title: ChIP-seq in siGPS2

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
The sequencing reads were aligned to mm8 by using bowtie aligner. 9 milions reads were randonly extracted from each sample for downstream analyses.
The bedgraph files were generated by using HOMER (http://homer.salk.edu/homer/).
Genome_build: mm8
Supplementary_files_format_and_content: bedgraph files displaying the continuous-valued data, as computed by HOMER (homer.salk.edu).

value: Pol-II (ac-055-100-adgenode)


title: AOX/NDI1 - day 9 rep 2

status: Public on Mar 21 2018

type: RNA

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

description: Gene expression from AOX/NDI1 - day 9

hyb_protocol: 12.5 μg of amplified biotin-aRNAs were fragmented and 10 μg were hybridized to each array for 16 hours at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console and Expression Console Software (AGCC; Version 3.2 and Expression Console; Version 1.2) using the MAS5 algorithm to generate .CHP files.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: mtDNA depleted + ectopic NADH oxidation

label_protocol: One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Plus kit protocol.

growth_protocol: all cells were grown in DMEM high glucose medium supplemented with uridine and pyruvate.

extract_protocol: RNA was isolated using the qiagen mini kits and the Qiashredder

treatment_protocol: HEK293 were exposed to doxycycline to induce the DN-POLG transgene

tag: cell line


title: DN-POLG - day 9 rep 3_methylation

type: genomic

first: Janine

last: Santos

address: 111 TW Alexander drive

department: GISBL

description: DN-POLG - day 9

hyb_protocol: Illumina InfiniumHD Methylation Protocol.

scan_protocol: Slides were scanned with an Illumina BeadArray Reader with BeadScan (version 3).

data_processing: Data obtained using Illumina GenomeStudio software (V2011.1).

label: Cy3 and Cy5

molecule: genomic DNA

source_name: mtDNA depleted

extract_protocol: DNA was isolated using the qiagen 20G kit and bisulfite converted using the Zymoresearch kit


title: AOX/NDI1 - day 0 rep 1_methylation

description: AOX/NDI1 - day 0

source_name: control + ectopic NADH oxidation

label_protocol: Illumina InfiniumHD Methylation Protocol.


title: ChIP-seq in siCTL

type: SRA

city: Boston

first: Valentina

last: Perissi

address: 72 E. Concord St

institute: Boston University

library_source: genomic

organism: Mus musculus

growth_protocol: 3T3-L1 cells were grown in 10% BCS/DMEM supplemented with 0.1 mM MEM non-essential aminoacids, 2mM L-glutamine, 1mM sodium pyruvate

extract_protocol: The library construction protocol followed  the manufacturer’s instructions.

treatment_protocol: siRNAs specific for GPS2 were purchased from Invitrogen (Silencer Select siRNAs).

tag: genotype/variation

value: control

tag: chip antibody


title: DN-POLG - day 3 rep 3_methylation

description: DN-POLG - day 3


title: DN-POLG - day 9 rep 2_methylation

description: DN-POLG - day 9


title: DN-POLG - day 6 rep 3_methylation

description: DN-POLG - day 6


title: DN-POLG - day 6 rep 3

description: Gene expression from DN-POLG - day 6


title: AOX/NDI1 - day 0 rep 1

description: Gene expression from AOX/NDI1 - day 0


title: DN-POLG - day 9 rep 3

description: Gene expression from DN-POLG - day 9


title: MT-37

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

country: China

institute: College of Life Sciences, Zhejiang University

description: Cell culture of JCS25-derived sectored colonies

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 24 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

scan_protocol: The data generated by GenePix Pro were exported as .gpr files and analyzed with a homemade software pipeline. Probes that were flagged by the software were deleted from the analysis.

data_processing: The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. The 635 nm/532 nm ratio was analyzed for each oligonucleotide. The average value of the median ratios of the control probes was calculated and used to normalize the ratios of the experimental probes to a value of 1 by dividing each probe ratio by the average control probe ratio. The Whole genome arrays were completed with Agilent platform with Design ID Agilent-027438 was used. Sectored colonies were mapped using Agilent platforsm with Design IDs Agilent-031671, which contains probes specific only to chromosome IV, and Agilent-047217, which contains many probes on chromsome IV, but few probes near the telomere and centromere of all chromosomes.

organism: Saccharomyces cerevisiae

label_protocol: DNA from these colonies was labeled with Cy5, and mixed with control DNA (DNA from the strain JSC24) labeled with Cy3. The two samples were mixed and competitively hybridized to the SNP microarrays.

growth_protocol: Yeast cells were grown in YPD medium at 30 degree.

extract_protocol: Genomic DNA were prepared by standard procedures (St. Charles et al., 2012)

treatment_protocol: JSC25 cells were cultured in YPD (5 mL) for 18 h at 30°C and then resuspended in fresh YPD medium (5 mL) containing MBC with initial OD600 of 0.1. The cells were incubated for 18 h and then plated onto YPD plates. All colonies appeared within a specific zone of a plate were selected for SNP microarray analysis.

tag: ploidy

value: diploid strain

tag: background

source_name: cell culture of JSC24

tag: strain

value: control strain JSC24


title: DN-POLG - day 3 rep 2_methylation

description: DN-POLG - day 3


title: MT-38

source_name: Cell culture of JCS25-derived sectored colonies


title: MT-34


title: DN-POLG - day 9 rep 2

description: Gene expression from DN-POLG - day 9


title: MT-35


title: MT-40


title: MT-36


title: MT-31


title: MT-33


title: MT-32


title: DN-POLG - day 3 rep 3

description: Gene expression from DN-POLG - day 3


title: DN-POLG - day 6 rep 2_methylation

description: DN-POLG - day 6


title: DN-POLG - day 6 rep 2

description: Gene expression from DN-POLG - day 6


title: DN-POLG - day 0 rep 2

description: Gene expression from DN-POLG - day 0

source_name: control


title: DN-POLG - day 3 rep 2

description: Gene expression from DN-POLG - day 3


title: DN-POLG - day 9 rep 1

description: Gene expression from DN-POLG - day 9


title: MT-30


title: DN-POLG - day 3 rep 1_methylation

description: DN-POLG - day 3


title: DN-POLG - day 0 rep 3

description: Gene expression from DN-POLG - day 0


title: DN-POLG - day 0 rep 2_methylation

description: DN-POLG - day 0


title: DN-POLG - day 6 rep 1

description: Gene expression from DN-POLG - day 6


title: RNA-seq of Col_M_1

city: Jinan

first: Yanchen

last: Tian

state: Shandong

address: No. 27, South Shanda Road

department: School of Life Sciences

institute: Shandong university

description: biological replicate 1

library_source: transcriptomic

data_processing:
The sequence reads were mapped to the Arabidopsis genome using HISAT and Bowtie2 software, and differential gene expression was analyzed using Noiseq software.
Genome_build: tair 10
Supplementary_files_format_and_content: XLS file for two sample comparison testing if a gene is differentially expressed

organism: Arabidopsis thaliana

source_name: hypocotyl

growth_protocol: Wild type Arabidopsis thaliana Columbia and bzr1-1D were grown in 1/2MS containing 2μM PPZ or 2 μM PPZ plus 1μM DPI or 2 μM PPZ plus 1μM DPI and 0.3mM H2O2 for 6 days in dark

extract_protocol:
Total RNA was extracted with Trizaol RNA extraction kit (Transgene)
the mRNA sequencing libraries construction and sequencing on the BGISEQ-500 platform were performed at Beijing Geonomics institute(BGI)

treatment_protocol: 2μM PPZ or 2 μM PPZ plus 1μM DPI or 2 μM PPZ plus 1μM DPI and 0.3mM H2O2 added in 1/2MS medium. M indicate 2μM PPZ; D indicate 2 μM PPZ plus 1μM DPI; DH indicate 2 μM PPZ plus 1μM DPI and 0.3mM H2O2

tag: tissue

value: hypocotyl

tag: genotype

value: wild type

tag: ecotype

value: Columbia

tag: development stage

value: 6day-dark growth seedling

tag: treatment

value: PPZ condition


title: DN-POLG - day 3 rep 1

description: Gene expression from DN-POLG - day 3


title: DN-POLG - day 6 rep 1_methylation

description: DN-POLG - day 6


title: RNA-seq of Col_M_2

description: biological replicate 2


title: RNA-seq of bzr1-1D_M_3

description: biological replicate 3


title: RNA-seq of Col_D_3

description: biological replicate 3

value: PPZ plus DPI condition


title: MT-25


title: MT-28


title: RNA-seq of bzr1-1D_M_1

description: biological replicate 1


title: MT-19


title: MT-18


title: MT-29


title: MT-23


title: DN-POLG - day 0 rep 1_methylation

description: DN-POLG - day 0


title: MT-15


title: DN-POLG - day 0 rep 1

description: Gene expression from DN-POLG - day 0


title: RNA-seq of bzr1-1D_DH_2

description: biological replicate 2

value: PPZ plus DPI and H2O2 condition


title: DN-POLG - day 9 rep 1_methylation

description: DN-POLG - day 9


title: MT-26


title: RNA-seq of Col_M_3

description: biological replicate 3


title: MT-27


title: RNA-seq of Col_D_2

description: biological replicate 2


title: MT-14


title: MT-21


title: MT-22


title: MT-24


title: RNA-seq of Col_D_1

description: biological replicate 1


title: MT-20


title: RNA-seq of bzr1-1D_D_1

description: biological replicate 1


title: MT-11


title: RNA-seq of bzr1-1D_M_2

description: biological replicate 2


title: RNA-seq of bzr1-1D_DH_1

description: biological replicate 1


title: MT-16


title: MT-39


title: MT-12


title: MT-17


title: HCT116-siCse1l-RNA.rep1

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

institute: Institute of Biophysics, CAS

data_processing:
Basecalls performed by BGI, Shenzhen.
Data were filtered using samtools to remove potential PCR duplicates
MeDIP sequencing reads were mapped to the Human genome (hg19) using Bowtie2.
Sequencing qualities were evaluated with FASTQC software and then the reads were aligned to hg19 genome sequences with a maximum of 2 mismatches allowed. Only the uniquely mapped reads were kept, and duplicate reads were removed. Mapped reads were extended to the average fragment sizes. Genome profile files were generated with IGV tools and linearly normalized to the same depth of 10 million reads.
RNA-Seq data were mapped by TopHat and quantitified by Crosslinks.
Genome_build: hg19
Supplementary_files_format_and_content: The transcription levels (RPKM) were quantified with Cufflinks (v2.0.2) software. Bigwig files were generated with IGV tools followed by UCSC utilities.

source_name: siCse1l treated HCT116 cells

extract_protocol:
Genomic DNA was isolated by conventional phenol extraction and proteinase K treatment. For sperm samples, 40 mM DTT were added during cell lysis.
According to standard protocols provided by Illumina Kits.

tag: parental cell line

value: HCT116 cell line

tag: cell type

value: somatic cell line

value: siCse1l treated HCT116 cells

value: colon cancer

tag: developmental stage

value: adult


title: RNA-seq of bzr1-1D_D_3

description: biological replicate 3


title: MT-8


title: HCT116-WT-RNA.rep2

source_name: WT HCT116 w/o treatment

value: WT HCT116 w/o treatment


title: MT-7


title: RNA-seq of bzr1-1D_D_2

description: biological replicate 2


title: MT-13


title: MT-6


title: HCT116-siCse1l-RNA.rep2


title: Control LPS-stimulated RAW264.7 cells Replicate 3

city: GULDFORD

first: RACHEL

last: SIMMONDS

state: Surrey

address: FHMS UNIVERSITY OF SURREY, STAG HILL CAMPUS

country: United Kingdom

institute: University of Surrey

description: Biological replicate 3 of 3, DMSO treated, LPS stimulated RAW264.7 cells

hyb_protocol: Pooled labelled cRNAs were fragemented at 60⁰C for 30min then applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After  overnight hybridization at 65⁰C in Agilent Hi-RPM Hybridisation buffer, slides were washed according to manufacturer's instructions.

