - resection

description: sarcoma - resection


title: 39 ADI sarcoma - resection

description: sarcoma - resection


title: 38 ADI sarcoma - resection

description: sarcoma - resection


title: 32 OTH sarcoma - resection

description: sarcoma - resection


title: 34 ADI sarcoma - resection

description: sarcoma - resection


title: 36 ADI sarcoma - resection

description: sarcoma - resection


title: 29 OTH sarcoma - resection

description: sarcoma - resection

source_name: Inflammatory myofibroblastic sarcoma


title: 37 LMS sarcoma - resection

description: sarcoma - resection


title: 33 LMS sarcoma - resection

description: sarcoma - resection


title: NRVM control siRNA treated


title: 47 SYN sarcoma - resection

description: sarcoma - resection


title: 43 ADI sarcoma - resection

description: sarcoma - resection


title: 28 LMS sarcoma - resection

description: sarcoma - resection


title: 26 OTH sarcoma - resection

description: sarcoma - resection


title: 27 OTH sarcoma - resection

description: sarcoma - resection


title: 24 LMS sarcoma - resection

description: sarcoma - resection


title: 19 LMS sarcoma - resection

description: sarcoma - resection


title: 25 OTH sarcoma - resection

description: sarcoma - resection


title: 23 OTH sarcoma - resection

description: sarcoma - resection

source_name: Malignant peripheral nerve sheath tumor


title: 17 OTH sarcoma - resection

description: sarcoma - resection


title: 15 OTH sarcoma - resection

description: sarcoma - resection

source_name: Haemangioendothelioma


title: 12 LMS sarcoma - resection

description: sarcoma - resection


title: 18 OTH sarcoma - resection

description: sarcoma - resection

source_name: Uterine adenosarcoma with heterologous elements


title: 11 LMS sarcoma - resection

description: sarcoma - resection


title: 10 OTH sarcoma - resection

description: sarcoma - resection

source_name: Rhabdomyosarcoma


title: 8 OTH sarcoma - resection

description: sarcoma - resection

source_name: Stromal sarcoma


title: MKI3111T

hyb_protocol: The RNA was converted to cRNA probes, which were hybridized to Murine Genome MOE430A GeneChips (Affymetrix, Santa Clara, CA) following the protocol of the manufacturer.

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G

data_processing: We asked for all transcripts that were induced or repressed in the tumor-bearing kidneys compared to the littermate control kidneys, requiring at least a 2-fold mean increase or decrease in expression and using ANOVA an FDR of p<.05 using the Benjamini-Hochberg correction for multiple comparisons.

source_name: Cultured fetal mouse kidney with tumors

label_protocol: IVT LABELING GENECHIP EXPRESSION 3'-AMP Kit (Affymetrix, 900449)

growth_protocol: Fetal kidneys were dissected at 10.5dpc, then grown in culture for 3-4 days.

extract_protocol: Total RNA from cultured mouse embryonic kidneys was prepared using Trizol reagent.

treatment_protocol: Pregnant mice were intraperitoneally injected with tamoxifen (2mg/40g body weight) at 10.5 dpc. After dissection, kidneys were grown on 12-well TranswellTM membranes saturated with  F12 medium/DMEM (1:1) containing 5ug/mL transferrin, 5ug/mL insulin and 5ng/mL selenium.

value: beta-catenin activated


title: MKI3016T


title: MKI3020T


title: MKI3110N

source_name: Normal cultured fetal mouse kidney

value: wild type


title: MKI3114T


title: MKI3109N


title: MKI3115N


title: 7 LMS sarcoma - resection

description: sarcoma - resection

source_name: Leiomyosarcoma


title: MKI3113T


title: MKI3017N


title: 4 OTH sarcoma - resection

description: sarcoma - resection

source_name: Malignant solitary fibrous tumor

value: responder


title: 6 LMS sarcoma - resection

description: sarcoma - resection


title: MKI3015T


title: MKI3018N


title: liver_8WK_female_rep6

status: Public on Feb 19 2017

city: Jefferson

first: Vikrant

last: Vijay

state: AR

address: 3900 NCTR Road

department: Division of Systems Biology

institute: US FDA National Center for Toxicological Research

description:
whole ground tissue homogenized
8WK-F6

hyb_protocol: Hybridizations were conducted accourding to manufacturer's protocol.

scan_protocol: Arrays were scanned using the Agilent High Resolution C Scanner according to manufacturer's protocols.

data_processing: A single file containing the raw intensities (gTotalGeneSignal) of miRNAs from all arrays was generated. An intensity value of 0.1 represent a placeholder indicating miRNA signal below the level of detection for the assay, equivalent to 'not expressed'. Intensity values of 0.1 were replaced by the global minimum intensity value (1.84) across all the arrays. This file containing the raw intensities of all arrays was used as the input file for further data pre-processing in SAS 9.3 to remove controls and target redundancy. Out of 15,744 array features, 2,204 features representing controls were removed, resulting in 13,540 features measuring sample miRNAs (677 unique miRNA × 20 replicates per miRNA). Redundant replicates (containing redundant values) were removed, resulting in a dataset containing 677 unique miRNAs. Next, those features which were not expressed (intensity = 1.84) in any of the arrays were discarded, leaving 314 unique features, which were expressed on at least one array. Raw intensity data for all arrays were transposed and transformed to log2 values, and normalization (75th percentile) was performed on the 314 miRNAs. To prevent generating false fold differences from placeholders, transformed 1.84 values were replaced by 0.012 (lowest transformed value among all samples with measured values). Statistical analysis was performed in SAS using a generalized linear model procedure (proc glm).  Model (RandomModelANOVA) and estimate statements were used to perform ANOVA and pairwise comparisons using least square method to measure the significance of group differences using log2 intensities as the dependent variable and age or sex as independent variables.  Significant age differences in miRNA expression were calculated separately for males and females.  Significant sex differences in miRNA expression were calculated at each age.  The ANOVA p-value and p-value from pairwise tests were adjusted to False Discovery Rate (FDR).  The magnitude of group differences was calculated as the difference of average log2 intensities; the anti-log of the resulting value was used as the fold-change value between groups.  When group absolute fold changes were greater than or equal to 1.5 and FDR for ANOVA as well as pairwise tests were significant (p < 0.05), miRNAs were determined to be differentially expressed by age. Differential expression by sex was determined using absolute fold changes greater than or equal to 1.5 between sexes of the same age and a pairwise t-test with FDR < 5%.

source_name: whole liver_8weeks_female

label_protocol: Single color (Cy3) Agilent Rat miRNA 8x15k microarrays and reagents were used according to manufacturer’s protocols using 100 nanograms of total RNA.

growth_protocol: Female Fischer 344 rats were obtained and housed under AAALAC-approved conditions with a 12-hr light/dark cycle (0600-1800).  Rats were housed two per cage in standard polycarbonate cages with hardwood chip bedding maintained at 23 degrees C with a relative humidity of ~50%

extract_protocol: Total RNA was isolated from ~30 mg of whole, homogenized, liver tissue of independent animals using Qiagen miRNeasy Mini Kit according to manufacturer’s protocol.  The yield of the extracted RNA was determined spectrophotometrically by measuring the optical density at 260 nm (Nanodrop-1000, Thermo Scientific, Wilmington, DE). The purity and quality of extracted RNA were evaluated using the RNA 6000 LabChip and Agilent 2100 Bioanalyzer. RNA samples with RNA integrity numbers (RINs) greater than 8.0 were used for microarray experiments with an average RIN of 8.3 for all samples.

treatment_protocol: No treatments

tag: Sex

value: female

value: 8 wks

value: whole liver


title: liver_8WK_male_rep1

description:
whole ground tissue homogenized
8WK-M1

source_name: whole liver_8weeks_male


title: FSH and T treated pubertal Sertoli cell samples

city: New Delhi

first: Sayon

last: Basu

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Immunology

description: cDNA probed on in situ oligonucleotide array

hyb_protocol: Samples were hybridized to Agilent Whole Human Genome Microarray Kit, 8x60K (Agilent-27114) using  Agilent’s In situ Hybridzation kit (Cat # 5184-3568) following manufacturers instruction.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.10.5.1.1).

data_processing:
Agilent Feature Extraction Software (v 10.5.1.1) was used for background  normalization.
Data analysis was done with Genespring Gx 11 using Percentile Shift normalization.
gProcessed signal indicates Dye normalized and background subtracted signal obtained from raw data file

organism: Macaca mulatta

source_name: Pubertal monkey Sertoli cell

label_protocol: Samples were labeled using the Agilent Quick-Amp labeling Kit following manufacturers instruction . Specific activity of labelled cRNA was checked using NanoDrop

growth_protocol: Infant sertoli cells were isolated from testis of infant male monkeys less than 3 months old. Juvenile, pre-pubertal male monkeys were implanted with indwelling catheter and given GnRH intermittently, 0.15 µg/min for 2 min every 3 h, for 4 to 5 weeks to induce puberty. Sertoli cells were isolated from testis of such pubertal animals.

