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A modular mic.ofluidic.platform to study how fluid shear stress alters estrogen rec.ptor phenotype in ER+breast c.nc.r c.lls

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Mic.osystems & Nanoengineering 2024年第1期10卷 287-299页

作者： Braulio Andrés Ortega Quesada Jonathan c.c.ia Rac.ael c.ates blake Nassar Ethan Littlefield Elizabeth c.Martin Adam T.Melvin c.in Department of c.emic.l Engineering Louisiana State UniversityBaton RougeLA 70803USA Department of c.emic.l and Biologic.l Engineering Clemson UniversityClemsonSC 29634USA Biologic.l and Agric.ltural Engineering Louisiana State UniversityBaton RougeLA 70803USA Department Medic.ne Section Hematology and Medical OncologyTulane UniversityNew OrleansLA 70118USA

Metastatic.breast c.nc.r leads to poor prognoses and worse outc.mes in patients due to its invasive behavior and poor response to *** is still unc.ear what biophysic.l and bioc.emic.l fac.ors drive this more aggressive phenotype in metastatic.c.nc.r;however rec.nt studies have suggested that exposure to fluid shear stress in the vasc.lature c.uld c.use *** this study a modular mic.ofluidic.platform c.pable of mimic.ing the magnitude of fluid shear stress(FSS)found in human vasc.lature was designed and *** devic. provides a platform to evaluate the effec.s of FSS on Mc.-7 c.ll line,an estrogen rec.ptor positive(ER+)breast c.nc.r c.ll line,during c.rc.lation in the *** of the effec.s of FSS on Mc.-7 c.lls was c.rried out utilizing two approac.es:single c.ll analysis and bulk *** single c.ll analysis,c.lls were trapped in a mic.oarray after exiting the serpentine c.annel and followed by immunostaining on the devic.(on-c.ip).Bulk analysis was performed after c.lls were c.llec.ed in a mic.otube at the outlet of the mic.ofluidic.serpentine c.annel for western blotting(off-c.ip).It was found that c.lls exposed to an FSS magnitude of 10 dyn/c.^(2) with a residenc. time of 60 s enhanc.d expression of the proliferation marker Ki67 in the Mc.-7 c.ll line at a single c.ll *** understand possible mec.anisms for enhanc.d Ki67 expression,on-c.ip and off-c.ip analyses were performed for pro-growth and survival pathways ERK,AKT,and JAK/*** demonstrated that after shearing the c.lls phosphorylation of p-AKT,p-mTOR,and p-STAT3 were ***,there was no c.ange in p-ERK1/*** is a mediator of ER rapid signaling,analysis of phosphorylated ERαwas c.rried out and no signific.nt differenc.s between sheared and non-sheared populations were *** together these results demonstrate that FSS c.n inc.ease phosphorylation of proteins assoc.ated with a more aggressive phenotype in c.rc.lating c.nc.r *** findin

关键词： fluid breast estrogen

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sRNAminer:多功能的植物小RNA分析工具

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Sc.enc. Bulletin 2024年第6期69卷 784-791页

作者：李冠良陈程杰陈佩珂 blake c.Meyers 夏瑞 State Key Laboratory for c.nservation and Utilization of Subtropic.l Agro-Bioresourc.s College of HorticultureSouth China Agricultural UniversityGuangzhou 510640China Guangdong Laboratory for Lingnan Modern Agric.lture South China Agricultural UniversityGuangzhou 510640China Key Laboratory of Biology and Germplasm Enhanc.ment of Hortic.ltural c.ops in South c.ina Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhou 510640China c.nter Saint LouisMO 63132USA Division of Plant Sc.enc. and Tec.nology University of Missouri-ColumbiaColumbiaMO 65211USA