scan_protocol: Scanned on an Agilent G2505C scanner Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Background correction by the normexp method; normalisation within arrays by Loess method and between arrays by Scale method; dyeswap correction; statistical analysis by  RankProd method

source_name: Control LPS-stimulated RAW264.7 cells

label_protocol: 0.15µg polysomal or subpolysomal RNA was spiked with Agilent RNA Spike-in Kit and labelled using Agilent Low input Quick Amp 2-colour labelling kit according to manufacturer's instructions

growth_protocol: RAW264.7 cells were grown in high glucose DMEM supplemented with 10% fetal bovine serum

extract_protocol: Cells treated with 10µg/ml cyclohexhamide for 10min and lysed in 15mM Tris pH7.4, 300mM NaCl, 15mM MgCl2, 100µg/ml cyclohexamide, 1mg/ml heparin. Polysomal and sub-polysomal RNA prepared by  10-60% sucrose gradient centrifugation and purified by LiCl precipitation

treatment_protocol: Cells were incubated with DMSO carrier or 125ng/ml mycolactone for 1hr then stimulated with 100ng/ml LPS for 4hr

value: Macrophage-like

tag: molecule

value: Sub-polysomal RNA

value: DMSO

value: Polysomal RNA


title: Mycolactone  treated LPS-stimulated RAW264.7 cells Replicate 3

description: Biological replicate 3 of 3, mycolactone treated, LPS stimulated RAW264.7 cells

value: 125ng/ml mycolactone


title: HCT116-WT-RNA.rep1


title: Control LPS-stimulated RAW264.7 cells Replicate1

description: Biological replicate 1 of 3, DMSO treated, LPS stimulated RAW264.7 cells


title: Mycolactone  treated LPS-stimulated RAW264.7 cells Replicate 2

description: Biological replicate 2 of 3, mycolactone treated, LPS stimulated RAW264.7 cells


title: Control LPS-stimulated RAW264.7 cells Replicate 2

description: Biological replicate 2 of 3, DMSO treated, LPS stimulated RAW264.7 cells


title: Mycolactone  treated LPS-stimulated RAW264.7 cells Replicate 1

description: Biological replicate 1 of 3, mycolactone treated, LPS stimulated RAW264.7 cells


title: HCT116-5Aza-RNA.rep2

source_name: 5-Aza treated HCT116 cells

value: 5-Aza treated HCT116 cells


title: MT-9

value: diploid strain

value: control strain JSC24


title: HCT116-5Aza-RNA.rep1


title: MT-10


title: B2-1-siNova1-siHdac1/2.rep2

source_name: siNova1/siHdac1/siHdac2 treated B2-1 cells

value: HEK-293 cell line

value: embryonic kidney

value: fetus


title: Oxidative Stress

city: Coimbatore

first: Manivannan

last: Jeganathan

state: Tamilnadu

address: Maruthamalai Road

department: Environmental Sciences

country: India

institute: Bharathiar University

data_processing:
The Illumina HiSeq 4000 generates raw images utilizing HCS(HiSeq Control Software) for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq. Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using NGS Toolkit.
Sequencing reads obtained were mapped to the chick genome using TopHat (v2.1.1)
To assemble the mapped reads from RNA-seq against NCBI gene structure annotation, Cufflinks (v2.2.1) was used and expression level for each transcript was estimated. A Cufflinks based probabilistic model of paired-end sequencing was used to evaluate abundances of isoforms, and detect ambiguous isoforms.
Differentially expressed transcripts were identified using CuffDiff protocol.
Genome_build: gg5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Gallus gallus

source_name: Heart

growth_protocol: Fertilized chicken eggs were incubated in a humidified incubator at 38°C and 70% humidity, until the chick embryos research the desired Hamburger-Hamilton (HH) stage of development

extract_protocol:
RNA was extracted using the GenElute Mammalian total RNA Miniprep kit (Sigma cat: RTN10-1KT) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In this study, we have created the oxidative environment with 2,2-azobis(2-amidinopropane) dihydrochloride (AAPH), a free radicals generator to study the effects of oxidative stress on the cardiovascular system during chick embryo development. Here we exposed the chick embryo to AAPH through injecting 100 µL of AAPH (2.6 µmol) into the air chamber of fertilized eggs containing HH 35 chick embryos. The injections were repeated on alternative days for up to 10th day. At HH37 (day 11) the hearts were harvested from all surviving embryos for total RNA isolation

tag: chemical

value: AAPH

tag: age

value: 11th day


title: Control

value: Saline


title: MT-2


title: MT-3


title: B2-1-siHdac1/2.rep1

source_name: siHdac1/siHdac2 treated B2-1 cells

tag: cell line

value: somatic cell line

value: siHdac1/siHdac2 treated B2-1 cells


title: B2-1-siNova1-siHdac1/2.rep1

tag: genotype/variation

value: siNova1/siHdac1/siHdac2 treated B2-1 cells


title: MT-1


title: B2-1-siHdac1/2.rep2


title: MT-5


title: MT-4


title: A2lox.i8TFs eVSM-dox, biological replicate 1

status: Public on Mar 20 2018

city: Monterotondo

first: Christophe

last: Lancrin

state: RM

address: Via Ramarini 32

department: EMBL Rome

country: Italy

institute: EMBL

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB3

hyb_protocol: Biotinylated cDNA was synthesized from 30 ng of total RNA using the Nugen Ovation Pico WTA System V2 kit. Following fragmentation and labelling of 5 μg of ssDNA (NuGen Encore Biotin Module), cDNA samples were hybridized for 16 hours at 45°C (60rpm) on Affymetrix Mouse Gene 2.0 ST Arrays (using Affymetrix GeneChip® Hybridization, Wash, and Stain Kit, catalogue number 900720). Arrays were washed and stained in the Affymetrix Fluidics Station 450 and scanned using the GeneChip Scanner 3000 7G.

scan_protocol: GeneChip Scanner 3000 7G

data_processing:
Transcript expression values from scanned arrays were imported and examined for quality control using Affymetrix GeneChip® Operating Software (GCOS v. 3.0)
normalization using oligo::rma function from oligo R package

source_name: A2lox.i8TFs eVSM–dox (24h post-HE culture) cells

label_protocol: Samples were processed using the WT Pico kit (appliedbiosystems)

growth_protocol: not applicable

extract_protocol: RNAeasy Plus Micro kit (Qiagen).

treatment_protocol: not applicable

value: A2lox.i8TFs cell line

value: eVSM population

value: -dox


title: A2lox.i8TFs eVSM, biological replicate 2

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB7

source_name: A2lox.i8TFs eVSM before HE culture (t0) cells

value: control


title: A2lox.i8TFs Endo, biological replicate 2

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB8

source_name: A2lox.i8TFs Endo before HE culture (t0) cells

value: Endo population


title: A2lox.i8TFs eVSM-dox, biological replicate 2

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB9


title: A2lox.i8TFs eVSM+dox, biological replicate 1

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB4

source_name: A2lox.i8TFs eVSM+dox (24h post-HE culture) cells

value: +dox


title: A2lox.i8TFs eVSM-dox, biological replicate 3

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB15


title: A2lox.i8TFs eVSM+dox, biological replicate 3

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB16


title: A2lox.i8TFs Endo, biological replicate 3

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB14


title: A2lox.i8TFs Endo-dox, biological replicate 1

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB5

source_name: A2lox.i8TFs Endo–dox (24h post-HE culture) cells


title: A2lox.i8TFs eVSM, biological replicate 3

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB13


title: A2lox.i8TFs Endo-dox, biological replicate 2

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB11


title: A2lox.i8TFs Endo+dox, biological replicate 2

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB12

source_name: A2lox.i8TFs Endo+dox (24h post-HE culture) cells


title: A2lox.i8TFs eVSM, biological replicate 1

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB1


title: A2lox.i8TFs eVSM+dox, biological replicate 2

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB10


title: A2lox.i8TFs Endo, biological replicate 1

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB2


title: A2lox.empty eVSM+dox, biological replicate 3

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB9_rIB_27

source_name: A2lox.empty eVSM+dox (24h post-HE culture) cells

value: A2lox.empty cell line


title: A2lox.empty eVSM-dox, biological replicate 3

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB8_rIB_26

source_name: A2lox.empty eVSM-dox (24h post-HE culture) cells


title: A2lox.empty eVSM+dox, biological replicate 2

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB6_rIB_24


title: A2lox.empty eVSM, biological replicate 3

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB7_rIB_25

source_name: A2lox.empty eVSM before HE culture (t0) cells


title: A2lox.empty eVSM, biological replicate 2

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB4_rIB_22


title: A2lox.empty eVSM, biological replicate 1

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB1_rIB_19


title: A2lox.i8TFs Endo+dox, biological replicate 1

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB6


title: A2lox.i8TFs Endo-dox, biological replicate 3

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB17


title: A2lox.i8TFs Endo+dox, biological replicate 3

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB18


title: A2lox.empty eVSM-dox, biological replicate 2

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB5_rIB_23


title: A2lox.empty eVSM+dox, biological replicate 1

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB3_rIB_21


title: lung ventilated zmpste24-deficient mouse, biological rep.3

city: Oviedo

first: Guillermo

middle: M

last: Albaiceta

address: Avenida de Roma s/n

country: Spain

institute: Instituto de Investigación Sanitaria del Principado de Asturias

hyb_protocol: Labeled RNA were hybridized to a Mouse Gene 2.0 ST Array. Washing and staining was done ina a GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: Scanning was performed using GeneChip Scanner 7G (Affymetrix)

data_processing: Data were analyzed (Background correction and normalization using the RMA algorithm) using the oligo and limma packages from Bioconductor, in the R platform.

label: Biotin

source_name: Zmpste24-/-, ventilated

label_protocol: 100 ng of total RNA were amplified and labeled using the WT Plus Reagent kit (Affymetrix), following manufacturer's instructions

growth_protocol: Lung tissue from 10 week old mice

extract_protocol: RNA was extracted using Trizol and purified using the RNAeasy minikit (Quiagen)

treatment_protocol: baseline were intact mice. The ventilation was performed using positive inspiratory pressure of 15cmH2O ZEEP, 100 breaths/min, inspiratory:expiratory ratio 1:1, inpired oxygen fraction 0.21, during 2.5 hours

tag: gender

value: female

value: lung

value: 10 weeks


title: lung intact zmpste24-deficient mouse, biological rep.2

source_name: Zmpste24-/-, baseline


title: lung ventilated zmpste24-deficient mouse, biological rep.1


title: lung ventilated wildtype mouse, biological rep.3

source_name: wildtype, ventilated

value: wildtype


title: A2lox.empty eVSM-dox, biological replicate 1

description:
differentiated murine embryonic stem cells (mus musculus)
IsaB2_rIB_20


title: Zebrafish_NiONP_96h_rep1

first: Jing

last: Hou

address: No. 19, XinJieKouWai St., HaiDian District

institute: Beijing Normal University

hyb_protocol: Fifteen micrograms of the fragmented cRNA were hybridized to each microarray at 45°C for 15 h in an Affymetrix GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA, USA).

scan_protocol: The microarray was washed after hybridization. Streptavidin phycoerythrinonan was used to stain the microarray on an Affymetrix Fluidics Station 450 (Affymetrix), and a GeneChip Scanner 3000 7G (Affymetrix) was used to scan the microarray.