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

treatment_protocol: in vtro sertoli cell cultures were treated with 100 nM Testosterone and 5ng/ml of FSH for 12 hrs.

value: 18-22 months treated with pulsatile GnRH for one month to induce puberty

value: testis

value: Primary sertoli cell culture

tag: treatment

value: FSH and Testosterone


title: 3 LMS sarcoma - resection

description: sarcoma - resection

value: Leiomyosarcoma


title: FSH and T treated infant Sertoli cell samples

source_name: Infant monkey sertoli cell


title: MKI3014N

tag: strain


title: liver_8WK_male_rep5

description:
whole ground tissue homogenized
8WK-M5

value: male


title: liver_8WK_male_rep4

description:
whole ground tissue homogenized
8WK-M4


title: liver_8WK_male_rep6

description:
whole ground tissue homogenized
8WK-M6


title: liver_8WK_male_rep2

description:
whole ground tissue homogenized
8WK-M2


title: 1 OTH sarcoma - resection

description: sarcoma - resection

source_name: Sclerosing epitheloid fibrosarcoma

value: Other sarcoma subtype


title: liver_8WK_female_rep4

description:
whole ground tissue homogenized
8WK-F4


title: liver_8WK_female_rep2

description:
whole ground tissue homogenized
8WK-F2


title: liver_78WK_male_rep5

description:
whole ground tissue homogenized
78WK-M5

source_name: whole liver_78weeks_male

value: 78 wks


title: liver_8WK_female_rep3

description:
whole ground tissue homogenized
8WK-F3


title: liver_78WK_male_rep6

description:
whole ground tissue homogenized
78WK-M6


title: liver_78WK_male_rep4

description:
whole ground tissue homogenized
78WK-M4


title: liver_78WK_male_rep2

description:
whole ground tissue homogenized
78WK-M2


title: liver_78WK_male_rep3

description:
whole ground tissue homogenized
78WK-M3


title: liver_78WK_female_rep4

description:
whole ground tissue homogenized
78WK-F4

source_name: whole liver_78weeks_female


title: liver_78WK_female_rep3

description:
whole ground tissue homogenized
78WK-F3


title: liver_78WK_female_rep2

description:
whole ground tissue homogenized
78WK-F2


title: liver_78WK_female_rep5

description:
whole ground tissue homogenized
78WK-F5


title: liver_6WK_male_rep5

description:
whole ground tissue homogenized
6WK-M5

source_name: whole liver_6weeks_male

value: 6 wks


title: liver_78WK_female_rep1

description:
whole ground tissue homogenized
78WK-F1


title: liver_6WK_male_rep4

description:
whole ground tissue homogenized
6WK-M4


title: liver_6WK_male_rep2

description:
whole ground tissue homogenized
6WK-M2


title: HUVEC_donor2_P18

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD Methylation Assay protocol.

scan_protocol: Standard Infinium HD Methylation Assay protocol

data_processing: Initial analysis was performed by the Genomestudio 2010.3 (Modul M Version 1.8.5). Data were normalized with internal controls according to Illumina´s standard procedures. Methylation level at each locus was calculated with the GenomeStudio Methylation module as beta-value (ranging from 0 to 1). The number of beads per feature varies between chips and beta-values were calculated as average of at least three technical replica.

label: Cy5 and Cy3

source_name: umbilical cord

growth_protocol: Human umbilical vein endothelial cells of three different donors (Lonza, Basel, Switzerland) were cultured in Endopan 3 medium (PAN-Biotech GmbH, Aidenbach, Germany) supplemented with 2% fetal bovine serum at 37° C in an atmosphere with 5% CO2. Cells were harvested by trypsinization when reaching 80% confluency and re-seeded in a density of 10,000 cells /cm2

extract_protocol: To isolate DNA of HUVECs the cells were permeabilized (15mM Tris/HCl ph7.6, 60mM KCl, 15mM NaCl, 4mM CaCl2, 300mM sucrose, 0.2% NP-40, 0.5mM beta-Mercaptoethanol), lysed (50mM Tris/HCl ph8.0, 20mM EDTA, 1% SDS) with addition of RNase A for 2h at 37°C and subsequent proteinase K digestion overnight at 37°C. DNA of HUVECs was then purified by phenol/chloroform extraction.

tag: donor

value: donor 2

tag: cell type

value: human umbilical vein endothelial cells

tag: passage

value: passage 18

value: 0 years


title: liver_6WK_female_rep6

description:
whole ground tissue homogenized
6WK-F6

source_name: whole liver_6weeks_female

tag: tissue


title: liver_6WK_male_rep3

description:
whole ground tissue homogenized
6WK-M3


title: liver_6WK_female_rep5

description:
whole ground tissue homogenized
6WK-F5


title: liver_8WK_female_rep5

description:
whole ground tissue homogenized
8WK-F5


title: liver_6WK_male_rep1

description:
whole ground tissue homogenized
6WK-M1


title: HUVEC_donor3_P13

label_protocol: Standard Infinium HD Methylation Assay protocol

value: donor 3

value: passage 13

tag: gender


title: HUVEC_donor1_P20

value: donor 1

value: passage 20


title: liver_5WK_female_rep3

description:
whole ground tissue homogenized
5WK-F3

source_name: whole liver_5weeks_female

value: female

value: 5 wks

value: whole liver


title: liver_6WK_female_rep2

description:
whole ground tissue homogenized
6WK-F2


title: liver_5WK_female_rep6

description:
whole ground tissue homogenized
5WK-F6


title: liver_6WK_female_rep1

description:
whole ground tissue homogenized
6WK-F1


title: liver_5WK_male_rep6

description:
whole ground tissue homogenized
5WK-M6

source_name: whole liver_5weeks_male


title: liver_5WK_male_rep4

description:
whole ground tissue homogenized
5WK-M4


title: liver_5WK_male_rep1

description:
whole ground tissue homogenized
5WK-M1


title: HUVEC_donor2_P4

value: passage 4


title: liver_5WK_female_rep2

description:
whole ground tissue homogenized
5WK-F2


title: liver_5WK_female_rep1

description:
whole ground tissue homogenized
5WK-F1


title: HUVEC_donor3_P4


title: liver_52WK_male_rep7

description:
whole ground tissue homogenized
52WK-M7

source_name: whole liver_52weeks_male

value: 52 wks


title: HUVEC_donor1_P4

value: male


title: liver_52WK_male_rep6

description:
whole ground tissue homogenized
52WK-M6


title: liver_52WK_male_rep10

description:
whole ground tissue homogenized
52WK-M10


title: liver_52WK_male_rep5

description:
whole ground tissue homogenized
52WK-M5


title: Sirt1+/+_MIRA_Sample3

description: MIRA-chip Sirt1+/+ ESC (methylated DNA)

hyb_protocol: The labeled MIRA products and corresponding input samples were hybridized to NimbleGen Mouse DNA Methylation 3x720K CpG Island Plus RefSeq Promoter tiling Array  according to the manufacturer’s instructions.