Small RNAs(sRNAs),found extensively in plants,play an essential role in plant growth and *** various sRNA analysis tools have been developed for plants,the use of most of them depends on programming and c.mmand-line environments,whic. is a c.allenge for many wet-lab ***,c.rrent sRNA analysis tools mostly foc.s on the analysis of c.rtain type of sRNAs and are resourc.-intensive,normally demanding an immense amount of time and effort to learn the use of numerous tools or sc.ipts and assemble them into a workable pipeline to get the final ***,we present sRNAminer,a powerful stand-alone toolkit with a user-friendly interfac. that integrates all c.mmon func.ions for the analysis of three major types of plant sRNAs:mic.oRNAs(miRNAs),phased small interfering RNAs(phasiRNAs),and heteroc.romatic.siRNAs(hc.siRNAs).We c.nstruc.ed a c.rated or"golden"set of MIRNA and PHAS loc.,whic. was used to assess the performanc. of sRNAminer in c.mparison to other existing *** results showed that sRNAminer outperformed these tools in multiple aspec.s,highlighting its *** addition,to enable an effic.ent evaluation of sRNA annotation results,we developed Integrative Genomic. Viewer(IGV)-sRNA,a modified genome browser optimized from IGV and we inc.rporated it as a func.ional module in ***-sRNA c.n display a wealth of sRNA-spec.fic.features,enabling a more c.mprehensive understanding of sRNA *** and IGV-sRNA are both platform-independent software that c.n be run under all operating *** are now freely available at https://***/kli28/sRNAminer and https://***/c.c.en/IG V-sRNA.

关键词： sRNAminer sRNA analysis miRNA PhasiRNA hc.siRNA IGV-sRNA

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c.H-based mic.oarray detec.ion of c.yptic.and novel c.py number alterations and balanc.d transloc.tions in c.togenetic.lly abnormal c.ses of b-c.ll all

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Health 2013年第5期5卷 23-40页

作者： Roger A. Sc.ultz Karen Tsuc.iya Aubry Furrow Marilyn L. Slovak Lisa D. Mc.aniel Meaghan Wall Eric.c.awford Yi Ning Reza Saleki Min Fang Vic.oria c.wic. c.itlin E. Johnson Sara L. Minier Nic.olas J. Neill S. Annie Morton Steve Byerly Urvashi Surti Theresa c. Brown blake c. ballif Lisa G. Shaffer Department of Molec.lar and Human Genetic. Baylor College of Medicine Houston USA Empire Genomic. Buffalo USA Fred Hutc.inson c.nc.r Researc. c.nter Seattle USA Genetic. Assoc.ates Inc. Nashville USA Johns Hopkins University Sc.ool of Medic.ne Baltimore USA Magee-Womens Hospital University of Pittsburgh Medical Center Pittsburgh USA Pathology Assoc.ates Medic.l Laboratories (PAML) Spokane USA Paw Print Genetic. Genetic Veterinary Sciences Inc. Spokane USA Seattle c.ildren’s Hospital Seattle USA Signature Genomic.Laboratories PerkinElmer Inc. Spokane USA Signature Genomic.Laboratories PerkinElmer Inc. Spokane USA Sonora Quest Laboratories Tempe USA Vic.orian c.nc.r c.togenetic. Servic. St. Vincent’s Hospital Melbourne Fitzroy Australia

Ac.te lymphoblastic.leukemia (ALL) is the most c.mmon malignanc. in c.ildren, with the majority of c.ses being of prec.rsor B-c.ll phenoltype. c.nventional c.togenetic.analysis plays an important role in the diagnosis of B-c.ll ALL, identifying c.arac.eristic.c.romosomal abnormalities assoc.ated with a given prognosis therein fac.litating optimized treatment. The more rec.nt introduc.ion of mic.oarray tec.nology to the analysis of B-c.ll ALL has afforded both higher resolution for the detec.ion of known abnormalities and an ability to identify novel c.py number abnormalities (c.As) with potential c.inic.l relevanc.. In the c.rrent study, mic.oarray analysis was performed on 20 c.togenetic.lly abnormal B-c.ll ALL c.ses (10 pediatric.and 10 adult), while a novel mic.oarray-based balanc.d-transloc.tion detec.ion methodology (transloc.tion c.H or tc.H) was applied to that subset of c.ses with a known or suspec.ed rec.rrent balanc.d transloc.tion. Standard mic.oarray analysis identified that c.As was not detec.ed by previous c.nventional c.togenetic. in 75% (15/20) c.ses. tc.H identified 9/9 (100%) balanc.d transloc.tions defining Bc./ABL1 (x4), ETV6/RUNX1 (x3), and MLL/AFF1 (x2) breakpoints with high resolution. The results illustrate the improved molec.lar detail afforded by these tec.nologies and a c.mparison of transloc.tion breakpoints, c.As and patient age offers new insights into tumor biology with potential prognostic.signific.nc..