data_processing: Microarray data were further analyzed with Microarray Suite version 5.0 at the default settings, and global scaling was used as the normalization method. Genes with a false discovery rate-adjusted fold-change ≥ 2 and p-value < 0.05 were considered differentially expressed.

organism: Danio rerio

source_name: gill, 96h, replicate 1

label_protocol: To avoid dye-based bias, the RNA sample was then labeled with cyanine 3 using the Low Input QuickAmp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) with a dye swap design. RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) was used to purify the labeled cRNA, which was then fragmented and hybridized on a D. rerio microarray.

growth_protocol: During the acclimation period (not less than 14 days), D. rerio were housed in 60-L tanks (40 cm height × 30 cm width × 50 cm length) at a maximum density of seven D. rerio per liter. The tanks were filled with water previously treated by aeration and kept under filtration at a temperature of 24 ± 2°C and pH of 7.0-8.0. Fish were fed commercially available dry flakes twice a day.

extract_protocol: Total RNA was isolated from the gills of D. rerio exposed to the NPs and the controls using Trizol reagent (Invitrogen, Carlsbad, CA, USA). To remove contaminated DNA, the isolated RNA sample was digested with DNase I at 37°C for 15 min.

treatment_protocol: After two weeks of acclimation, D. rerio were exposed to eight concentrations of each NP solution (ZnO: 1.0, 2.0, 4.0, 8.0, 16.0, 32.0, 64.0, and 128.0 mg/L; CuO: 0.0625, 0.125, 0.25, 0.5, 1.0, 2.0, 4.0, and 8.0 mg/L; NiO: 2.0, 4.0, 8.0, 16.0, 32.0, 64.0, 128.0, and 256.0 mg/L) with a day/night cycle of 16/8 h. Three biological replicates were used in each treatment and each replicate consisted of 10 individuals. D. rerio were exposed for 96 h without feeding.

value: Gill

tag: develomental stage

value: Adult

value: NiONP treated


title: lung intact wildtype mouse, biological rep.2

source_name: wildtype, baseline


title: Zebrafish_ZnONP_96h_rep3

source_name: gill, 96h, replicate 3

value: ZuONP treated


title: lung ventilated wildtype mouse, biological rep.2


title: lung intact zmpste24-deficient mouse, biological rep.3


title: lung intact wildtype mouse, biological rep.1


title: lung intact wildtype mouse, biological rep.3


title: Zebrafish_CuONP_96h_rep3

value: CuONP treated


title: Zebrafish_ZnONP_96h_rep1


title: lung ventilated zmpste24-deficient mouse, biological rep.2


title: Zebrafish_CK_96h_rep2

source_name: gill, 96h, replicate 2

value: untreated


title: lung intact zmpste24-deficient mouse, biological rep.1


title: Zebrafish_CK_96h_rep3


title: lung ventilated wildtype mouse, biological rep.1


title: Zebrafish_CuONP_96h_rep2


title: Zebrafish_ZnONP_96h_rep2


title: Zebrafish_CK_96h_rep1


title: Zebrafish_CuONP_96h_rep1


title: Zebrafish_NiONP_96h_rep3


title: Zebrafish_NiONP_96h_rep2


title: IL5_Transgenic_GMP_3

city: Parkville

first: Carolyn

middle: A

last: de Graaf

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

description:
IL5 Transgenic GMP
sample name in non-normalized data file:
iltp1674-4-23-123-il5gmpb&c

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Normalized data was restricted to a curated selection of probes that were supported by an Ensembl transcript and that were found on both V1.1 and V2.0 beadchips. The dataset was normalized with the normexp background correction followed by quantile normalization

source_name: IL5 Transgenic Bone Marrow

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

growth_protocol: All cells were purified from mice between 7 and 12 weeks of age.

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.

treatment_protocol: Bone marrow was collected from femurs and tibiae. Peripheral blood was collected from the retro-orbital sinus into microtainer tubes containing EDTA. Cells were purified using monoclonal monoclonal antibodies and then isolated on a fluorescence-activated cell sorter.

value: BALB/c

tag: cell type abbreviation

value: GMP

tag: cell type full

value: Granulocyte Macrophage Progenitor

tag: antibodies

value: Lin- Sca-1- c-Kit+ CD34+ FcR+

value: Bone Marrow

value: IL5 Transgenic


title: IL5_Transgenic_CMP_1

description:
IL5 Transgenic CMP
sample name in non-normalized data file:
iltp1674-15-26-126-il5cmp

tag: strain

value: CMP

value: Common Myeloid Progenitor

value: Lin- Sca-1- c-Kit+ CD34+ FcRlo

tag: tissue

tag: genotype


title: IL5_Transgenic_CMP_3

description:
IL5 Transgenic CMP
sample name in non-normalized data file:
iltp1674-9-25-125-il5cmp


title: IL5_Transgenic_EoH_Bld_2

description:
IL5 Transgenic EoH Bld
sample name in non-normalized data file:
iltp1436-13-4b

source_name: IL5 Transgenic Peripheral Blood

value: EoH Bld

value: SiglecF High Eosinophil in the peripheral blood

value: Siglec-F Hi IL-5ra+ c-Kit lo

value: Peripheral Blood


title: IL5_Transgenic_EoM_BM_3

description:
IL5 Transgenic EoM BM
sample name in non-normalized data file:
iltp1436-8-8a

value: EoM BM

value: SiglecF Medium Eosinophil in the bone marrow

value: Siglec-F Med IL-5ra+ c-Kit lo


title: IL5_Transgenic_EoM_BM_2

description:
IL5 Transgenic EoM BM
sample name in non-normalized data file:
iltp1436-6-6a


title: IL5_Transgenic_CMP_2

description:
IL5 Transgenic CMP
sample name in non-normalized data file:
iltp1674-3-22-118-il5gmpb&c


title: IL5_Transgenic_EoH_Bld_3

description:
IL5 Transgenic EoH Bld
sample name in non-normalized data file:
iltp1436-16-8b


title: IL5_Transgenic_EoH_BM_2

description:
IL5 Transgenic EoH BM
sample name in non-normalized data file:
iltp1436-2-2a

value: EoH BM

value: SiglecF High Eosinophil in the bone marrow


title: IL5_Transgenic_GMP_2

description:
IL5 Transgenic GMP
sample name in non-normalized data file:
iltp1674-16-27-127-il5gmp

value: BALB/c

value: GMP


title: IL5_Transgenic_EoH_BM_4

description:
IL5 Transgenic EoH BM
sample name in non-normalized data file:
iltp1436-7-7a


title: IL5_Transgenic_EoH_BM_3

description:
IL5 Transgenic EoH BM
sample name in non-normalized data file:
iltp1436-5-5a


title: RppH rep2

city: Mainz

first: René

last: Ketting

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

data_processing:
The quality of raw sequenced reads was accessed with FastQC, illumina adatpers were then removed with cutadapt (-O 8 -m 26 -M 38), reads with low-quality calls were filtered out with fastq_quality_filter ( -q 20 -p 100 -Q 33). Using information from unique molecule identifiers (UMIs) added during library preparation, reads with the same sequence (including UMIs) were collapsed to removed putative PCR duplicates using a custom script. Prior to mapping, UMIs were trimmed (seqtk trimfq) and library quality re-assessed with FastQC.
Reads were aligned against the C. elegans genome assembly WBcel235 with bowtie v0.12.8 (--tryhard --best --strata --chunkmbs 256 -p 8 -v 1 -M 1). For the analysis, only reads mapping to a single genomic location were used.
To create genome browser tracks for 22G small RNAs, reads  whose sequence is exactly 22 nucleotides long and have a guanine at their 5’ where selected, and the genome coverage determined with genomeCoverageBed (normalization to total number of mapped reads). The bigwig files were then generated with bedGraphToBigWig.
Genome_build: WBcel235
Supplementary_files_format_and_content: Bigwig tracks summarizing the genomic coverage of 22G small RNAs

organism: Caenorhabditis elegans

source_name: L2 animals

growth_protocol: worms were grown in NGM plates seeded with OP50

extract_protocol:
Gravid adults were washed off plate with M9 buffer and lysed in 250 µL of Worm Lysis Buffer (0.2M NaCl, 0.1M Tris pH 8.5, 50 mM EDTA, 0.5% SDS) with 150 µg Proteinase K (Sigma-Aldrich #P2308) for at least 90 minutes at 65oC. 750 uL of Trizol LS were added per sample and extraction followed manufacturer’s instructions, with the exception that phase-lock tubes were used to facilitate phase-separation. Total RNA extraction was followed by TURBO DNase treatment (Life Technologies #AM1907) according to manufacturer’s instructions. Small RNAs were isolated from DNase-treated total RNA using MirVana (Life Technologies #AM1561).
A single RNA sample was divided into 6 technical replicates. Three of these technical replicates were treated with Tobacco Acid Phosphatase (TAP, Epicentre) and the other three, with RNA 5’Pyrophosphohydrolase (RppH, New England Biolabs, #M0356S). For TAP-treated samples, 1 µg of total RNA was incubated for 2 hours at 37C, with 5 units of TAP enzyme and 10X TAP buffer. For RppH treated samples, 1µg of RNA was incubated for 1 hour at 37°C, with 5 units of RppH enzyme and 10X NEB Buffer 2. To stop the RppH treatment, 500mM EDTA was added and samples were incubated for 5 minutes at 65°C. Small RNAs (16-30nt) were enriched by performing size selection of the RNA prior to library preparation. RNA samples were run on a 15% TBE-Urea polyacrylamide gel (BioRad), and purified with sodium chloride/isopropanol precipitation. Library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England BioLabs) as recommended by the manufacturer (protocol version v2.0 8/13), but replacing the RNA ligation adapters with adapters with 4 additional random bases at their 3’ ends to allow identification of PCR clonal artefacts (synthesized by Bioo Scientific). Fourteen PCR cycles were used for library amplification The PCR-amplified cDNA was purified using AMPure XP beads (Beckman Coulter). Size selection of the small RNA library was done on LabChip XT instrument (Perkin Elmer) using DNA 300 assay kit extracting the 135-170 bp fraction. The 135-170 bp library fractions of the RppH and TAP-treated libraries were pooled in equal molar ratio. The resulting 4 nM pool was denatured and diluted to 9 pM with 5% PhiX spike-in and sequenced as single-read on MiSeq (Illumina) for 68 cycles. Libraries for an untreated sample, originating from a different biological replicate, were also prepared using the protocol above, but were sequenced as single-read on HiSeq 2500 (Illumina).

treatment_protocol: Caenorhabditis elegans populations were grown according to standard conditions (Brenner, 1974). Wild-type N2 worms were grown at 20oC on nematode growth medium (NGM) plates seeded with E. coli OP50. For synchronization, gravid adult worm populations were bleached and the resulting eggs were allowed to hatch with an overnight incubation at 20oC, in M9 buffer. Synchronized L1 larvae were plated the next day on OP50 plates and allowed to grow at 20oC for 60-63 hours until adulthood.