scan_protocol: Two-color NimbleGen arrays were scanned with the MS2000 Microarray Scanner and generated both Cy3 (532) and Cy5 (635) image files.

data_processing:
Each paired image files were imported into Roche NimbleScan Software (v2.6). With the aid of this software, the two image files were bursted into 3-paired single image files which were 3 green (532) and 3 red (635) image files. The 3-paired image files were further analyzed using the same software and the log2 ratio (Cy5/Cy3) data were generated and reported in the GFF file (.gff).
The pair files for 6 samples (3-samples for each genotype ESC) were imported into Partek software and the ratio of signals were calculated and normalized using Loess method. A one-way ANOVA was set up for the different cell types with contrasts comparing Sirt1+/+ versus Sirt1-/- ESC. The MAT algorithm was used to detect regions of statically significant DNA methylation peaks using default cut-off setting (p-value threshold=0.05, average ChIP fragment length=300, minimum number of probes in a region=3, fraction of highest and lowest probes exculded from calculation mean=0.01)

source_name: MIRA DNA from Sirt1+/+ ESCs

label_protocol: The MIRA products and corresponding input samples were labeled using the NimbleGen Dual-Color DNA labeling kits

growth_protocol: ESCs were cultured under 0.1% gelatin coated dish

extract_protocol: The CpG methylated DNA was enriched using MethylCollector™ Ultra Kit (Active Motif) from 1 ug of genomic DNA fragmented by Mse I restriction enzyme. The recovered methylated DNA was amplified using two round primer extension, followed by PCR amplification of primed DNA. Amplified MIRA product was purified using the MinElute cleanup kit (Qiagen).

treatment_protocol: ESCs were grown under normal culture condition

tag: genotype

tag: methylated dna

value: MIRA

source_name: Input DNA from Sirt1+/+ ESCs

value: none, input DNA


title: liver_52WK_female_rep9

description:
whole ground tissue homogenized
52WK-F9

source_name: whole liver_52weeks_female

tag: age


title: liver_52WK_female_rep8

description:
whole ground tissue homogenized
52WK-F8


title: liver_52WK_female_rep6

description:
whole ground tissue homogenized
52WK-F6


title: liver_52WK_female_rep5

description:
whole ground tissue homogenized
52WK-F5


title: Sirt1+/+_MIRA_Sample1

description: MIRA-chip Sirt1+/+ ESC (methylated DNA)


title: Sirt1-/-_MIRA_Sample2

description: MIRA-chip Sirt1-/- ESC (methylated DNA)

source_name: MIRA DNA from Sirt1-/- ESCs


title: liver_2WK_male_rep2

description:
whole ground tissue homogenized
2WK-M2

source_name: whole liver_2weeks_male

value: 2 wks


title: liver_2WK_female_rep6

description:
whole ground tissue homogenized
2WK-F6

source_name: whole liver_2weeks_female


title: liver_2WK_male_rep3

description:
whole ground tissue homogenized
2WK-M3


title: Sirt1+/+_MIRA_Sample2

description: MIRA-chip Sirt1+/+ ESC (methylated DNA)


title: liver_2WK_male_rep1

description:
whole ground tissue homogenized
2WK-M1


title: liver_2WK_male_rep4

description:
whole ground tissue homogenized
2WK-M4


title: liver_2WK_female_rep3

description:
whole ground tissue homogenized
2WK-F3


title: liver_2WK_female_rep4

description:
whole ground tissue homogenized
2WK-F4


title: liver_2WK_male_rep5

description:
whole ground tissue homogenized
2WK-M5


title: liver_21WK_male_rep6

description:
whole ground tissue homogenized
21WK-M6

source_name: whole liver_21weeks_male

value: 21 wks


title: liver_2WK_female_rep5

description:
whole ground tissue homogenized
2WK-F5


title: liver_2WK_female_rep1

description:
whole ground tissue homogenized
2WK-F1


title: Sirt1-/-_MIRA_Sample1

description: MIRA-chip Sirt1-/- ESC (methylated DNA)


title: liver_21WK_male_rep1

description:
whole ground tissue homogenized
21WK-M1


title: liver_21WK_male_rep3

description:
whole ground tissue homogenized
21WK-M3


title: liver_21WK_male_rep5

description:
whole ground tissue homogenized
21WK-M5


title: liver_21WK_male_rep4

description:
whole ground tissue homogenized
21WK-M4


title: Sirt1-/-_MIRA_Sample3

description: MIRA-chip Sirt1-/- ESC (methylated DNA)


title: liver_52WK_female_rep1

description:
whole ground tissue homogenized
52WK-F1


title: liver_21WK_female_rep6

description:
whole ground tissue homogenized
21WK-F6

source_name: whole liver_21weeks_female


title: liver_52WK_male_rep1

description:
whole ground tissue homogenized
52WK-M1


title: liver_21WK_female_rep4

description:
whole ground tissue homogenized
21WK-F4


title: liver_21WK_female_rep3

description:
whole ground tissue homogenized
21WK-F3


title: liver_15WK_female_rep5

description:
whole ground tissue homogenized
15WK-F5

source_name: whole liver_15weeks_female

value: 15 wks


title: liver_15WK_female_rep6

description:
whole ground tissue homogenized
15WK-F6


title: liver_21WK_female_rep1

description:
whole ground tissue homogenized
21WK-F1


title: liver_15WK_male_rep3

description:
whole ground tissue homogenized
15WK-M3

source_name: whole liver_15weeks_male


title: liver_15WK_male_rep6

description:
whole ground tissue homogenized
15WK-M6


title: liver_15WK_male_rep1

description:
whole ground tissue homogenized
15WK-M1


title: liver_15WK_male_rep4

description:
whole ground tissue homogenized
15WK-M4


title: liver_15WK_female_rep1

description:
whole ground tissue homogenized
15WK-F1


title: liver_15WK_male_rep2

description:
whole ground tissue homogenized
15WK-M2


title: liver_104WK_male_rep4

description:
whole ground tissue homogenized
104WK-M4

source_name: whole liver_104weeks_male

value: 104 wks


title: liver_15WK_female_rep4

description:
whole ground tissue homogenized
15WK-F4


title: liver_15WK_female_rep2

description:
whole ground tissue homogenized
15WK-F2


title: liver_104WK_male_rep3

description:
whole ground tissue homogenized
104WK-M3


title: liver_104WK_male_rep2

description:
whole ground tissue homogenized
104WK-M2


title: liver_104WK_male_rep5

description:
whole ground tissue homogenized
104WK-M5


title: liver_104WK_female_rep5

description:
whole ground tissue homogenized
104WK-F5

source_name: whole liver_104weeks_female


title: liver_104WK_female_rep2

description:
whole ground tissue homogenized
104WK-F2


title: liver_104WK_female_rep8

description:
whole ground tissue homogenized
104WK-F8


title: liver_5WK_male_rep3

description:
whole ground tissue homogenized
5WK-M3


title: liver_104WK_female_rep1

description:
whole ground tissue homogenized
104WK-F1


title: liver_104WK_female_rep7

description:
whole ground tissue homogenized
104WK-F7


title: liver_5WK_female_rep4

description:
whole ground tissue homogenized
5WK-F4


title: liver_21WK_female_rep2

description:
whole ground tissue homogenized
21WK-F2


title: liver_6WK_female_rep4

description:
whole ground tissue homogenized
6WK-F4

value: 6 wks


title: hcr1-2, biological rep3

city: Montpellier

first: Christophe

last: Maurel

state: Languedoc Rousillon

address: 2, Place Viala

department: Aquaporines

country: France

institute: CNRS

hyb_protocol: Hybridization was carried out at 45 °C for 16 h

scan_protocol: The arrays were scanned using GeneAtlas Imaging Station (Affymetrix)

data_processing:
The quality of hybridization was evaluated using the Expression Console software (Affymetrix). Normalized expression signals were calculated from Affymetrix CEL files using the Robust Multi-Array average (RMA) normalization method.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.0.38

organism: Arabidopsis thaliana

source_name: roots of hcr1-2 grown in potassium-replete hypoxia

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip® WT Expression Arrays Technical Manual, 2013, Affymetrix).