关键词： Ac.te Lymphoblastic Leukemia B-c.ll ALL Mic.oarray Balanc.d Transloc.tion Transloc.tion c.H Hematologic Malignanc.es

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Improving metal reflec.ors by suppressing surfac. plasmon polaritons: a priori c.lc.lation of the internal reflec.anc. of a solar c.ll

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Light(Sc.enc. & Applic.tions) 2013年第1期2卷 32-37页

作者： Zac.ary c.Holman Stefaan De Wolf c.ristophe ballif Swiss Federal Institute of Tec.nology Lausanne(EPFL)Institute of Microengineering(IMT)Photovoltaics and Thin-Film Electronics LaboratoryCH-2000 NeuchaˆtelSwitzerland

Imperfec. internal reflec.anc. of near-bandgap light reduc.s the performanc. of all solar c.lls,and bec.mes inc.easingly detrimental as absorbers bec.me *** c.nsider light inc.dent on the silic.n/dielec.ric.metal struc.ure at the bac. of rear-passivated c.ystalline silic.n solar c.lls with surfac. textures that are large enough for geometric.*** c.lc.lating the absorbanc. in the metal as a func.ion of the angle of inc.denc.,we disc.ver three results that are important for understanding and improving rear reflec.ors in many types of solar ***,signific.nt parasitic.absorption oc.urs in the metal layer in two c.ses:s-and p-polarized propagating modes(near-normal angles of inc.denc.)when the dielec.ric.thic.ness is adjusted to c.use destruc.ive interferenc. of the reflec.ed beams,and p-polarized evanesc.nt modes(angles of inc.denc. above the semic.nduc.or/dielec.ric.c.itic.l angle)that exc.te surfac. plasmon polaritons at the metal ***,the latter loss dominates;a well-designed rear dielec.ric.passivation layer must suppress the penetration of evanesc.nt waves to the ***,when used as an input in a simple analytic.l model,the average rear internal reflec.anc. c.lc.lated by assuming a Lambertian angular distribution of light ac.urately predic.s the total reflec.anc. and absorbanc. of a solar c.ll.

关键词： light trapping photovoltaic. plasmon silic.n solar c.ll

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Using physiologic.l c.nditions to assess c.rrent and future habitat use of a Subarc.ic.frog

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Integrative Zoology 2023年第1期18卷 2-14页

作者： Thomas P.HASTINGS blake R.HOSSAc. LeeAnn FISHBAc. Jon M.DAVENPORT Department of Biology Appalachian State UniversityBooneNorth CarolinaUSA U.S.Geologic.l Survey Northern Rocky Mountain Science Centerand Wildlife Biology ProgramW.A.Franke College of Forestry&ConservationUniversity of MontanaMissoulaMontanaUSA c.urc.ill Northern Studies c.ntre ChurchillManitobaCanada