tag: genoptype/variation

value: wild-type

value: Gravid adult

tag: treatment

value: RppH


title: TAP rep2

value: TAP


title: IL5_Transgenic_EoH_Bld_1

description:
IL5 Transgenic EoH Bld
sample name in non-normalized data file:
iltp1436-1-1a

value: IL5 Transgenic


title: IL5_Transgenic_EoM_BM_1

description:
IL5 Transgenic EoM BM
sample name in non-normalized data file:
iltp1436-11-11a

value: Bone Marrow


title: RppH rep3


title: TAP rep3


title: TAP rep1


title: RppH rep1


title: IL5_Transgenic_EoH_BM_1

description:
IL5 Transgenic EoH BM
sample name in non-normalized data file:
iltp1436-10-10a


title: HCT116-HiChIP-SMC1

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Library strategy: HiChIP-Seq
HiChIP paired-end reads were first tested for the presence of a junction, which was removed if detected. All paired-end reads (whether trimmed or not) were aligned using bowtie with configuration -p 8 -k 1 -m 1 --sam. Paired-end reads where both ends mapped were further processed using origami to build the HiChIP contact map and call loops, as described in Weintraub et al 2018.
hg19
Supplementary_files_format_and_content: BEDPE file has the called SMC1 loops in HCT-116 using the origami score 0.9 and removing called loops in adjacent bins

source_name: Colorectal Cancer Cell Line

growth_protocol: HCT-116 cells were cultured in 10% FCS DMEM with pen/strep super standard

extract_protocol:
HiChIP was performed essentially as described (Mumbach et al., 2016). 10 million HCT116 cells were crosslinked, nuclei were isolated and DNA was digested with MboI. Ends were filled in and proximity ligation was performed in situ before the nuclei were lysed and DNA was sonicated. Sonicated DNA was precipitated with SMC1A antibody and DNA was washed and purified. Sequencing libraries then were generated using transposase and the Nextera kit from Illumina.
sonication

treatment_protocol: normal HCT-116 cells

tag: chip antibody

tag: antibody manu.

value: Bethyl

tag: antibody catalog

tag: system

value: Colorectal Cancer


title: BCBL1_NaB_48hrs_rep2

city: Chapel Hill

first: Jennifer

last: Webster-Cyriaque

address: 385 S. Columbia St.

department: Dental Research

institute: University of North Carolina at Chapel Hill

hyb_protocol: Samples were applied to array in a hybridization chamber and placed at 65°C overnight. Coverslips were removed with 2X SSC with 0.25% SDS, washed once in 1X SSC for 3-5 min, then washed twice in 0.2X SSC for 3-5 min at 50-65°C. Slides were spun at 500 rpm for 4 min.

scan_protocol: Microarrays were scanned and gridded with GenePix 3.0 (Axon Corp.)

data_processing: The limma package from Bioconductor was used.  background subtracted using normexp, normalized using print-tip loess and G-quantiles normalization. M values were calculated as the log2 of the spot intensity for the sample treated with a viral replication inducer over the spot intensity of the untreated sample and spots representing the same gene were averaged.

source_name: BCBL-1 untreated 48hrs

label_protocol: cDNA was synthesized using  Reverse transcriptase PCR with Taq polymerase (Roche) and N6 primers. Primers annealed at 50°C, followed by 35 cycles of 94°C for 45 seconds, 50°C  for 45 seconds, 75°C for 4 seconds, plus 2 seconds for each cycle.  Cy3 and Cy5 dyes were incorporated into the control and treatment samples, respectively.

growth_protocol: BCBL-1, a latently infected KSHV body cavity-based, lymphoma-derived cell line, were maintained in 5% CO2 at 37°C in RPMI 1640 medium supplemented with 10% FBS containing penicillin, streptomycin, sodium pyruvate, and L-glutamine (GIBCO-BRL, Gaithersburg, MD).

extract_protocol: RNA was isolated from BCBL-1 cells that were either untreated or treated with NaB, TPA, or spent medium from P. gingivalis using the RNeasy kit from Qiagen (Valencia, CA). Any DNA contamination was then removed from the RNA using the DNAfree kit from Ambion, and the RNA was concentrated.

treatment_protocol: BCBL-1 cells were left untreated or treated for 48 hours with 1:20 P. gingivalis spent media, 0.3 mM NaB, or 0.25 ng/mL TPA.

tag: cell type

tag: treated with

value: none (untreated control)

source_name: BCBL-1 NaB 48hrs

value: 0.3 mM NaB for 48 hrs


title: BCBL1_TPA_48hrs_rep1

tag: cell line

value: latently infected KSHV body cavity-based, lymphoma-derived cell line

source_name: BCBL-1 TPA 48hrs

value: 0.25 ng/mL TPA for 48hrs


title: BCBL1_NaB_48hrs_rep3


title: BCBL1_PG_48hrs_rep2

source_name: BCBL-1 PG 48hrs

value: 1:20 P. gingivalis spent media for 48hrs


title: BCBL1_TPA_48hrs_rep2


title: BCBL1_NaB_48hrs_rep1


title: BCBL1_PG_48hrs_rep1


title: Y10063T

city: Seoul

first: Yong-Min

last: Huh

address: 50 Shinchon-ro

country: South Korea

institute: Yonsei University

description: SAMPLE 7

hyb_protocol: Illumina TotalPrep™ RNA Amplification Kit was used for cRNA synthesis.

data_processing: Genomestudio, quantile normalization

source_name: Human gastric cancer

extract_protocol: RecoverAll™ total nucleic acid isolation kit (Ambion) or the mirVana RNA Isolation Labeling Kit (Ambion) were used. Quality control was performed with NanoDrop 2000 (Thermo Fischer Scientific) and RNA Nano 6000 chip (Agilent).

value: gastric cancer

tag: age

tag: Sex

value: female

tag: ptstage

tag: pnstage

tag: death

tag: duration overall survival


title: Y10079T

description: SAMPLE 9

label_protocol: Illumina TotalPrep™ RNA Amplification Kit was used for cRNA synthesis.

tag: tissue

value: male


title: Y10087T

description: SAMPLE 11


title: Y10060T

description: SAMPLE 6


title: Y2597T

description: SAMPLE 398

hyb_protocol: HumanHT-12 v3.0 Expression BeadChip array (Illumina) was used.

label_protocol: Illumina TotalPrep™ RNA Amplification Kit was used for synthesis of labeled cRNA.


title: Y2523T

description: SAMPLE 395


title: Y10055T

description: SAMPLE 2


title: Y10052T

description: SAMPLE 1


title: Y10081T

description: SAMPLE 10


title: Y2358T

description: SAMPLE 392


title: Y10058T

description: SAMPLE 5


title: Y10056T

description: SAMPLE 3


title: Y10065T

description: SAMPLE 8


title: Y3203T

description: SAMPLE 388


title: Y2609T

description: SAMPLE 400


title: Y2622T

description: SAMPLE 399


title: Y3376T

description: SAMPLE 390


title: Y2433T

description: SAMPLE 393


title: Y2264T

description: SAMPLE 386


title: Y2637T

description: SAMPLE 401


title: Y3404T

description: SAMPLE 389


title: Y2659T

description: SAMPLE 396


title: Y2566T

description: SAMPLE 397


title: Y2769T

description: SAMPLE 394


title: Y3886T

description: SAMPLE 373


title: IL5_Transgenic_GMP_1

description:
IL5 Transgenic GMP
sample name in non-normalized data file:
iltp1674-10-24-124-il5gmp