growth_protocol: Plants were grown under hypoxia (pO2 = 11.1 ± 1.1 % ) in hydroponics in a growth chamber at 70 % relative humidity with cycles of 16 h of light (250 µmol m-2 s-1) at a constant temperature of 20 °C.

tag: ecotype

value: Hydraulic conductivity of Root 1 (HCR1) mutant

value: 21 days

value: roots


title: hcr1-2, biological rep1

tag: genotype/variation


title: hcr1-1, biological rep3

source_name: roots of hcr1-1 grown in potassium-replete hypoxia


title: hcr1-2, biological rep2


title: 8_CTGF

city: Oslo

first: Ingvild

middle: Tronstad

last: Moe

address: Sognsvannsveien 20

country: Norway

institute: University of Oslo

description: SAMPLE 8

data_processing: The data were quantile normalized using GenomeStudio v2010.1, Gene Expression module 1.6.0 (Illumina)

source_name: cardiac fibroblasts_CCN2/CTGF

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep-96 RNA Amplification Kit (Ambion)

growth_protocol: Primary cardiac fibroblasts were maintained in uncoated culture wells (Invitrogen Inc.) in Dulbecco’s modified Eagle’s medium (Life Technologies, MD, USA) supplemented with 10% fetal calf serum and 40 μg/mL gentamycin.

extract_protocol: Total RNA was extracted using Rneasy system (Qiagen, Germany). The amount and quality of the RNA were measured by a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DE, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA), respectively.

treatment_protocol: Cardiac fibroblasts were cultured in the absence (n=4) or presence (n=4) of 500 nmol/L GDF15 or 200 nmol/L CCN2 for 48 hours.

value: 10-16 weeks

value: Primary cardiac fibroblasts

tag: treated with

value: 200 nmol/L CCN2 for 48 h


title: 9_GDF15

description: SAMPLE 9

source_name: cardiac fibroblasts_GDF15

value: female

value: 500 nmol/L GDF15 for 48hr


title: 10_GDF15

description: SAMPLE 10


title: 11_GDF15

description: SAMPLE 11


title: Col-0, biological rep3

source_name: roots of Col-0 grown in potassium-replete hypoxia

value: wild type


title: Col-0, biological rep1


title: hcr1-1, biological rep2


title: Col-0, biological rep2


title: 3_control

description: SAMPLE 3

source_name: cardiac fibroblasts_control

value: none (control)


title: 12_GDF15

description: SAMPLE 12


title: 2_control

description: SAMPLE 2


title: 6_CTGF

description: SAMPLE 6


title: hcr1-1, biological rep1


title: 4_control

description: SAMPLE 4


title: 7_CTGF

description: SAMPLE 7


title: 1_control

description: SAMPLE 1


title: 5_CTGF

description: SAMPLE 5


title: C42B NOV-FL-OE +R+Dox Rep #2

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: SAMPLE 10

hyb_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

data_processing: The data were processed and normalised using Illumina GenomeStudio

source_name: C42B NOV-FL-OE +R+Dox

growth_protocol: Cells were maintained in RPMI supplemented with 10% FBS and 1% PS.

extract_protocol: Total RNA were extracted using Trizol according to manufacturer's instructions. The quantity and quality of the isolated RNAs was determined using ND-1000 Spectrophotometer.

treatment_protocol: LNCaP/C4-2B cells stably expressing doxycycline inducible NOV were cultured in medium with charcoal stripped FBS for 3 days. Cell were then treated with Ethanol (EtOH) or androgen (R1881) and water (Ctrl) or doxycycline (NOV) for 24h before being harvested.

tag: cell line

value: NOV-FL-OE +R+Dox

value: Doxycycline and R1881


title: C42B NOV-FL-OE +R-Dox Rep #1

description: SAMPLE 7

scan_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

source_name: C42B NOV-FL-OE +R-Dox

value: NOV-FL-OE +R-Dox


title: LNCaP Ctrl EtOH Rep #2

description: SAMPLE 4

source_name: LNCaP Ctrl EtOH

label_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

value: LNCaP

value: Ctrl

value: EtOH


title: LNCaP NOV R1881 Rep #2

description: SAMPLE 6

source_name: LNCaP NOV R1881

value: NOV


title: LNCaP NOV R1881 Rep #1

description: SAMPLE 3


title: LNCaP Ctrl R1881 Rep #1

description: SAMPLE 2

source_name: LNCaP Ctrl R1881


title: LNCaP Ctrl EtOH Rep #1

description: SAMPLE 1


title: C42B NOV-FL-OE +R-Dox Rep #2

description: SAMPLE 9


title: LNCaP Ctrl R1881 Rep #2

description: SAMPLE 5


title: FS1801

city: Camperdown

first: Zac

last: Chatterton

state: Australia

address: 97 Mallet St, ME30K

department: Brain and Mind Centre

country: Australia

institute: The University of Sydney

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised 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: minfi sofftware in R Language 3.03

label: cy3, cy5

source_name: fetal DLPFC exposed

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from fetal DLPFC samples using QIAamp DNA Mini Kit (Qiagen) according to standard instructions

value: M

tag: Stage

tag: maternal smoking

value: Yes smoking

value: developing dorsolateral prefrontal cortex (DLPFC)


title: FS3880


title: FS5864


title: FS6519


title: FS3646

value: F


title: FS1010


title: FS2664


title: d10

status: Public on Feb 18 2017

city: Dallas

first: Souparno

last: Bhattacharya

state: TEXAS

address: NC7.126  2201 Inwood Rd

department: Radiation Oncology

institute: UT southwestern medical center

hyb_protocol: Samples were processed and hybridized to Illumina Human HT12v4 arrays (Illumina, Inc.) using standard Illumina protocols.

scan_protocol: The slides were scanned on an Illumina BeadStation (Illumina, Inc.; Genomics Core, UT Southwestern Medical Center).

data_processing:
The two-step normalization procedure and the Associative analysis functions are implemented in MatLab (Mathworks, MA) and available from authors upon request. These algorithms are also obtainable from an R package diffGeneAnalysis, available as a part of Bioconductor packages (http://www.bioconductor.org/packages/2.5/bioc/html/diffGeneAnalysis.html).
Methods for data normalization and analysis are based on the use of internal standards (Rocke and Durbin 2001) that characterize some aspects of the system's behavior, such as technical variability, as presented elsewhere (Dozmorov and Centola 2003; Dozmorov and Lefkovits 2009). The comparison of these methods with some other normalization and analysis procedures was presented in (Dozmorov, ea, 2010).

label_protocol: Total RNA was amplified using the Illumina TotalPrep RNA amplification kit with biotin UTP (Enzo) labeling. The Illumina TotalPrep RNA amplification kit uses T7 oligo(dT) primer to generate single-stranded cDNA followed by a second strand synthesis to generate double-stranded cDNA which is then column purified. In vitro transcription was done to synthesize biotin-labeled cRNA using T7 RNA polymerase. The cRNA was then column purified and then checked for size and yield using the Bio-Rad Experion system. 1 µg of cRNA was hybridized for each array using standard Illumina protocols with streptavidin-Cy3 (Amersham) being used for detection.

growth_protocol: HT1080 cells were grown in Minimum Essential Medium (MEM) alpha supplemented with 10% fetal bovine serum, 100 mg/ml streptomycin sulfate, and 100 U/ml penicillin.

extract_protocol: Total RNA was isolated from mock-treated and irradiated cell pellets using the Qiagen RNeasy kit (217004, Qiagen), according to manufacturer's instructions.