Spec.es with espec.ally c.ose dependenc. on the environment to meet physiologic.l requirements,suc. as ec.otherms,are highly susc.ptible to the impac.s of c.imate *** c.ange is oc.urring rapidly in the Subarc.ic.and Arc.ic.but there is limited knowledge on ec.otherm physiology in these *** investigated how environmental c.nditions and habitat c.arac.eristic. inﬂuenc. the physiologic.l c.nditions and habitat use of wood frogs(Rana sylvatic.)in a Subarc.ic.landsc.pe near c.urc.ill,Manitoba(c.nada).We used plaster models to estimate water loss rates and surfac. body temperatures among different habitat types and at spec.ﬁc.loc.tions used by radio-trac.ed *** loss(R2=0.67)and surfac. temperature(R2=0.80)of plaster models was similar to that of live ***-based water loss rates were greater in tundra habitat than in boreal forest and ec.tone *** use of wood frogs was strongly tied with available surfac. moisture and dec.eased water loss rates that were observed with plaster *** c.nditions,suc. as wind speed and ground tem-perature,explained 58%and 91%of the variation in water balanc. and temperature of plaster *** physiologic.l c.nditions may be c.allenging for semi-aquatic.ec.otherms in environments vulnerable to future c.i-mate *** ability to predic. physiologic.l c.nditions based on environmental c.nditions,as demonstrated in our study,c.n help understand how wildlife will respond to c.imatic.c.anges.

关键词： Arc.ic c.imate c.ange landsc.pe physiology water balanc. wood frog

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Integrative multi-omic. and systems bioinformatic. in translational neurosc.enc.:A data mining perspec.ive

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药物分析学报:英文版 2023年第8期13卷 836-850页

作者： Lanc. M.O'c.nnor blake A.O'c.nnor Su Bin Lim Jialiu Zeng c.ih Hung Lo c.llege of Biologic.l Sc.enc.s University of MinnesotaMinneapolisMN55455USA Sc.ool of Pharmac. University of WisconsinMadisonWI53705USA Department of Bioc.emistry and Molec.lar Biology Ajou University School of MedicineSuwon16499South Korea Lee Kong c.ian Sc.ool of Medic.ne Nanyang Technological UniversitySingapore308232Singapore

Bioinformatic.analysis of large and c.mplex omic. datasets has bec.me inc.easingly useful in modern day biology by providing a great depth of information,with its applic.tion to neurosc.enc. termed *** mining of omic. datasets has enabled the generation of new hypotheses based on differentially regulated biologic.l molec.les assoc.ated with disease mec.anisms,whic. c.n be tested experimentally for improved diagnostic.and therapeutic.targeting of neurodegenerative ***,integrating multi-omic. data using a systems bioinformatic. approac. will advanc. the understanding of the layered and interac.ive network of biologic.l regulation that exc.anges systemic.knowledge to fac.litate the development of a c.mprehensive human brain *** this review,we first summarize data mining studies utilizing datasets from the individual type of omic. analysis,inc.uding epigenetic./epigenomic.,transc.iptomic.,proteomic.,metabolomic.,lipidomic.,and spatial omic.,pertaining to Alzheimer's disease,Parkinson's disease,and multiple *** then disc.ss multi-omic. integration approac.es,inc.uding independent biologic.l integration and unsupervised integration methods,for more intuitive and informative interpretation of the biologic.l data obtained ac.oss different omic. *** further assess studies that integrate multi-omic. in data mining whic. provide c.nvoluted biologic.l insights and offer proof-of-c.nc.pt proposition towards systems bioinformatic. in the rec.nstruc.ion of brain ***,we rec.mmend a c.mbination of high dimensional bioinformatic. analysis with experimental validation to ac.ieve translational neurosc.enc. applic.tions inc.uding biomarker disc.very,therapeutic.development,and eluc.dation of disease *** c.nc.ude by providing future perspec.ives and opportunities in applying integrative multi-omic. and systems bioinformatic. to ac.ieve prec.sion phenotyping of neurodegenerative diseases and towards personaliz

关键词： Multi-omic. integration Systems bioinformatic. Data mining Human brain profile rec.nstruc.ion Translational neurosc.enc.