tag: strain

value: BALB/c

tag: cell type abbreviation

value: GMP

tag: cell type full

value: Granulocyte Macrophage Progenitor

tag: antibodies

value: Lin- Sca-1- c-Kit+ CD34+ FcR+

tag: genotype


title: Y2685T

description: SAMPLE 384


title: Y10057T

description: SAMPLE 4


title: Y4121T

description: SAMPLE 377


title: Y598T

description: SAMPLE 383


title: Y3830T

description: SAMPLE 372


title: Y4032T

description: SAMPLE 376


title: Y2656T

description: SAMPLE 379


title: Y597T

description: SAMPLE 382


title: Y3034T

description: SAMPLE 380


title: Y3105T

description: SAMPLE 361


title: Y2555T

description: SAMPLE 381


title: Y2736T

description: SAMPLE 385


title: Y3823T

description: SAMPLE 371


title: Y4123T

description: SAMPLE 378


title: Y3368T

description: SAMPLE 362


title: Y4780T

description: SAMPLE 359


title: Y4698T

description: SAMPLE 366


title: Y4029T

description: SAMPLE 375


title: Y3151T

description: SAMPLE 370


title: Y3117T

description: SAMPLE 365


title: Y3244T

description: SAMPLE 360


title: Y3341T

description: SAMPLE 367


title: Y3333T

description: SAMPLE 368


title: Y2985T

description: SAMPLE 364


title: Y3344T

description: SAMPLE 369


title: Y4001T

description: SAMPLE 374


title: Y2691T

description: SAMPLE 363


title: Y4472T

description: SAMPLE 358


title: Y4771T

description: SAMPLE 357


title: Y4546T

description: SAMPLE 353


title: Y3100T

description: SAMPLE 350


title: Y583T

description: SAMPLE 347


title: Y2221T

description: SAMPLE 351


title: Y585T

description: SAMPLE 349


title: Y2873T

description: SAMPLE 335


title: Y3098T

description: SAMPLE 352


title: Y584T

description: SAMPLE 348


title: Y2860T

description: SAMPLE 336


title: Y3527T

description: SAMPLE 333


title: Y3594T

description: SAMPLE 334


title: Y2224T

description: SAMPLE 391


title: Y3499T

description: SAMPLE 332


title: Y4770T

description: SAMPLE 356


title: Y580T

description: SAMPLE 344


title: Y4712T

description: SAMPLE 354


title: Y3649T

description: SAMPLE 340


title: Y4667T

description: SAMPLE 330


title: Y582T

description: SAMPLE 346


title: Y3054T

description: SAMPLE 337


title: Y3747T

description: SAMPLE 339


title: Y577T

description: SAMPLE 342


title: Y3467T

description: SAMPLE 331


title: Y581T

description: SAMPLE 345


title: Y578T

description: SAMPLE 343


title: Y4662T

description: SAMPLE 329


title: Y3082T

description: SAMPLE 338


title: Y4635T

description: SAMPLE 328


title: Y4296T

description: SAMPLE 319


title: Y3512T

description: SAMPLE 317


title: Y3614T

description: SAMPLE 311


title: Y4736T

description: SAMPLE 355


title: Y4427T

description: SAMPLE 324


title: Y3643T

description: SAMPLE 313


title: Y4360T

description: SAMPLE 322


title: Y4535T

description: SAMPLE 325


title: Y3768T

description: SAMPLE 315


title: Y3769T

description: SAMPLE 316


title: Y4348T

description: SAMPLE 321


title: Y4409T

description: SAMPLE 323


title: Y4299T

description: SAMPLE 320


title: Y4634T

description: SAMPLE 327


title: Y3734T

description: SAMPLE 308


title: Y3607T

description: SAMPLE 310


title: Y3625T

description: SAMPLE 304


title: Y3657T

description: SAMPLE 306


title: Y3646T

description: SAMPLE 305


title: Y3672T

description: SAMPLE 314


title: Y3624T

description: SAMPLE 303


title: Y3737T

description: SAMPLE 309


title: Y4282T

description: SAMPLE 318


title: Y3572T

description: SAMPLE 300


title: Y2423T

description: SAMPLE 301


title: Y3628T

description: SAMPLE 312


title: Y3715T

description: SAMPLE 307


title: Y2569T

description: SAMPLE 302


title: Y3381T

description: SAMPLE 298


title: Y3473T

description: SAMPLE 299


title: Y539T

description: SAMPLE 281


title: Y533T

description: SAMPLE 280


title: Y595T

description: SAMPLE 293


title: Y516T

description: SAMPLE 275


title: Y522T

description: SAMPLE 279


title: Y587T

description: SAMPLE 285


title: Y589T

description: SAMPLE 287


title: Y592T

description: SAMPLE 290


title: Y2359T

description: SAMPLE 270


title: Y591T

description: SAMPLE 289


title: Y590T

description: SAMPLE 288


title: Y588T

description: SAMPLE 286


title: Y510T

description: SAMPLE 272


title: Y519T

description: SAMPLE 277


title: Y594T

description: SAMPLE 292


title: Y518T

description: SAMPLE 276


title: Y3514T

description: SAMPLE 297


title: Y521T

description: SAMPLE 278


title: Y596T

description: SAMPLE 294


title: Y540T

description: SAMPLE 282


title: Y593T

description: SAMPLE 291


title: Y586T

description: SAMPLE 284


title: Y515T

description: SAMPLE 274


title: Y514T

description: SAMPLE 273


title: Y506T

description: SAMPLE 271


title: Y558T

description: SAMPLE 283


title: Y4570T

description: SAMPLE 326


title: Y2234T

description: SAMPLE 268


title: Y2339T

description: SAMPLE 269


title: Y2711T

description: SAMPLE 267


title: Y2473T

description: SAMPLE 264


title: Y2411T

description: SAMPLE 262


title: Y3417T

description: SAMPLE 259


title: Y3382T

description: SAMPLE 256


title: Y3307T

description: SAMPLE 251


title: Y2658T

description: SAMPLE 266


title: Y3437T

description: SAMPLE 249


title: Y3402T

description: SAMPLE 257


title: Y3455T

description: SAMPLE 250


title: Y572T

description: SAMPLE 247


title: Y3361T

description: SAMPLE 255


title: Y2417T

description: SAMPLE 263


title: Y568T

description: SAMPLE 244


title: Y3317T

description: SAMPLE 253


title: Y2540T

description: SAMPLE 265


title: Y3309T

description: SAMPLE 252


title: Y569T

description: SAMPLE 245


title: Y3347T

description: SAMPLE 254


title: Y566T

description: SAMPLE 242


title: Y571T

description: SAMPLE 246


title: Y2372T

description: SAMPLE 260


title: Y567T

description: SAMPLE 243


title: Y550T

description: SAMPLE 238


title: Y563T

description: SAMPLE 240


title: Y564T

description: SAMPLE 241


title: Y561T

description: SAMPLE 239


title: Y3262T

description: SAMPLE 237


title: Y2400T

description: SAMPLE 261


title: Y3099T

description: SAMPLE 233


title: Y3090T

description: SAMPLE 232


title: Y3233T

description: SAMPLE 236


title: Y573T

description: SAMPLE 248


title: Y3024T

description: SAMPLE 229


title: Y3164T

description: SAMPLE 234


title: Y2776T

description: SAMPLE 215


title: Y3089T

description: SAMPLE 231


title: Y2833T

description: SAMPLE 227


title: Y3561T

description: SAMPLE 209


title: Y3428T

description: SAMPLE 208


title: Y2869T

description: SAMPLE 228


title: Y3426T

description: SAMPLE 206


title: Y2818T

description: SAMPLE 216


title: Y3569T

description: SAMPLE 211


title: Y3554T

description: SAMPLE 193


title: Y3551T

description: SAMPLE 192


title: Y3036T

description: SAMPLE 230


title: Y3420T

description: SAMPLE 205


title: Y3427T

description: SAMPLE 207


title: Y3566T

description: SAMPLE 210


title: Y3577T

description: SAMPLE 212


title: Y3555T

description: SAMPLE 194


title: Y3603T

description: SAMPLE 214


title: MC3T3-E1, Wnt3a overexpression

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

description: osteoblastic cells, MC3T3-E1, cultured in proliferation medium after overexpression of the Wnt3a gene with Adenovirus vector

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: osteoblastic cells, MC3T3-E1

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: Cultures in alpha-MEM with 10% FBS, containing 100 units/mL penicillin, and 100 microgram/mL streptomycin

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

treatment_protocol: Overexpression of the genes with recombinant Adenovirus vector

tag: genotype/variation


title: MC3T3-E1, control with GFP expression

description: osteoblastic cells, MC3T3-E1, cultured in proliferation medium after overexpression of the GFP gene with Adenovirus vector


title: Y3589T

description: SAMPLE 213


title: Y3544T

description: SAMPLE 190


title: FECD_cultured_corneal_endothelial_cells_005_rep1

city: Québec

first: Stéphanie

last: Proulx

state: Qc

address: 1050 Chemin Ste-Foy

country: Canada

institute: Université Laval

description: Gene expression of passage 2 cells after 14 days of post-confluency

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10,7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: primary corneal endothelial cell population

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50-200 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions

growth_protocol: Cell populations were expanded in culture medium made of OptiMem-I, 8 % fetal bovine serum, 5 ng/mL human epidermal growth factor, 20 ng/mL nerve growth factor, 100 μg/mL bovine pituitary extract, 20 μg/mL ascorbic acid, 0.08 % chondroitin sulfate, 25 μg/mL gentamicin sulfate and 100 IU/mL penicillin G. Cells were maintained in 37°C and 8% CO2 incubators.

extract_protocol:
Isolation protocol: Cells were isolated from mechanically peeled Descemet's membrane using EDTA 0.02% treatment. They were then seeded in culture dishes for expansion.
Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Cat#74104)

treatment_protocol: Cells were cultivated post-confluency for a minimum of 14 days in the same culture medium, with 0.4 μg/mL hydrocortisone added for the last 7 days.

tag: disease

value: FECD


title: FECD_cultured_corneal_endothelial_cells_003_rep1


title: FECD_cultured_corneal_endothelial_cells_004_rep1


title: FECD_cultured_corneal_endothelial_cells_001_rep1


title: EyeBank_cultured_corneal_endothelial_cells_006_rep1

value: no corneal pathology associated


title: Y3532T

description: SAMPLE 188


title: Y3409T

description: SAMPLE 258


title: FECD_cultured_corneal_endothelial_cells_006_rep1


title: N3

first: Xia

last: Lin

address: Jiefang Road 88

institute: Zhejiang University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: 4T1 cell

growth_protocol: 4T1 cells were cultivated in 96-well plate at the concentration of one cell per well with 300μL complete RPMI-1640. After 14 days of culture, SC and NSC were separated for further study.

extract_protocol:
4T1 cells were cultivated in 96-well plate at the concentration of one cell per well with 200 μL complete RPMI-1640. After 14 days of culture, 10 SC clones and 10 NSC clones were randomly collected. We collect three batches of SC and NSC from 3 independent experiments. Total RNA was extracted using the RNeasy kit (Qiagen, Germany). The quality of the total RNA was verified with the BioAnalyzer (Agilent, Santa Clara, CA, USA).
mRNA-seq library is prepared for sequencing using standard Illumina protocols.

value: BALB/C

value: breast cancer cell

tag: cell type


title: Y3533T

description: SAMPLE 189


title: Y3516T

description: SAMPLE 187


title: S3

value: breast cancer stem cell


title: N1


title: Y3515T

description: SAMPLE 186


title: N2


title: EyeBank_cultured_corneal_endothelial_cells_005_rep1


title: EyeBank_cultured_corneal_endothelial_cells_001_rep1


title: EyeBank_cultured_corneal_endothelial_cells_004_rep1


title: EyeBank_cultured_corneal_endothelial_cells_002_rep1


title: Y3501T

description: SAMPLE 185


title: Y3496T

description: SAMPLE 184


title: EyeBank_cultured_corneal_endothelial_cells_003_rep1


title: S2


title: S1


title: FECD_cultured_corneal_endothelial_cells_002_rep1


title: Y3491T

description: SAMPLE 173


title: Y3489T

description: SAMPLE 172


title: Y4265T

description: SAMPLE 158


title: Y4263T

description: SAMPLE 157


title: Y4277T

description: SAMPLE 160


title: TUMOR_WR_GRADE4

city: beijing

first: xin

last: chen

address: 6 tiantanxili

institute: Beijing Tiantan Hospital

description: Gene expression data from embryos in BSGs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip miRNA 4.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RMA for Affymetrix data as normalization method.

source_name: TUMOR OF GRADE4

label_protocol: MiRNAs were labelled using the FlashTag™ Biotin RNA Labeling Kit

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

tag: age (y)

tag: gender

value: F

tag: pathology diagnosis

value: GBM

tag: os (m)

tag: alive/dead

value: Dead


title: Y4305T

description: SAMPLE 161

tag: age

tag: Sex

tag: ptstage

tag: pnstage


title: MC3T3-E1, Wnt4 overexpression

description: osteoblastic cells, MC3T3-E1, cultured in proliferation medium after overexpression of the Wnt4 gene with Adenovirus vector


title: Y3485T

description: SAMPLE 171

tag: tissue

tag: death

tag: duration overall survival


title: Y3480T

description: SAMPLE 168


title: Y3482T

description: SAMPLE 169


title: TUMOR_ZBF_GRADE4

value: M


title: Y3558T

description: SAMPLE 195


title: TUMOR_ZSQ_GRADE4


title: Y3194T

description: SAMPLE 235


title: Y4245T

description: SAMPLE 153


title: Y4260T

description: SAMPLE 156


title: Y4788T

description: SAMPLE 152


title: TUMOR_LXX_GRADE4


title: Y4256T

description: SAMPLE 155


title: TUMOR_MJF_GRADE4


title: Y4273T

description: SAMPLE 159


title: Y4253T

description: SAMPLE 154


title: Y4737T

description: SAMPLE 151


title: Y3484T

description: SAMPLE 170


title: Y4721T

description: SAMPLE 149


title: Y4708T

description: SAMPLE 148


title: Y4724T

description: SAMPLE 150


title: Y4689T

description: SAMPLE 147


title: Y4658T

description: SAMPLE 146


title: TUMOR_LBY_GRADE4


title: TUMOR_HDX_GRADE4


title: TUMOR_SJN_GRADE3

source_name: TUMOR OF GRADE3

value: AA


title: Y4638T

description: SAMPLE 145

value: gastric cancer


title: Y4889T

description: SAMPLE 137


title: Y4869T

description: SAMPLE 136


title: TUMOR_JB_GRADE3


title: Y4188T

description: SAMPLE 143

value: female


title: Y4236T

description: SAMPLE 132

value: male


title: TUMOR_GHY_GRADE4


title: TUMOR_LMQ_GRADE3


title: TUMOR_DGY_GRADE4


title: TUMOR_HMY_GRADE4


title: TUMOR_RQY_GRADE2

source_name: TUMOR OF GRADE2

value: A

value: Alive


title: Y4617T

description: SAMPLE 144


title: MC3T3-E1, Wnt5a overexpression

description: osteoblastic cells, MC3T3-E1, cultured in proliferation medium after overexpression of the Wnt5a gene with Adenovirus vector