treatment_protocol: HT1080 cells were transfected with a mammalian expression plasmid containing tetracycline-inducible Rad51 shRNA and selected in presence of hygromycin (75 µg/ml). To down-regulate RAD51 protein levels, cells were cultured in the presence of doxycycline (DOX, 1μg/mL) for 72 h. After 72h, WT and sh RAD51 HT1080 cells were exposed to 1 Gy high-LET iron (Fe) particles generated at the NASA Space Radiation Laboratory in Brookhaven National Laboratory, Long Island, NY. The energy of the used Fe-particles was 1 GeV/nucleon and the dose rate ranged from 50 to 200 cGy/min. The linear energy transfer (LET) of the Fe-particles was 150 keV/µm. Cell pellets were collected from mock and irradiated cells at different time intervals (4h and 8h) and stored at -80°C until use.

value: fibrosarcoma cell line

value: WT

value: IR

tag: time


title: d9

tag: treatment


title: FS2903


title: FS4483


title: FS1062


title: C42B NOV-FL-OE +R+Dox Rep #1

description: SAMPLE 8


title: FS5271


title: FS8245

source_name: fetal DLPFC unexposed

value: No smoking


title: No_treatment_Rep2

city: Research Triangle Park

first: Xuting

last: Wang

address: 111 TW Alexander Dr

institute: NIEHS/NIH

description: RMA expression value derived from Expression Console software; core-gene analysis

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the NIEHS Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Gene expression data were analyzed through Affymetrix Expression Console using gene-level RMA summarization and sketch-quantile normalization methods.

source_name: no treatment, 0h, Replicate 2

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

growth_protocol: Human lymphoblastoid GM12878 (Coriell Cell Repositories, Camden, NJ), were cultured  in RPMI 1640 medium supplemented with 15% heat-inactivated fetal bovine serum (Life Technologies) and 1X antibiotics/antimycotics (Life Technologies). Cells were incubated at 37 C with 5% CO2.

extract_protocol: Total RNAs were extracted using Qiagen total RNA Miniprep kit (Qiagen, cat #74104 ) with DNase 1 digestion according to the manufacturer’s instructions.

treatment_protocol: Lymphoblastoid cells were seeded at 900,000 cell/ml in a 100X20mm dish and treated with 10 uM sulforaphane or vehicle (0.1% DMSO) for 8h or 24h.

value: B-Lymphocyte


title: No_treatment_Rep3

source_name: no treatment, 0h, Replicate 3


title: d7

description: RAD51 K/D_IR4h_rep1

value: RAD51 K/D


title: FS6836


title: No_treatment_Rep1

source_name: no treatment, 0h, Replicate 1


title: d12

description: RAD51 K/D_IR8h_rep2


title: FS7628


title: d6


title: d11

description: RAD51 K/D_IR8h_rep1


title: FS3211


title: SFN8h_Rep2

source_name: SFN treated, 8h, Replicate 2


title: SFN8h_Rep1

source_name: SFN treated, 8h, Replicate 1


title: SFN24h_Rep3

source_name: SFN treated, 24h, Replicate 3


title: FS3958


title: FS6793


title: FS0850


title: SFN24h_Rep2

source_name: SFN treated, 24h, Replicate 2


title: d4

description: RAD51 K/D_control_rep2

source_name: HT1080, RAD51 K/D, control

value: mock


title: FS5394


title: d3

description: RAD51 K/D_control_rep1


title: FS6487


title: FS5777


title: SFN24h_Rep1

source_name: SFN treated, 24h, Replicate 1


title: FS3886


title: FS0362


title: FS7035


title: d5


title: d2

source_name: HT1080, WT, control


title: SFN8h_Rep3

source_name: SFN treated, 8h, Replicate 3


title: d1


title: MCF10A-HER2 3

city: Columbia

first: Hexin

last: Chen

state: SC

address: 715 Sumter Street,PSC621

department: Biological sciences

institute: University of South Carolina

description:
Replicate 2
Experiemnt 1

data_processing: The data were normalized using the default quantile normalisation with R/bioconductor package lumi version 3.2.2

source_name: Cultured cells of MCF10A breast epithelial cel line

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

growth_protocol: MCF10A was maintained in DMEM/F12 containing 5% horse serum, 10 ug/ml insulin, 0.5 ug/ml hydrocortisone and 100 ng/ml cholera toxin.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Breast epithelial cells transduced with human HER2-cDNA expressing pBABE retrovirus


title: MCF10A-Vector 4

description:
Replicate 2
Experiemnt 2

value: Breast epithelial cells transduced with pBABE retroviral vector


title: MCF10A-Vector 3

description:
Replicate 2
Experiemnt 1


title: MCF10A-HER2 1

description:
Replicate 1
Experiemnt 1


title: MCF10A-HER2 2

description:
Replicate 1
Experiemnt 2


title: MCF10A-Vector 1

description:
Replicate 1
Experiemnt 1


title: MCF10A-HER2 4

description:
Replicate 2
Experiemnt 2


title: T_PRE

status: Public on Feb 17 2017

city: Copenhagen

first: Malene

middle: Maag

last: Kristensen

address: Blegdamsvej 3

country: Denmark

institute: University of Copenhagen

description:
T1
Hy3: 1_Exiqon_14326122_S01.txt
Hy5: 0_Exiqon_14326122_S01.txt

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 6th GEN (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 16.0.

scan_protocol: The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).

data_processing:
The quantified signals were background corrected and normalised using LOESS in marray and linear models for microarray analysis (LIMMA).
Please note that only capture probes targeting human miRNAs as well as all control probes on the array platform were included during the normalization step. Following normalization, all control probes were removed and probe set level expression data were summarized for each human miRNA by the average value of the corresponding probe sets.

source_name: subcutaneous adipose tissue, male, baseline

label_protocol: 500 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: 13 severely obese individuals (seven women and six men) underwent a 15-week weight loss intervention including moderate daily exercise and a hypo-caloric diet.

extract_protocol: Total RNA was extracted from approximately 350 mg of subcutaneous adipose tissue using Trizol (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: Subcutaneous adipose tissue biopsies were sampled at baseline and after the 15-week intervention. In short, a small incision was made in the skin after anesthetising with lidocaine (10 mg/mL). 10-15 g tissue was extracted by use of a needle with partial vacuum after injection of 15 mL isotonic NaCl into the subcutaneous adipose tissue. Biopsies were washed in isotonic NaCl and snap-frozen in liquid nitrogen and stored at -80°C immediately.

tag: phenotype

value: obese

value: male

value: subcutaneous adipose tissue

value: hypo-caloric diet and moderate exercise

tag: timepoint

value: pre-treatment

tag: individual identifier

value: T

source_name: reference pool of subcutaneous adipose tissue

tag: sample type

value: Common references pool (equal pool of all test samples)


title: R_POST

description:
R2
Hy3: 1_Exiqon_14326120_S01.txt
Hy5: 0_Exiqon_14326120_S01.txt

source_name: subcutaneous adipose tissue, female, post-intervention

value: female

tag: tissue

value: post-treatment

value: R


title: T_POST

description:
T2
Hy3: 1_Exiqon_14326123_S01.txt
Hy5: 0_Exiqon_14326123_S01.txt

source_name: subcutaneous adipose tissue, male, post-intervention

tag: gender


title: MCF10A-Vector 2

description:
Replicate 1
Experiemnt 2

tag: cell type


title: Pcyt2+/- Male - 8 mon, biological rep4

city: Guelph

first: Marica

last: Bakovic

state: Ontario

address: 50 Stone Rd E

department: Human Health and Nutritional Sciences

country: Canada

institute: University of Guelph

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Mouse Gene 2.1 ST array strips, according to manufacturer's instructions. GeneChips were washed and stained on the GeneAltas platform.

scan_protocol: GeneChips were scanned on the GeneAltas platform.

data_processing:
The data were analyzed with GeneSpring GX Software v. 14.8 using default Affymetrix settings.
RMA

source_name: Pcyt2+/- Male - 8 mon

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA

growth_protocol: The mice were collected at 8 months of age, 3-4 hours after lights on.

extract_protocol: Total RNA was extracted using the Purelink RNA extraction kit according to the manufacturer's instructions.