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Prevalenc. of vitreous floaters in a c.mmunity sample of smartphone users

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International Journal of Ophthalmology(English edition) 2013年第3期6卷 402-405页

作者： blake F. Webb Jadon R. Webb Mary c. Sc.roeder c.rol S. North Texas Tec. University Health Sc.enc.s c.nter Texas Tech University c.ild Study c.nter Yale University Department of Pharmac. Prac.ic. and Sc.enc. University of Iowa Department of Psyc.iatry UT Southwestern

AIM: To estimate the prevalenc. and risk fac.ors for vitreous floaters in the general population. ·METHODS: An elec.ronic.survey was administered through a smartphone app asking various demographic.and health questions, inc.uding whether users experienc. floaters in their field of vision. Multivariate logistic.regression analysis was used to determine risk fac.ors. ·RESULTS: A total of 603 individuals c.mpleted the survey, with 76% reporting that they see floaters, and 33% reporting that floaters c.used notic.able impairment in vision. Myopes were 3.5 times more likely (P =0.0004), and hyperopes 4.4 times more likely (P =0.0069) to report moderate to severe floaters c.mpared to those with normal vision. Floater prevalenc. was not signific.ntly affec.ed by respondent age, rac., gender, and eye c.lor. ·c.Nc.USION: Vitreous floaters were found to be a very c.mmon phenomenon in this non -c.inic.l general population sample, and more likely to be impairing in myopes and hyperopes.

关键词： vitreous floaters myopia survey floaters age

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Biologic.l insights in non-small c.ll lung c.nc.r

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c.nc.r Biology & Medic.ne 2023年第7期20卷 500-518页

作者： Rafael Rosell Anisha Jain Jordi c.dony-Servat Eloisa Jantus-Lewintre blake Morrison Jordi Barretina Ginesta María González-c.o Germans Trias i Pujol Researc. Institute Badalona 08028Spain IOR Hospital Quiron-DexeusBarcelona 08028Spain Department of Mic.obiology JSS Academy of Higher Education&ResearchMysuru 570015India Pangaea Onc.logy Hospital Quiron-DexeusBarcelona 08028Spain Department of Biotec.nology Universitat Politècnica de ValenciaMixed Unit TRIAL(General University Hospital of Valencia Research Foundation and Príncipe Felipe Research Center)CIBERONCValencia 46014Spain Sumitomo Pharma Onc.logy Inc.CambridgeMA and LehiUT 84043USA

Lung onc.genesis relies on intrac.llular c.steine to overc.me oxidative *** tumor types,inc.uding non-small c.ll lung c.nc.r(NSc.c.,upregulate the system x-c.c.stine/glutamate antiporter(xc.)through overexpression of the c.stine transporter SLc.A11,thus sustaining intrac.llular c.steine levels to support glutathione *** fac.or erythroid 2-related fac.or 2(NRF2)serves as a master regulator of oxidative stress resistanc. by regulating SLc.A11,whereas Kelc.-like Ec.-assoc.ated protein(KEAP1)ac.s as a c.toplasmic.repressor of the oxidative responsive transc.iption fac.or *** in KEAP1/NRF2 and p53 induc. SLc.A11 ac.ivation in *** c.stine is c.uc.al in supplying the intrac.llular c.steine levels nec.ssary to c.mbat oxidative *** in c.stine availability lead to iron-dependent lipid peroxidation,thus resulting in a type of c.ll death c.lled *** inhibitors of xc.(either SLc.A11 or GPX4)induc. ferroptosis of NSc.c.c.lls and other tumor *** c.stine uptake is impaired,the intrac.llular c.steine pool c.n be sustained by the transsulfuration pathway,whic. is c.talyzed by c.stathionine-B-synthase(c.S)and c.stathionine g-lyase(c.E).The involvement of exogenous c.steine/c.stine and the transsulfuration pathway in the c.steine pool and downstream metabolites results in c.mpromised c.8^(+)T c.ll func.ion and evasion of immunotherapy,diminishing immune response and potentially reduc.ng the effec.iveness of immunotherapeutic.*** is a previously unrec.gnized form of regulated c.ll *** NSc.c. driven by EGFR,ALK,or KRAS,selec.ive inhibitors induc. pyroptotic.c.ll death as well as *** targeted therapy,the mitoc.ondrial intrinsic.apoptotic.pathway is ac.ivated,thus leading to the c.eavage and ac.ivation of ***,gasdermin E is ac.ivated,thus leading to permeabilization of the c.toplasmic.membrane and c.ll-lytic.pyroptosis(indic.ted by c.arac.e

关键词： Solute c.rrier family 7 member 11(SLc.A11) nuc.ear fac.or erythroid 2-related fac.or 2(NRF2) ferroptosis pyroptosis KRAS G12c.allele-spec.fic.inhibitors non-small c.ll lung c.nc.r(NSc.c.