title: TUMOR_ZYB_GRADE3


title: Y4812T

description: SAMPLE 134


title: TUMOR_CHY_GRADE3


title: Y4222T

description: SAMPLE 131


title: Y4863T

description: SAMPLE 135


title: Y4244T

description: SAMPLE 133


title: Y3550T

description: SAMPLE 191


title: TUMOR_KLT_GRADE2


title: TUMOR_LDQ_GRADE2


title: TUMOR_ZJH_GRADE1

source_name: TUMOR OF GRADE1

value: PA


title: TUMOR_CLL_GRADE2


title: TUMOR_LCX_GRADE1


title: TUMOR_WRY_GRADE1


title: Y4221T

description: SAMPLE 130


title: Y4216T

description: SAMPLE 129


title: TUMOR_CLS_GRADE1


title: TUMOR_FBL_GRADE1


title: Y4214T

description: SAMPLE 128


title: Y3983T

description: SAMPLE 119


title: Y3976T

description: SAMPLE 118


title: Y4162T

description: SAMPLE 120


title: Y3944T

description: SAMPLE 116


title: Y4180T

description: SAMPLE 121


title: Y3958T

description: SAMPLE 117


title: Y4430T

description: SAMPLE 114


title: Y4189T

description: SAMPLE 122


title: Y4588T

description: SAMPLE 113


title: Y4568T

description: SAMPLE 111


title: Y4198T

description: SAMPLE 126


title: Y4197T

description: SAMPLE 125


title: Y4580T

description: SAMPLE 112


title: Y2827T

description: SAMPLE 115


title: Y4204T

description: SAMPLE 127


title: Y4194T

description: SAMPLE 124


title: Y4190T

description: SAMPLE 123


title: Y4548T

description: SAMPLE 110


title: Y4531T

description: SAMPLE 109


title: Y4101T

description: SAMPLE 103


title: Y4142T

description: SAMPLE 107


title: Y4109T

description: SAMPLE 105


title: Y4507T

description: SAMPLE 108


title: Y4092T

description: SAMPLE 101


title: Genomic DNA from prostate_32_tumor

city: London

first: Bekim

last: Sadikovic

state: Ontario

address: 800 Commissioners Rd E

department: Pathology and Laboratory Medicine

institute: University of Western Ontario

description: SAMPLE 47

hyb_protocol: According to the manufacturer's protocol

scan_protocol: iScan

data_processing: Illumina Normalization method with background coorection, using minfi package in R 3.4.2

label: Cy5 and Cy3

extract_protocol: Archival formalin-fixed paraffin-embedded tissues were collected. The slides were reviewed by a pathologist to identify representative tumor tissue blocks. Enrichment of tumor cells was performed by tissue macro-dissection of predetermined areas, as outlined by Haemotoxylin and Eosin staining. Seven-micron thick sections in isolated areas of interest with at least 50% tumor cellularity were dissected to be used as tumor samples. Normal prostate samples were obtained from the adjacent tissues demonstrating no tumor involvement.

tag: sample preparation

value: FFPE

tag: tumor cellularity

value: prostate tumor

tag: source id


title: Y4138T

description: SAMPLE 106


title: Y3934T

description: SAMPLE 100


title: Y4107T

description: SAMPLE 104


title: Y4095T

description: SAMPLE 102


title: Genomic DNA from prostate_16_tumor

description: SAMPLE 46

label_protocol: According to the manufacturer's protocol


title: Y3903T

description: SAMPLE 94


title: Y2849T

description: SAMPLE 93


title: Y3831T

description: SAMPLE 96


title: Y3926T

description: SAMPLE 98


title: Y4444T

description: SAMPLE 92


title: Genomic DNA from prostate_29_tumor

description: SAMPLE 42


title: Y4083T

description: SAMPLE 91


title: Genomic DNA from prostate_16_normal

description: SAMPLE 44

value: Adjacent normal prostate tissue


title: Genomic DNA from prostate_31_tumor

description: SAMPLE 45


title: Genomic DNA from prostate_27_tumor

description: SAMPLE 36


title: Genomic DNA from prostate_14_normal

description: SAMPLE 37


title: Y4074T

description: SAMPLE 90


title: Genomic DNA from prostate_14_tumor

description: SAMPLE 39


title: Genomic DNA from prostate_15_normal

description: SAMPLE 41


title: Genomic DNA from prostate_13_tumor

description: SAMPLE 35


title: Genomic DNA from prostate_12_tumor

description: SAMPLE 34


title: Y4064T

description: SAMPLE 89


title: TUMOR_LYC_GRADE2

value: OA


title: Genomic DNA from prostate_22_tumor

description: SAMPLE 40


title: Genomic DNA from prostate_28_tumor

description: SAMPLE 38


title: Genomic DNA from prostate_12_normal

description: SAMPLE 32


title: Genomic DNA from prostate_13_normal

description: SAMPLE 33


title: Y4053T

description: SAMPLE 87


title: Y4063T

description: SAMPLE 88


title: Genomic DNA from prostate_9_tumor

description: SAMPLE 27


title: Genomic DNA from prostate_11_normal

description: SAMPLE 29


title: Y4046T

description: SAMPLE 86


title: Y3932T

description: SAMPLE 99


title: Y3920T

description: SAMPLE 97


title: Y4009T

description: SAMPLE 85


title: Genomic DNA from prostate_10_tumor

description: SAMPLE 28


title: Genomic DNA from prostate_11_tumor

description: SAMPLE 31


title: Y3316T

description: SAMPLE 83


title: Y3746T

description: SAMPLE 81


title: Genomic DNA from prostate_9_normal

description: SAMPLE 25


title: Genomic DNA from prostate_18_tumor

description: SAMPLE 30


title: Y2245T

description: SAMPLE 78


title: Genomic DNA from prostate_17_tumor

description: SAMPLE 24


title: Y2449T

description: SAMPLE 80


title: Y2582T

description: SAMPLE 77


title: Genomic DNA from prostate_8_tumor

description: SAMPLE 23


title: Y3412T

description: SAMPLE 76


title: Genomic DNA from prostate_30_tumor

description: SAMPLE 43


title: Y3220T

description: SAMPLE 75


title: Y2252T

description: SAMPLE 79


title: Y2979T

description: SAMPLE 74


title: Genomic DNA from prostate_26_tumor

description: SAMPLE 22


title: Genomic DNA from prostate_8_normal

description: SAMPLE 21


title: Y2847T

description: SAMPLE 71


title: Genomic DNA from prostate_25_tumor

description: SAMPLE 20


title: Y3912T

description: SAMPLE 95


title: Y3477T

description: SAMPLE 70


title: Genomic DNA from prostate_19_tumor

description: SAMPLE 18


title: Genomic DNA from prostate_6_tumor

description: SAMPLE 16


title: Genomic DNA from prostate_5_tumor

description: SAMPLE 15


title: Genomic DNA from prostate_6_normal

description: SAMPLE 14


title: Y3679T

description: SAMPLE 82


title: Y3062T

description: SAMPLE 69


title: Y3462T

description: SAMPLE 73


title: Genomic DNA from prostate_7_tumor

description: SAMPLE 19


title: Y3092T

description: SAMPLE 67


title: Y2993T

description: SAMPLE 72


title: Genomic DNA from prostate_7_normal

description: SAMPLE 17


title: Y2845T

description: SAMPLE 66


title: Genomic DNA from prostate_4_normal

description: SAMPLE 9


title: Y3988T

description: SAMPLE 84


title: 181: cell free DNA from plasma

type: other

city: Vilnius

first: Algimantas

last: Krisciunas

address: Sauletekio al. 7

country: Lithuania

institute: Vilnius University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing:
The sample data were processed using R package minfi (Aryee et al. 2014). Raw modification values were extracted using getM and preprocessRaw functions. At each of the 485,577 cytosines interrogated by the microarray, cytosine modification level was summarized by calculating the M value defined as log2 ( (M+100)/ (U+100)), where M and U are the methylated (M) and unmethylated (U) signal intensities (Du et al. 2010). Cytosines were annotated using the Illumina HumanMethylation450 manifest file (GEO GPL13534) and those from sex chromosomes were removed. In addition, polymorphic cytosines and cross-hybridizing probes were also removed (Chen et al. 2013) (total 382,378 cytosines). Outlying samples were identified from the obtained modification data using the following algorithm: first, a k-nearest neighbour imputation algorithm (impute.knn) was used to fill missing cytosine values. Next, using the raw data matrix each sample was projected into two-dimensional space using multidimensional scaling (cmdscale) that preserves sample distances while reducing dimensionality. For each sample, its mean distance to the 15 nearest samples was computed. The samples that deviated from the mean of the resulting distribution by more than three standard deviations were identified as outliers and removed from subsequent analysis (N=18)
minfi Quantile normalised Average Beta values. NAs inserted for outlier samples.
Unmethylated and methylated signal intensities

molecule: other

source_name: plasma

label_protocol: Standard Illumina Protocol

extract_protocol: cell free DNA was extracted and purified from plasma samples using QIAmp Circulating Nucleic Acid Kit according to manufacturer instructions

tag: diagnosis

value: prostrate cancer

value: plasma

tag: individual id

tag: visit

tag: center

value: BC

tag: cohort

value: Pilot

tag: treatment respsonse

value: Sensitive

tag: psa amount

tag: visit time point

tag: outlier

value: TRUE

tag: phenotype

value: Sensitive to AA treatment


title: Genomic DNA from prostate_5_normal

description: SAMPLE 13


title: Y3094T

description: SAMPLE 63

value: gastric cancer

tag: age

tag: Sex

tag: ptstage

tag: pnstage


title: Genomic DNA from prostate_20_tumor

description: SAMPLE 12

tag: sample preparation

tag: tissue


title: Y2885T

description: SAMPLE 64

tag: death

tag: duration overall survival


title: 179: cell free DNA from plasma

tag: diagnosis

tag: individual id

value: FALSE


title: Y3045T

description: SAMPLE 65

value: male


title: 178: cell free DNA from plasma

tag: visit

tag: center


title: Y2785T

description: SAMPLE 62

value: female


title: Y2695T

description: SAMPLE 68


title: Genomic DNA from prostate_3_tumor

description: SAMPLE 8

tag: tumor cellularity

tag: source id


title: 177: cell free DNA from plasma

value: BL

tag: cohort

tag: treatment respsonse

tag: psa amount

tag: visit time point


title: Y3456T

description: SAMPLE 61

tag: age

tag: Sex


title: Genomic DNA from prostate_3_normal

description: SAMPLE 6


title: Genomic DNA from prostate_4_tumor

description: SAMPLE 11


title: 176: cell free DNA from plasma

value: EoT

tag: outlier

tag: phenotype


title: Y3065T

description: SAMPLE 60

tag: tissue

tag: ptstage

tag: pnstage


title: Genomic DNA from prostate_2_tumor

description: SAMPLE 7

tag: sample preparation

value: FFPE


title: Y2755T

description: SAMPLE 59

tag: death

tag: duration overall survival


title: 173: cell free DNA from plasma

tag: diagnosis

tag: individual id

tag: visit

tag: center


title: 175: cell free DNA from plasma

tag: cohort

tag: treatment respsonse


title: 171: cell free DNA from plasma

tag: psa amount

tag: visit time point


title: Y4730T

description: SAMPLE 57

tag: age

tag: Sex


title: Y2602T

description: SAMPLE 58


title: 180: cell free DNA from plasma

tag: outlier

tag: phenotype


title: Genomic DNA from prostate_24_tumor

description: SAMPLE 4

tag: tumor cellularity

tag: tissue

value: prostate tumor

tag: source id


title: 169: cell free DNA from plasma


title: Genomic DNA from prostate_1_tumor

description: SAMPLE 3

tag: sample preparation


title: Y4670T

description: SAMPLE 55

tag: ptstage

tag: pnstage

tag: death

tag: duration overall survival


title: Y4561T

description: SAMPLE 53


title: Y2663T

description: SAMPLE 56


title: Y4595T

description: SAMPLE 54


title: DNA methylation of normal esophagus sample

city: Shantou

first: Qian

last: Yang

state: Guangdong

address: Xinling 22 Road

institute: Medical College of Shantou University

description: normal esophagus tissue

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: GenomeStudio Methylation Module v1.8

source_name: esophagus tissue

extract_protocol: genomic DNA was extracted and purified according to standard instructions in Illumina