treatment_protocol: The hearts were collected and snap frozen in liquid nitrogen and stored at -80°C.

value: myocardium


title: Pcyt2+/- Female - 8 mon, biological rep3

source_name: Pcyt2+/- Female - 8 mon


title: Pcyt2+/- Male - 8 mon, biological rep1


title: R_PRE

description:
R1
Hy3: 1_Exiqon_14326119_S01.txt
Hy5: 0_Exiqon_14326119_S01.txt

source_name: subcutaneous adipose tissue, female, baseline


title: Pcyt2+/- Male - 8 mon, biological rep3


title: LB05-0240

city: Lyon

first: Zdenko

last: Herceg

address: 25 avenue Tony Garnier CS 90627

department: EGM

institute: IARC

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation 450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged with standard recommended Illumina scanner settings

data_processing:
Idat files were loaded into R and analyzed with R/Bioconductor packages
Normalized betas (FunNorm normalization - minfi R package). Probes were filtered out for SNPs, XY chromosomes and cross-reactive probes.

source_name: Oropharynx

extract_protocol: QIAamp DNA mini kit (Qiagen)

tag: anatomical site

value: Oropharynx

tag: tissue storage

value: fresh frozen

tag: hpv status

value: Positive

tag: center

value: Pasteur

value: F

tag: organ group


title: Pcyt2+/- Female - 8 mon, biological rep1


title: Pcyt2+/- Female - 8 mon, biological rep2


title: Pcyt2+/- Female - 8 mon, biological rep4


title: Pcyt2+/- Male - 8 mon, biological rep2


title: Q_PRE

description:
Q1
Hy3: 1_Exiqon_14326117_S01.txt
Hy5: 0_Exiqon_14326117_S01.txt

value: Q


title: LB08-0603

source_name: Hypopharynx

value: Hypopharynx

value: M

value: Neck


title: Q_POST

description:
Q2
Hy3: 1_Exiqon_14326118_S01.txt
Hy5: 0_Exiqon_14326118_S01.txt

value: obese

value: male

value: subcutaneous adipose tissue

value: hypo-caloric diet and moderate exercise


title: H05.8546

source_name: Oral Tongue

value: Oral Tongue

value: Negative

value: CAL

value: Oral Cavity


title: d8

description: RAD51 K/D_IR4h_rep2

tag: cell line

value: fibrosarcoma cell line

tag: genotype/variation

value: RAD51 K/D

value: IR


title: LB05-0476

value: fresh frozen

value: Pasteur


title: P_PRE

description:
P1
Hy3: 1_Exiqon_14326115_S01.txt
Hy5: 0_Exiqon_14326115_S01.txt

value: female

value: pre-treatment

value: P

value: Common references pool (equal pool of all test samples)


title: P_POST

description:
P2
Hy3: 1_Exiqon_14326116_S01.txt
Hy5: 0_Exiqon_14326116_S01.txt

value: obese

value: post-treatment


title: J_POST

description:
J2
Hy3: 1_Exiqon_14326110_S01.txt
Hy5: 0_Exiqon_14326110_S01.txt

value: subcutaneous adipose tissue

value: J


title: L_PRE

description:
L1
Hy3: 1_Exiqon_14326111_S01.txt
Hy5: 0_Exiqon_14326111_S01.txt

value: male

value: hypo-caloric diet and moderate exercise

value: L


title: H_POST

description:
H2
Hy3: 1_Exiqon_14326106_S01.txt
Hy5: 0_Exiqon_14326106_S01.txt

value: H


title: LB08-0357

value: Hypopharynx

value: Negative

value: M

value: Neck


title: F_POST

description:
F2
Hy3: 1_Exiqon_14326103_S01.txt
Hy5: 0_Exiqon_14326103_S01.txt

value: F


title: H_PRE

description:
H1
Hy3: 1_Exiqon_14326104_S01.txt
Hy5: 0_Exiqon_14326104_S01.txt

value: female


title: F_PRE

description:
F1
Hy3: 1_Exiqon_14326101_S01.txt
Hy5: 0_Exiqon_14326101_S01.txt

value: pre-treatment


title: E_PRE

description:
E1
Hy3: 1_Exiqon_14326099_S01.txt
Hy5: 0_Exiqon_14326099_S01.txt

value: E


title: L_POST

description:
L2
Hy3: 1_Exiqon_14326112_S01.txt
Hy5: 0_Exiqon_14326112_S01.txt

value: Common references pool (equal pool of all test samples)


title: D_POST

description:
D2
Hy3: 1_Exiqon_14326096_S01.txt
Hy5: 0_Exiqon_14326096_S01.txt

value: obese

value: D


title: D_PRE

description:
D1
Hy3: 1_Exiqon_14326095_S01.txt
Hy5: 0_Exiqon_14326095_S01.txt

value: subcutaneous adipose tissue


title: LB09-0246

value: Oropharynx

value: fresh frozen

value: Positive

value: Pasteur


title: LB05-0247


title: C_POST

description:
C2
Hy3: 1_Exiqon_14326094_S01.txt
Hy5: 0_Exiqon_14326094_S01.txt

value: male

value: hypo-caloric diet and moderate exercise

value: post-treatment

value: C


title: C_PRE

description:
C1
Hy3: 1_Exiqon_14326093_S01.txt
Hy5: 0_Exiqon_14326093_S01.txt


title: B_POST

description:
B2
Hy3: 1_Exiqon_14326092_S01.txt
Hy5: 0_Exiqon_14326092_S01.txt

value: B


title: B_PRE

description:
B1
Hy3: 1_Exiqon_14326091_S01.txt
Hy5: 0_Exiqon_14326091_S01.txt


title: A_POST

description:
A2
Hy3: 1_Exiqon_14326090_S01.txt
Hy5: 0_Exiqon_14326090_S01.txt

value: A


title: A_PRE

description:
A1
Hy3: 1_Exiqon_14326089_S01.txt
Hy5: 0_Exiqon_14326089_S01.txt

value: female


title: LB08-0804

source_name: Base of tongue

value: Base of tongue

value: M


title: Normal [Sample 151]

city: Miami

first: Denise

last: Yan

state: FL

address: 1601 NW 12th Ave

department: Otolaryngology

institute: University of Miami

hyb_protocol: Each PCR reaction is prepared by combining 5 μl template DNA (15-150 ng), 10 μl mixture of amplification primer and 10 μl mixture of amplification reagent to the 25 μl reaction system individually. The amplification was performed in a Master Cycler nexus X2e (Oppendorf) by setting the temperature rate using the RAMP function of the PCR instrument under the following conditions: 37oC for 10min, 95oC for 15 min; 96oC for 1 min; then: 94oC for 30 sec, ramp (0.4 C/s) to 55oC, hold for 30 sec; ramp (0.2 C/s) to 70oC, hold for 45 sec for 32 cycles; followed by 60o C for 10 min, 4o C soak. Amplified products from the two tubes were mixed, and the amplicons were then captured by magnetic beads. Captured amplicons were denatured by NaOH, and only the single stranded DNA attached to the magnetic beads was collected and dissolved in hybridization buffer. First, an aliquot of 30 μg streptavidin-coated magnetic beads was washed twice with 2x binding and washing (B&W) buffer (10 mM Tris–HCl (pH 7.5), 1 mM EDTA, 2 M NaCl) and resuspended in 6 μL 2x B&W buffer after removing the supernatant with a external magnet. Then, an equal volume of biotinylated anti-tags solution was added, mixed gently with the magnetic beads suspension, incubated for 15 min at room temperature. After washing three times with 1x B&W buffer, the anti-tag-coated magnetic beads were resuspended in 15 μL hybridization buffer (9x SSC, 7.5x Denhardt's reagent, 37.5% (v/v) formamide, 0.15% (w/v) SDS). Approximately 30 µL of the hybridization solution was then injected into the sample inlet to cover the central hexagonal array region. The sample inlet and the air outlet were then sealed and the chip was placed into the Easy Array 3A (CapitalBio Corporation) for a dynamic hybridization at 55 oC for 20 min followed by washing at 42oC for 2 min.