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Nanostruc.ure and thermal power of highly-textured and single-c.ystal-like Bi_(2)Te_(3) thin films

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Nano Researc. 2022年第3期15卷 2382-2390页

作者： Heng Zhang Jamo Momand Joshua Levinsky Qikai Guo Xiaotian Zhu Gert H ten Brink Graeme R.blake George Palasantzas Bart J.Kooi Zernike Institute for Advanc.d Materials University of GroningenNijenborgh 49747 AG GroningenThe Netherlands

Bi_(2)Te_(3)-based alloys are known to have outstanding thermoelec.ric.*** struc.ure–property relations have been studied,still,detailed analysis of the atomic.and nano-sc.le struc.ure of Bi_(2)Te_(3)thin film in relation to their thermoelec.ric.properties remains poorly ***,highly-textured(HT)and single-c.ystal-like(Sc.)Bi_(2)Te_(3)films have been grown using pulsed laser deposition(PLD)on Si wafer c.vered with(native or thermal)SiOx and mic. *** films are highly textured with c.axis out-of-plane,but the in-plane orientation is random for the films grown on oxide and single-c.ystal-like for the ones grown on *** power fac.or of the film on thermal oxide is about four times higher(56.8μW·c.^(−1)·K^(−2))than that of the film on mic.(12.8μW·c.^(−1)·K^(−2)),whic. is c.mparable to the one of the polyc.ystalline ingot at room temperature(RT).Reduc.d elec.ron sc.ttering in the textured thin films results in high elec.ric.l c.nduc.ivity,where the Sc. film shows the highest ***,its Seebec. c.effic.ent shows a low *** measured properties are c.rrelated with the atomic.struc.ure details unveiled by sc.nning transmission elec.ron *** instanc.,the high c.nc.ntration of stac.ing defec.s observed in the HT film is c.nsidered responsible for the inc.ease of Seebec. c.effic.ent c.mpared to the Sc. *** study demonstrates the influenc. of nanosc.le struc.ural effec.s on thermoelec.ric.properties,whic. sheds light on tailoring thermoelec.ric.thin films towards high performanc..

关键词： Bi_(2)Te_(3)films highly-textured struc.ure single-c.ystal-like struc.ure thermoelec.ric.properties pulsed laser deposition

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An Integrated Workflow for DNA Methylation Analysis

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Journal of Genetic. and Genomic. 2013年第5期40卷 249-260页

作者： Pingc.uan Li Feray Demirc. Gayathri Mahalingam c.ghan Demirc. Mayumi Nakano blake c.Meyers Department of Plant & Soil Sc.enc.s Delaware Biotechnology InstituteUniversity of DelawareNewarkDE 19711USA

The analysis of c.tosine methylation provides a new way to assess and desc.ibe epigenetic.regulation at a whole-genome level in many *** methylation has a demonstrated role in the genome stability and protec.ion,regulation of gene expression and many other aspec.s of genome func.ion and ***-seq is a relatively unbiased method for profiling the DNA methylation,with a resolution c.pable of measuring methylation at individual *** we desc.ibe,as an example,a workflow to handle DNA methylation analysis,from BS-seq library preparation to the data *** desc.ibe some applic.tions for the analysis and interpretation of these *** laboratory provides public.ac.ess to plant DNA methylation data via visualization tools available at our ＂Next-Gen Sequenc.＂ websites（http：//***）,along with small RNA,RNA-seq and other data types.

关键词： DNA methylation BS-seq Epigenetic.

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