tag: gender

value: Male

value: normal esophagus


title: 166: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

tag: individual id

tag: visit

tag: center

value: PMH

tag: cohort


title: Y4549T

description: SAMPLE 52

tag: age

tag: Sex


title: 167: cell free DNA from plasma

value: plasma

tag: treatment respsonse

tag: psa amount

tag: visit time point

tag: outlier

tag: phenotype


title: Genomic DNA from prostate_1_normal

description: SAMPLE 1

tag: sample preparation

tag: tumor cellularity

tag: tissue

value: Adjacent normal prostate tissue

tag: source id


title: DNA methylation of fibrosarcoma with ESCC sample

description: fibrosarcoma with ESCC tissue

tag: gender

value: fibrosarcoma with ESCC


title: Genomic DNA from prostate_23_tumor

description: SAMPLE 2


title: Y3275T

description: SAMPLE 48

tag: ptstage

tag: pnstage

tag: death

tag: duration overall survival


title: Y3372T

description: SAMPLE 50


title: 164: cell free DNA from plasma

tag: diagnosis

tag: individual id

tag: visit

tag: center

tag: cohort

value: Pilot

value: Sensitive

value: TRUE


title: 168: cell free DNA from plasma

tag: age

tag: treatment respsonse

tag: psa amount

tag: visit time point

value: Sensitive to AA treatment


title: 165: cell free DNA from plasma

tag: outlier

value: FALSE

tag: phenotype


title: 172: cell free DNA from plasma

tag: tissue

value: BC


title: 174: cell free DNA from plasma


title: 161: cell free DNA from plasma

value: Resistant

value: Resistant to AA treatment


title: Genomic DNA from prostate_2_normal

description: SAMPLE 5

tag: sample preparation

value: FFPE

tag: tumor cellularity

tag: source id


title: Genomic DNA from prostate_21_tumor

description: SAMPLE 10

value: prostate tumor


title: Genomic DNA from prostate_10_normal

description: SAMPLE 26


title: 163: cell free DNA from plasma


title: Y3252T

description: SAMPLE 49

value: gastric cancer

tag: Sex

value: female

tag: ptstage

tag: pnstage

tag: death


title: Y3320T

description: SAMPLE 46

value: male

tag: duration overall survival


title: Y3335T

description: SAMPLE 45


title: Y4539T

description: SAMPLE 51


title: Y3396T

description: SAMPLE 47


title: 162: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

tag: individual id

tag: visit

tag: center

value: PMH


title: Y2497T

description: SAMPLE 42

tag: age


title: 159: cell free DNA from plasma

value: plasma

tag: cohort

tag: treatment respsonse

tag: psa amount

tag: visit time point


title: 160: cell free DNA from plasma

tag: tissue

value: BL

tag: outlier

tag: phenotype


title: 158: cell free DNA from plasma

value: EoT


title: 153: cell free DNA from plasma


title: Y3894T

description: SAMPLE 38

tag: Sex


title: 157: cell free DNA from plasma


title: Y2498T

description: SAMPLE 43

tag: ptstage


title: 155: cell free DNA from plasma


title: 156: cell free DNA from plasma


title: 154: cell free DNA from plasma


title: Y2509T

description: SAMPLE 39

tag: pnstage


title: Y2499T

description: SAMPLE 44

tag: death


title: 150: cell free DNA from plasma

value: Sensitive


title: 152: cell free DNA from plasma


title: Y2488T

description: SAMPLE 41

tag: duration overall survival


title: Y3885T

description: SAMPLE 35


title: 151: cell free DNA from plasma

tag: diagnosis

value: TRUE


title: Y3887T

description: SAMPLE 36


title: Y2507T

description: SAMPLE 40


title: Y3892T

description: SAMPLE 37


title: 149: cell free DNA from plasma

tag: individual id


title: 146: cell free DNA from plasma

tag: visit


title: 147: cell free DNA from plasma

tag: center


title: 148: cell free DNA from plasma

tag: age

value: Sensitive to AA treatment


title: 145: cell free DNA from plasma

tag: cohort

value: FALSE


title: 144: cell free DNA from plasma

value: BC

tag: treatment respsonse


title: 143: cell free DNA from plasma

value: Resistant

tag: psa amount


title: Y3884T

description: SAMPLE 34


title: Y3873T

description: SAMPLE 32


title: Y3846T

description: SAMPLE 27


title: Y3838T

description: SAMPLE 25


title: Y3883T

description: SAMPLE 33


title: Y3863T

description: SAMPLE 29


title: Y3868T

description: SAMPLE 30


title: 139: cell free DNA from plasma

tag: visit time point


title: Y3819T

description: SAMPLE 24

tag: tissue


title: Y3847T

description: SAMPLE 28


title: 141: cell free DNA from plasma

tag: outlier

value: Resistant to AA treatment


title: 140: cell free DNA from plasma

tag: phenotype


title: 138: cell free DNA from plasma


title: Y3872T

description: SAMPLE 31

tag: Sex


title: 136: cell free DNA from plasma


title: 135: cell free DNA from plasma


title: 170: cell free DNA from plasma

value: Pilot


title: 137: cell free DNA from plasma


title: 134: cell free DNA from plasma


title: 133: cell free DNA from plasma


title: Y3844T

description: SAMPLE 26

tag: ptstage


title: 142: cell free DNA from plasma


title: 131: cell free DNA from plasma


title: 128: cell free DNA from plasma


title: 129: cell free DNA from plasma


title: 127: cell free DNA from plasma


title: 126: cell free DNA from plasma


title: 124: cell free DNA from plasma


title: 125: cell free DNA from plasma


title: Y3804T

description: SAMPLE 23

tag: pnstage


title: 132: cell free DNA from plasma


title: Y4494T

description: SAMPLE 16

tag: death


title: Y4438T

description: SAMPLE 15

tag: duration overall survival


title: Y4325T

description: SAMPLE 17


title: 123: cell free DNA from plasma

tag: diagnosis


title: Y4349T

description: SAMPLE 13


title: Y4310T

description: SAMPLE 22


title: Y4439T

description: SAMPLE 18


title: Y4429T

description: SAMPLE 12


title: Y4344T

description: SAMPLE 20


title: Y4386T

description: SAMPLE 19


title: Y4367T

description: SAMPLE 14


title: 130: cell free DNA from plasma

tag: individual id


title: Y4397T

description: SAMPLE 9


title: Y4396T

description: SAMPLE 11


title: Y4390T

description: SAMPLE 10


title: Y4314T

description: SAMPLE 6


title: Y4442T

description: SAMPLE 8


title: 122: cell free DNA from plasma

tag: visit


title: 121: cell free DNA from plasma

tag: center


title: Y4313T

description: SAMPLE 21

tag: age


title: 120: cell free DNA from plasma

tag: cohort


title: Y4426T

description: SAMPLE 7


title: Y4317T

description: SAMPLE 5


title: 118: cell free DNA from plasma

tag: treatment respsonse


title: 115: cell free DNA from plasma

tag: psa amount


title: 112: cell free DNA from plasma

tag: visit time point


title: 111: cell free DNA from plasma

tag: tissue


title: 117: cell free DNA from plasma

tag: outlier


title: 114: cell free DNA from plasma

tag: phenotype


title: 116: cell free DNA from plasma


title: 119: cell free DNA from plasma


title: 113: cell free DNA from plasma


title: Y4340T

description: SAMPLE 4

tag: Sex


title: Y10192T

description: SAMPLE 76

tag: ptstage


title: Y10195T

description: SAMPLE 78

tag: pnstage


title: Y4404T

description: SAMPLE 2

tag: death


title: Y10200T

description: SAMPLE 82

tag: duration overall survival


title: Y4316T

description: SAMPLE 3


title: Y10189T

description: SAMPLE 73


title: Y10191T

description: SAMPLE 75


title: Y10199T

description: SAMPLE 81


title: Y10186T

description: SAMPLE 71


title: Y10196T

description: SAMPLE 79


title: Y10179T

description: SAMPLE 65


title: Y10198T

description: SAMPLE 80


title: Y10193T

description: SAMPLE 77


title: Y10180T

description: SAMPLE 66


title: 106: cell free DNA from plasma

tag: diagnosis


title: 103: cell free DNA from plasma

tag: individual id


title: 110: cell free DNA from plasma

tag: visit


title: 109: cell free DNA from plasma

tag: center


title: 108: cell free DNA from plasma

tag: age


title: Y10188T

description: SAMPLE 72


title: 104: cell free DNA from plasma

tag: cohort


title: 102: cell free DNA from plasma

tag: treatment respsonse


title: 107: cell free DNA from plasma

tag: psa amount


title: 105: cell free DNA from plasma

tag: visit time point


title: Y10182T

description: SAMPLE 68

tag: tissue


title: Y10184T

description: SAMPLE 70


title: Y10181T

description: SAMPLE 67


title: Y10190T

description: SAMPLE 74


title: Y10183T

description: SAMPLE 69


title: 101: cell free DNA from plasma

tag: outlier


title: Y4080T

description: SAMPLE 1


title: 97: cell free DNA from plasma

tag: phenotype


title: 100: cell free DNA from plasma


title: 99: cell free DNA from plasma


title: 95: cell free DNA from plasma


title: 96: cell free DNA from plasma


title: 93: cell free DNA from plasma


title: 98: cell free DNA from plasma


title: 92: cell free DNA from plasma


title: Wildtype_CMP_3

description:
Wildtype CMP
sample name in non-normalized data file:
iltp2455-30

source_name: Wildtype Bone Marrow

tag: strain

value: BALB/c

tag: cell type abbreviation

value: CMP

tag: cell type full

value: Common Myeloid Progenitor

tag: antibodies

value: Lin- Sca-1- c-Kit+ CD34+ FcRlo

value: Bone Marrow

tag: genotype

value: Wildtype


title: Y10174T

description: SAMPLE 62

value: gastric cancer

tag: Sex

value: male

tag: ptstage

tag: pnstage

tag: death

tag: duration overall survival


title: Wildtype_GMP_1

description:
Wildtype GMP
sample name in non-normalized data file:
iltp2455-22

value: GMP

value: Granulocyte Macrophage Progenitor

value: Lin- Sca-1- c-Kit+ CD34+ FcR+


title: Wildtype_GMP_3

description:
Wildtype GMP
sample name in non-normalized data file:
iltp2455-3


title: Y10178T

description: SAMPLE 64

tag: age

value: female


title: Wildtype_GMP_2

description:
Wildtype GMP
sample name in non-normalized data file:
iltp2455-25


title: Wildtype_EoP_3

description:
Wildtype EoP
sample name in non-normalized data file:
iltp2455-4

value: EoP

value: Eosinophil Progenitor

value: Lin- c-Kit+ Sca1- CD34+ CD16/32+ IL5Ra+


title: 91: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

value: plasma

tag: individual id

tag: visit

tag: center

value: PMH

tag: cohort

tag: treatment respsonse

value: Resistant

value: FALSE

value: Resistant to AA treatment


title: Y10173T

description: SAMPLE 61

tag: tissue


title: Y10172T

description: SAMPLE 60


title: 90: cell free DNA from plasma

value: BL

value: BC

value: Sensitive

tag: psa amount

tag: visit time point

tag: outlier

tag: phenotype

value: Sensitive to AA treatment


title: Y10177T

description: SAMPLE 63

value: gastric cancer

tag: Sex


title: Wildtype_EoP_2

description:
Wildtype EoP
sample name in non-normalized data file:
iltp2455-24

tag: strain

value: BALB/c

tag: cell type abbreviation

tag: cell type full

tag: antibodies

value: Bone Marrow

tag: genotype

value: Wildtype


title: Wildtype_CMP_2

description:
Wildtype CMP
sample name in non-normalized data file:
iltp2455-19

value: CMP

value: Common Myeloid Progenitor

value: Lin- Sca-1- c-Kit+ CD34+ FcRlo


title: 94: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

tag: age


title: 89: cell free DNA from plasma