scan_protocol: The hybridization results were recorded by a microarray scanner LuxScan™ 10K (CapitalBio), the laser power and photomultiplier tube (PMT) were set to 70 and 700, respectively.

data_processing: First, each microarray was scanned to obtain an image. Second, the absolute median signal intensities (AMSIs) for each spot, which were calculated by subtracting the local background from the median signal intensity, were extracted. Third, the system discriminated positive and negative signals according to the cut off value of each probe. On the basis of the distribution and the value of the signal, the reference values of the probes were made by ROC analysis. For a probe, if the detection signal value was greater than or equal to the reference value, the target was considered positive; if the detection signal value was less than the reference value of the probe, the target was considered negative.

source_name: Normal

label_protocol: The tag sequences in the tag-array were designed as described previously (Li et al., Hum. Mutat., 29 (2008), pp. 306-314). The tag probes were synthesized with a poly(dT) spacer and a 5' amino group for their immobilization onto the aldehyde-modified glass slides. The anti-tag probes complementary to the corresponding tag probes were synthesized with a poly(dT) spacer and a 5' biotin modification to validate the decoding performance of the tag-array. All probes and primers were dissolved in sterilized distilled and deionized water and quantified by UV absorbance at 260 nm. The tag probes were further diluted in 50% dimethyl sulfoxide (DMSO) to a final concentration of 15 μM and spotted with a SmartArrayer™ 136 spotter (CapitalBio, Beijing, China) on the aldehyde-functionalized glass slides (CapitalBio). Each tag probe was repeatedly spotted in triplicate.

extract_protocol: Genomic DNA was extracted from the whole blood using the Genetra Puregene DNA isolation kit (QIAGEN, Hilden, Germany) by following the instruction recommended by the manufacturer. Agarose gel and Qubit (Life Technologies, CA, USA) were used for DNA quantity and quality assessment.

tag: disease state

value: Normal

tag: population

value: European descent

value: Whole blood

value: WT


title: H09.3505

value: Oral Tongue

value: Negative

value: CAL

value: Oral Cavity


title: Normal [Sample 147]


title: H05.8214

value: fresh frozen

value: Positive

value: Oropharynx


title: Normal [Sample 150]


title: Normal [Sample 145]


title: Normal [Sample 148]


title: Normal [Sample 158]


title: Normal [Sample 153]


title: Normal [Sample 156]


title: Normal [Sample 154]


title: Normal [Sample 157]


title: Normal [Sample 155]


title: Normal [Sample 159]


title: Normal [Sample 160]


title: Normal [Sample 149]


title: Normal [Sample 152]


title: Normal [Sample 144]


title: Normal [Sample 142]


title: Normal [Sample 143]


title: Normal [Sample 140]


title: Normal [Sample 138]


title: Normal [Sample 141]


title: Normal [Sample 136]


title: Normal [Sample 137]


title: Normal [Sample 146]


title: Normal [Sample 139]


title: Normal [Sample 134]


title: Normal [Sample 132]


title: Normal [Sample 130]


title: Normal [Sample 131]


title: Normal [Sample 128]


title: Normal [Sample 133]


title: Normal [Sample 129]


title: Normal [Sample 135]


title: Normal [Sample 126]


title: Normal [Sample 124]


title: Normal [Sample 125]


title: Normal [Sample 121]


title: Normal [Sample 122]


title: Normal [Sample 127]


title: Normal [Sample 123]


title: Normal [Sample 120]


title: H05.8088


title: Normal [Sample 119]


title: Normal [Sample 118]


title: P19

first: Jin

last: Gu

address: FIT Building 1-112C

department: Automation

institute: Tsinghua University

description:
Sample 54
PVTT from patient #19

hyb_protocol: Prepare hybridization buffers and perform array hybridization at 50℃ in Hybridization Over (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US ) .After 16 hours hybridization, arrays were washed in Fluidics Station (Cat#00-0079, Affymetrix, Santa Clara, CA, US)according to Affymetrix CytoScan™ Assay User Manual (Cat#703038 Rev. 3, Affymetrix, Santa Clara, CA, US).

scan_protocol: Arrays were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing:
Raw data passed quality control were further analyzed by Affymetrix® Chromosome Analysis Suite (Affymetrix, Santa Clara, CA, US) .
In affymetrix CYCHP segmentation file format.

source_name: PVTT from HCC patient

label_protocol: Sample DNA was digested by restriction enzymes NspI, adaptors were ligated to the fragment DNA to perform a PCR amplification. Amplified DNA was labeled and further fragmented using Affymetrix Cytoscan HD array kit and reagent kit bundle, (Cat#901835, Affymetrix, Santa Clara, CA,US)followed the manufacturer’s instruction Affymetrix CytoScan™ Assay User Manual (Cat#703038 Rev. 3, Affymetrix, Santa Clara, CA, US) to obtain biotin labeled DNA.

growth_protocol: Fresh-frozen clinical tissue samples

extract_protocol: Sample DNA was extracted using DNeasy Blood &Tissue Kit (Cat#69506, QIAGEN, GmBH, Germany), following the manufacturer’s instructions. We used Nano Drop (Cat#ND-1000, Thermo Fisher, Waltham, MA, US) and ran a 1% agarose gel electrophoresis to check the quantity and quality of purified DNA.

tag: subject status

value: hepatocellular carcinoma (HCC) patient

tag: patient id

value: patient #19

value: male

tag: age (yrs)

value: Portal vein tumor thrombosis (PVTT)

tag: tumor size (cm)

tag: hbv infection

value: Yes

tag: cirrhosis


title: P11

description:
Sample 46
PVTT from patient #11

value: patient #11

tag: gender

tag: tissue


title: P12

description:
Sample 47
PVTT from patient #12

value: patient #12

value: female


title: P25

description:
Sample 59
PVTT from patient #25

value: patient #25

value: No


title: P10

description:
Sample 45
PVTT from patient #10

value: patient #10


title: P18

description:
Sample 53
PVTT from patient #18

value: patient #18


title: P20

description:
Sample 55
PVTT from patient #20

value: patient #20


title: P8

description:
Sample 44
PVTT from patient #8

value: patient #8


title: P16

description:
Sample 51
PVTT from patient #16

value: patient #16


title: T24

description:
Sample 38
Primary tumor from patient #24

source_name: Primary tumor from HCC patient

value: patient #24

value: Primary tumor


title: P26

description:
Sample 60
PVTT from patient #26

value: hepatocellular carcinoma (HCC) patient

value: patient #26


title: P24

description:
Sample 58
PVTT from patient #24

value: male


title: Normal [Sample 117]

value: Normal

value: European descent

value: Whole blood

value: WT


title: P7

description:
Sample 43
PVTT from patient #7

value: patient #7

value: Portal vein tumor thrombosis (PVTT)

value: Yes


title: P13

description:
Sample 48
PVTT from patient #13

value: patient #13


title: T25

description:
Sample 39
Primary tumor from patient #25

value: patient #25

value: No


title: P17

description:
Sample 52
PVTT from patient #17

value: patient #17


title: P14

description:
Sample 49
PVTT from patient #14

value: patient #14

value: female


title: T21

description:
Sample 36
Primary tumor from patient #21

value: patient #21

value: Primary tumor


title: P21

description:
Sample 56
PVTT from patient #21

value: hepatocellular carcinoma (HCC) patient


title: P3

description:
Sample 41
PVTT from patient #3

value: patient #3


title: Normal [Sample 116]

value: Normal


title: Normal [Sample 115]

value: European descent


title: P6

description:
Sample 42
PVTT from patient #6

value: patient #6

value: male


title: T22

description:
Sample 37
Primary tumor from patient #22

value: patient #22


title: T20

description:
Sample 35
Primary tumor from patient #20

value: patient #20


title: Normal [Sample 114]

value: Whole blood

value: WT


title: P15

description:
Sample 50
PVTT from patient #15

value: patient #15

value: Portal vein tumor thrombosis (PVTT)

value: Yes


title: Normal [Sample 113]


title: Normal [Sample 112]


title: P22

description:
Sample 57
PVTT from patient #22

value: No


title: T19

description:
Sample 34
Primary tumor from patient #19

value: patient #19


title: T18

description:
Sample 33
Primary tumor from patient #18

value: patient #18


title: Normal [Sample 111]


title: T26

description:
Sample 40
Primary tumor from patient #26

value: patient #26

value: Primary tumor


title: Normal [Sample 110]


title: Normal [Sample 109]


title: T17

description:
Sample 32
Primary tumor from patient #17

value: hepatocellular carcinoma (HCC) patient

value: patient #17


title: Normal [Sample 108]

value: Normal

value: European descent


title: Normal [Sample 106]


title: Normal [Sample 107]


title: Normal [Sample 105]


title: Normal [Sample 104]


title: T16

description:
Sample 31
Primary tumor from patient #16

value: patient #16

value: male


title: Normal [Sample 103]


title: T15

description:
Sample 30
Primary tumor from patient #15


title: Normal [Sample 102]


title: T14

description:
Sample 29
Primary tumor from patient #14

value: patient #14

value: female


title: Deaf [Sample 101]

source_name: Deafness

value: Deaf

value: Whole blood

value: WT


title: T11

description:
Sample 26
Primary tumor from patient #11

value: patient #11

value: Yes


title: N25

description:
Sample 19
Adjacent normal from patient #25

source_name: Adjacent normal from HCC patient

value: patient #25

value: Adjacent normal

value: No


title: T7

description:
Sample 23
Primary tumor from patient #7

value: patient #7

value: Primary tumor


title: Deaf [Sample 97]


title: T12

description:
Sample 27
Primary tumor from patient #12

value: hepatocellular carcinoma (HCC) patient

value: patient #12


title: T8

description:
Sample 24
Primary tumor from patient #8

value: patient #8


title: T10

description:
Sample 25
Primary tumor from patient #10

value: patient #10


title: T13

description:
Sample 28
Primary tumor from patient #13

value: patient #13

value: male


title: Deaf [Sample 99]

value: European descent


title: Deaf [Sample 100]

value: Deaf


title: Deaf [Sample 95]

value: Whole blood


title: N12

description:
Sample 7
Adjacent normal from patient #12

value: female


title: N11

description:
Sample 6
Adjacent normal from patient #11

value: patient #11


title: Deaf [Sample 94]

value: WT


title: N18

description:
Sample 13
Adjacent normal from patient #18

value: patient #18

value: Yes


title: Deaf [Sample 93]


title: Deaf [Sample 98]


title: Deaf [Sample 91]


title: T3

description:
Sample 21
Primary tumor from patient #3

value: patient #3


title: Deaf [Sample 96]


title: Deaf [Sample 92]


title: N22

description:
Sample 17
Adjacent normal from patient #22

value: patient #22

value: Adjacent normal

value: No


title: N14

description:
Sample 9
Adjacent normal from patient #14

value: hepatocellular carcinoma (HCC) patient

value: patient #14


title: N16

description:
Sample 11
Adjacent normal from patient #16

value: patient #16


title: N13

description:
Sample 8
Adjacent normal from patient #13

value: patient #13


title: Deaf [Sample 88]


title: Deaf [Sample 87]


title: N15

description:
Sample 10
Adjacent normal from patient #15

value: patient #15

value: male


title: N17

description:
Sample 12
Adjacent normal from patient #17

value: patient #17


title: Deaf [Sample 82]

value: Deaf

value: European descent

value: Whole blood


title: Deaf [Sample 89]

value: WT


title: P26 [methylation]

data_processing:
GenomeStudio Methylation Module v1.8, Methylated signal intensity/( Mehtylated signal intensity + Unmethylated signal intensity + 100 )
normalized data matrix (*.txt) contains Average Beta values

source_name: PVTT from patient #26

value: patient #26

value: Male

tag: age

value: Portal vein tumor thrombosis (PVTT)


title: Deaf [Sample 83]


title: Deaf [Sample 80]


title: Deaf [Sample 79]


title: P25 [methylation]

source_name: PVTT from patient #25

value: patient #25

value: Yes


title: N26

description:
Sample 20
Adjacent normal from patient #26

value: Adjacent normal


title: N8

description:
Sample 4
Adjacent normal from patient #8

value: hepatocellular carcinoma (HCC) patient

value: patient #8

value: No


title: Deaf [Sample 78]


title: N19

description:
Sample 14
Adjacent normal from patient #19

value: patient #19


title: T6

description:
Sample 22
Primary tumor from patient #6

value: patient #6

value: Primary tumor


title: N7

description:
Sample 3
Adjacent normal from patient #7

value: patient #7

value: male


title: P22 [methylation]

source_name: PVTT from patient #22

value: patient #22


title: Deaf [Sample 77]

value: Deaf

value: European descent

value: Whole blood


title: P21 [methylation]

source_name: PVTT from patient #21

value: patient #21

value: Male


title: Deaf [Sample 75]

value: WT


title: N20

description:
Sample 15
Adjacent normal from patient #20

value: patient #20

value: Yes


title: Deaf [Sample 76]


title: N10

description:
Sample 5
Adjacent normal from patient #10

value: hepatocellular carcinoma (HCC) patient

value: patient #10

value: Adjacent normal


title: P20 [methylation]

source_name: PVTT from patient #20

value: Portal vein tumor thrombosis (PVTT)


title: P19 [methylation]

source_name: PVTT from patient #19

value: patient #19


title: P18 [methylation]

source_name: PVTT from patient #18

value: patient #18


title: Deaf [Sample 73]


title: Deaf [Sample 72]


title: P17 [methylation]

source_name: PVTT from patient #17

value: patient #17


title: P16 [methylation]

source_name: PVTT from patient #16

value: patient #16


title: P15 [methylation]

source_name: PVTT from patient #15

value: patient #15


title: N3

description:
Sample 1
Adjacent normal from patient #3

value: patient #3

value: female


title: P14 [methylation]

source_name: PVTT from patient #14

value: patient #14

value: Female


title: Deaf [Sample 71]

value: Deaf

value: European descent

value: Whole blood


title: Deaf [Sample 74]

value: WT


title: Deaf [Sample 69]


title: Deaf [Sample 68]


title: Deaf [Sample 67]


title: P12 [methylation]

source_name: PVTT from patient #12

value: hepatocellular carcinoma (HCC) patient

value: patient #12

value: Yes


title: P11 [methylation]

source_name: PVTT from patient #11

value: patient #11

value: Male

value: Portal vein tumor thrombosis (PVTT)


title: P10 [methylation]

source_name: PVTT from patient #10

value: patient #10


title: P8 [methylation]

source_name: PVTT from patient #8

value: patient #8

value: No


title: Deaf [Sample 66]

source_name: Deafness


title: Deaf [Sample 70]


title: Deaf [Sample 64]


title: P7 [methylation]

source_name: PVTT from patient #7

value: patient #7


title: P13 [methylation]

source_name: PVTT from patient #13

value: patient #13


title: Deaf [Sample 62]


title: Deaf [Sample 90]


title: Deaf [Sample 61]


title: P6 [methylation]

source_name: PVTT from patient #6

value: patient #6


title: N6

description:
Sample 2
Adjacent normal from patient #6

source_name: Adjacent normal from HCC patient

value: male

value: Adjacent normal


title: Deaf [Sample 81]

value: Deaf

value: European descent


title: N24

description:
Sample 18
Adjacent normal from patient #24

value: patient #24


title: Deaf [Sample 65]

value: Whole blood

value: WT


title: P3 [methylation]

source_name: PVTT from patient #3

value: hepatocellular carcinoma (HCC) patient

value: patient #3

value: Female

value: Yes


title: Deaf [Sample 84]