value: plasma

tag: individual id

tag: visit


title: Y10166T

description: SAMPLE 54

value: female

tag: ptstage

tag: pnstage

tag: death

tag: duration overall survival


title: Y10167T

description: SAMPLE 55

tag: tissue

value: male


title: Y10168T

description: SAMPLE 56


title: Wildtype_EoP_1

description:
Wildtype EoP
sample name in non-normalized data file:
iltp2455-10

value: EoP

value: Eosinophil Progenitor

value: Lin- c-Kit+ Sca1- CD34+ CD16/32+ IL5Ra+


title: Y10171T

description: SAMPLE 59


title: Y10170T

description: SAMPLE 58


title: Y10165T

description: SAMPLE 53


title: 87: cell free DNA from plasma

tag: center

value: PMH

tag: cohort

tag: treatment respsonse

value: Resistant

tag: psa amount

tag: visit time point

tag: outlier

value: FALSE

value: Resistant to AA treatment


title: Wildtype_CMP_1

description:
Wildtype CMP
sample name in non-normalized data file:
iltp2455-16

tag: strain

value: BALB/c

tag: cell type abbreviation

tag: cell type full

tag: antibodies


title: 84: cell free DNA from plasma

tag: diagnosis

tag: age

tag: individual id

tag: phenotype


title: Y10169T

description: SAMPLE 57

value: gastric cancer

tag: Sex

tag: ptstage

tag: pnstage

tag: death


title: 85: cell free DNA from plasma

tag: tissue

tag: visit

value: EoT

tag: center

tag: cohort


title: 88: cell free DNA from plasma

tag: treatment respsonse

tag: psa amount

tag: visit time point

tag: outlier


title: 83: cell free DNA from plasma


title: Y10164T

description: SAMPLE 52

tag: duration overall survival


title: IL5_Transgenic_EoP_3

description:
IL5 Transgenic EoP
sample name in non-normalized data file:
iltp2455-29

source_name: IL5 Transgenic Bone Marrow

tag: strain

tag: cell type abbreviation

tag: cell type full

tag: antibodies

value: Bone Marrow

tag: genotype

value: IL5 Transgenic


title: IL5_Transgenic_GMP_5

description:
IL5 Transgenic GMP
sample name in non-normalized data file:
iltp2455-9

value: GMP

value: Granulocyte Macrophage Progenitor

value: Lin- Sca-1- c-Kit+ CD34+ FcR+


title: Y10161T

description: SAMPLE 51

tag: age

tag: Sex

tag: ptstage


title: IL5_Transgenic_CMP_5

description:
IL5 Transgenic CMP
sample name in non-normalized data file:
iltp2455-27

value: CMP

value: Common Myeloid Progenitor

value: Lin- Sca-1- c-Kit+ CD34+ FcRlo

tag: tissue


title: 86: cell free DNA from plasma

tag: diagnosis

value: prostrate cancer

value: plasma

tag: individual id

tag: visit

tag: phenotype


title: 82: cell free DNA from plasma

tag: center

value: PMH

tag: cohort

tag: treatment respsonse

tag: psa amount


title: Y10159T

description: SAMPLE 50

value: female

tag: pnstage

tag: death

tag: duration overall survival


title: IL5_Transgenic_GMP_4

description:
IL5 Transgenic GMP
sample name in non-normalized data file:
iltp2455-20

tag: strain

tag: cell type abbreviation

tag: cell type full

tag: antibodies


title: 81: cell free DNA from plasma

tag: age

value: BC

value: Resistant

tag: visit time point

tag: outlier

value: FALSE


title: IL5_Transgenic_EoP_2

description:
IL5 Transgenic EoP
sample name in non-normalized data file:
iltp2455-17

value: BALB/c

value: EoP

value: Eosinophil Progenitor

value: Lin- c-Kit+ Sca1- CD34+ CD16/32+ IL5Ra+

tag: tissue

tag: genotype


title: IL5_Transgenic_EoP_1

description:
IL5 Transgenic EoP
sample name in non-normalized data file:
iltp2455-11

value: Bone Marrow

value: IL5 Transgenic


title: IL5_Transgenic_CMP_4

description:
IL5 Transgenic CMP
sample name in non-normalized data file:
iltp2455-2


title: Y10158T

description: SAMPLE 49

value: gastric cancer

tag: Sex

value: male

tag: ptstage


title: 80: cell free DNA from plasma

tag: diagnosis

tag: individual id

tag: visit

tag: center

tag: cohort

value: Sensitive

tag: phenotype

value: Sensitive to AA treatment


title: Y10155T

description: SAMPLE 48

tag: pnstage

tag: death

tag: duration overall survival


title: 78: cell free DNA from plasma

value: prostrate cancer

tag: treatment respsonse

tag: psa amount

value: Resistant to AA treatment


title: Y10152T

description: SAMPLE 45

tag: age


title: Y10154T

description: SAMPLE 47


title: 77: cell free DNA from plasma

value: plasma

value: PMH

tag: visit time point

tag: outlier


title: Snai2 WT ERBB2 nulliparous with metastasis mouse, biological replicate 1

city: Salamanca

first: Jesús

last: Pérez Losada

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

description: Luminal tumor ERBB2+

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The RMA function provided by the package oligo from R/Bioconductor was applied to the raw expression data.

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Ambion)

growth_protocol: All mice were maintained in ventilated filter cages under specific-pathogen-free (SPF) conditions and were fed ad libitum.

treatment_protocol: Not applicable

tag: tissue

value: Mammary tumor

tag: genotype

value: Snai2 WT

tag: erbb2 status

value: nulliparous

tag: metastasis status

value: with metastasis


title: Snai2 WT ERBB2 nulliparous with metastasis mouse, biological replicate 4

description: Luminal tumor ERBB2+


title: Snai2 WT ERBB2 nulliparous with metastasis mouse, biological replicate 2

description: Luminal tumor ERBB2+


title: Snai2 WT ERBB2 nulliparous with metastasis mouse, biological replicate 3

description: Luminal tumor ERBB2+


title: Y10146T

description: SAMPLE 42

tag: Sex

tag: ptstage


title: 76: cell free DNA from plasma

tag: diagnosis

tag: individual id

tag: visit

tag: center

value: BC

value: Resistant

value: FALSE


title: Y10150T

description: SAMPLE 44

tag: pnstage

tag: death


title: Snai2 WT ERBB2 parous with metastasis mouse, biological replicate 4

description: Luminal tumor ERBB2+

source_name: Snai2 WT ERBB2 parous with metastasis

tag: cohort

value: parous


title: Y10148T

description: SAMPLE 43

tag: duration overall survival


title: 75: cell free DNA from plasma

tag: age

tag: treatment respsonse

tag: psa amount

tag: phenotype


title: Snai2 WT ERBB2 parous with metastasis mouse, biological replicate 2

description: Luminal tumor ERBB2+

tag: tissue

tag: genotype


title: 74: cell free DNA from plasma

value: EoT

tag: visit time point

tag: outlier


title: Y10144T

description: SAMPLE 41

value: gastric cancer

tag: Sex

tag: ptstage


title: 79: cell free DNA from plasma

tag: diagnosis

tag: individual id


title: Snai2 WT ERBB2 parous with metastasis mouse, biological replicate 3

description: Luminal tumor ERBB2+

tag: erbb2 status

tag: metastasis status


title: Snai2 WT ERBB2 parous with metastasis mouse, biological replicate 1

description: Luminal tumor ERBB2+


title: Snai2 KO ERBB2 nulliparous without metastasis mouse, biological replicate 2

description: Luminal tumor ERBB2+

value: Snai2 KO

value: without metastasis


title: Snai2 KO ERBB2 nulliparous without metastasis mouse, biological replicate 3

description: Luminal tumor ERBB2+


title: 72: cell free DNA from plasma

tag: visit

tag: center


title: Snai2 KO ERBB2 nulliparous without metastasis mouse, biological replicate 1

description: Luminal tumor ERBB2+

tag: cohort


title: Y10140T

description: SAMPLE 38

tag: age

value: male

tag: pnstage

tag: death

tag: duration overall survival


title: Y10143T

description: SAMPLE 40

tag: tissue


title: Y10133T

description: SAMPLE 33


title: 70: cell free DNA from plasma

value: prostrate cancer

tag: treatment respsonse

tag: psa amount

tag: phenotype


title: Y10136T

description: SAMPLE 34

tag: Sex


title: 73: cell free DNA from plasma

value: BL

tag: visit time point

tag: outlier

value: Resistant to AA treatment


title: Snai2 KO ERBB2 nulliparous with metastasis mouse

description: Luminal tumor ERBB2+

tag: genotype


title: 69: cell free DNA from plasma

tag: diagnosis

value: plasma

tag: individual id


title: Snai2 KO ERBB2 parous without metastasis mouse, biological replicate 3

description: Luminal tumor ERBB2+

value: Mammary tumor

tag: erbb2 status

tag: metastasis status


title: Y10132T

description: SAMPLE 32

tag: ptstage


title: 67: cell free DNA from plasma

tag: age

tag: visit

tag: center

tag: cohort


title: 68: cell free DNA from plasma

tag: tissue


title: Y10131T

description: SAMPLE 31

tag: pnstage

tag: death

tag: duration overall survival


title: Y10130T

description: SAMPLE 30

tag: Sex


title: Y10129T

description: SAMPLE 29


title: Snai2 KO ERBB2 parous without metastasis mouse, biological replicate 2

description: Luminal tumor ERBB2+


title: Snai2 KO ERBB2 parous with metastasis mouse, biological replicate 2

description: Luminal tumor ERBB2+

source_name: Snai2 KO ERBB2 parous with metastasis


title: 66: cell free DNA from plasma

tag: treatment respsonse

tag: psa amount

tag: visit time point

tag: phenotype


title: Snai2 KO ERBB2 parous with metastasis mouse, biological replicate 3

description: Luminal tumor ERBB2+

tag: genotype


title: 64: cell free DNA from plasma

tag: diagnosis

tag: individual id

value: PMH

value: Sensitive

tag: outlier

value: Sensitive to AA treatment


title: 71: cell free DNA from plasma

tag: age

value: BC


title: Snai2 KO ERBB2 parous without metastasis mouse, biological replicate 1

description: Luminal tumor ERBB2+

tag: erbb2 status

tag: metastasis status


title: 63: cell free DNA from plasma

tag: visit

tag: center

tag: cohort


title: 61: cell free DNA from plasma

tag: tissue


title: 62: cell free DNA from plasma


title: 65: cell free DNA from plasma


title: miRNA expression of matched normal esophagus tissue

description:
After the homogenization of the sample hybridization signal, the signal value after logarithmic transformation was performed on the base of 2.
B771N_NS

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)

data_processing: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.

source_name: normal esophagus tissue

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

tag: gender

value: Male

value: normal esophagus


title: Y10121T

description: SAMPLE 24

tag: Sex

tag: ptstage

tag: pnstage

tag: death

tag: duration overall survival


title: Snai2 KO ERBB2 parous with metastasis mouse, biological replicate 1

description: Luminal tumor ERBB2+

tag: genotype

value: parous

value: with metastasis


title: Y10123T

description: SAMPLE 25

value: gastric cancer


title: miRNA expression of a fibrosarcoma with ESCC tissue

description:
After the homogenization of the sample hybridization signal, the signal value after logarithmic transformation was performed on the base of 2.
B771T_NS

source_name: fibrosarcoma with ESCC tissue

extract_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

value: fibrosarcoma with ESCC


title: 59: cell free DNA from plasma

tag: diagnosis

tag: treatment respsonse

tag: psa amount

tag: visit time point

value: FALSE

tag: phenotype


title: 60: cell free DNA from plasma

tag: age

tag: individual id

value: Resistant

tag: outlier