生物技术通报 ›› 2025, Vol. 41 ›› Issue (2): 77-84.doi: 10.13560/j.cnki.biotech.bull.1985.2024-0783
收稿日期:
2024-08-14
出版日期:
2025-02-26
发布日期:
2025-02-28
通讯作者:
马涛,男,博士,副研究员,研究方向 :反刍动物营养与调控技术;E-mail: matao@caas.cn作者简介:
孙同玉,男,硕士研究生,研究方向 :反刍动物营养;E-mail: 1612541223@qq.com
基金资助:
SUN Tong-yu1(), RONG Fei-fei2, GAO Zhan2, MA Tao1(
)
Received:
2024-08-14
Published:
2025-02-26
Online:
2025-02-28
摘要:
母乳不仅含有幼龄反刍动物生长必要的营养物质,还含有多种生物活性成分如微小核糖核酸(microRNA)。乳源microRNA存在于胞外囊泡之中,后者是一类脂质双分子层包裹的膜状结构,可以被宿主肠道细胞吸收,对幼龄反刍动物的生长发育起到调控作用,具有一定的抗逆性。分析乳源microRNA组成前通常要先提取胞外囊泡,主要采用差速离心法、密度梯度离心法和沉淀法,每种提取方法都有其优缺点,需要根据样本特点和试验条件选择合适的提取方法,提取到的胞外囊泡还需要经过电子显微镜、流式细胞术或纳米颗粒追踪分析等进行鉴定。乳源microRNA组成分析主要分为测序和生物信息分析两部分,前者需要选择合适的测序平台,后者主要包括数据质控、数据库比对、差异表达microRNA分析和microRNA功能预测等多个步骤,每个步骤都有多种类型分析软件可供选择,需要根据测序数据和分析软件的特点合理搭配分析方法,对测序数据进行精确且有效的信息挖掘。本文主要总结了近年来针对反刍动物乳源microRNA分析技术的研究进展,旨在为合理利用相应的技术研究乳源microRNA的组成和功能,从而有效调控幼龄反刍动物生长发育提供参考。
孙同玉, 荣飞飞, 高展, 马涛. 反刍动物乳源microRNA分析技术研究进展[J]. 生物技术通报, 2025, 41(2): 77-84.
SUN Tong-yu, RONG Fei-fei, GAO Zhan, MA Tao. Research Advances in the Analytical Technology of Milk-derived microRNA from Ruminant[J]. Biotechnology Bulletin, 2025, 41(2): 77-84.
年份 Year | 胞外囊泡提取方法 Extracellular vesicles isolation method | 测序平台 Sequencing platform | 质量控制软件 Quality control software | 序列比对软件 Sequence alignment software | 新型microRNA预测软件 Novel microRNA prediction software | 差异表达分析软件 Differential expression analysis software | 靶标预测软件 Target prediction software | 基因组数据库 Genome database | 文献 Reference |
---|---|---|---|---|---|---|---|---|---|
2010 | 无 | Illumina Genome Analyzer | N | SOAP | MIRAEP(RNAfold) | N | N | miRBase V 13.0 | [ |
2015 | 蔗糖密度 梯度离心 | Illumina Genome Analyzer II | Cutadapt v1.3/Sickle | SOAP/miRDeep2 | Mireap | EdgeR v2.4.6 | RNAhybrid | Rfam\mirBAse\ Repeat\Reference mRNA databases | [ |
2019 | 无 | Illumina HiSeq 2500 | Cutadapt v1.16/STAR v.21 | miRDeep2/oasis | miRDeep2 | DESeq2 | N | miRBase | [ |
2020 | 差速离心法 | Illumina | N | miRDeep2/srna-tools-cli | miRDeep2/miREvo | DESeq | miRanda | miRBase20.0 | [ |
2020 | 蔗糖密度 梯度离心 | Illumina HiSeq2500 | Btrim | N | N | DESeq2 | miRTarBase | miRBase v21/RNAcentral | [ |
2021 | 差速离心 | Illumina HiSeq | sRNAbench | sRNAbench | N | ANOVA | N | miRBase v22 | [ |
2022 | 血浆/血清外泌体提纯方法(试剂盒) | Illumina HiSeq 4000 SR | miRdeep2/sRNAbench | miRdeep2/sRNAbench | N | DESeq2 | TargetScan | N | [ |
2023 | 碘二醇密度 梯度离心 | Illumina Hiseq 4000 SR | miRdeep2 | miRdeep2 | N | DESeq2 | TargetScan | N | [ |
2023 | 蔗糖密度 梯度离心 | Illumina NextSeq 500 system | N | N | miRPara | N | N | miRBase v20 | [ |
2023 | 差速离心 | Illumina HiSeq 4000 | Cutadapt | miRDeep2 | miRDeep2 | DESeq2 | Tarbase v8/Diana mirPath v3 | miRBase v.22 | [ |
2024 | 无 | N | N | N | N | DESeq2 | TargetScan v8.0 | N | [ |
2024 | 差速离心 | Illumina NextSeq 500 | N | Feature Count | N | DESeq2 | MiRWalk 3.0 | miRBase v.22 | [ |
2024 | 差速离心 | DNBSEQ | N | N | N | N | TargetScan\miRTarbase\miRDB | N | [ |
表1 乳源胞外囊泡的提取方法及microRNA测序数据分析方法
Table 1 Extraction method of milk derived extracellular vesicles and analysis method of microRNA sequencing data
年份 Year | 胞外囊泡提取方法 Extracellular vesicles isolation method | 测序平台 Sequencing platform | 质量控制软件 Quality control software | 序列比对软件 Sequence alignment software | 新型microRNA预测软件 Novel microRNA prediction software | 差异表达分析软件 Differential expression analysis software | 靶标预测软件 Target prediction software | 基因组数据库 Genome database | 文献 Reference |
---|---|---|---|---|---|---|---|---|---|
2010 | 无 | Illumina Genome Analyzer | N | SOAP | MIRAEP(RNAfold) | N | N | miRBase V 13.0 | [ |
2015 | 蔗糖密度 梯度离心 | Illumina Genome Analyzer II | Cutadapt v1.3/Sickle | SOAP/miRDeep2 | Mireap | EdgeR v2.4.6 | RNAhybrid | Rfam\mirBAse\ Repeat\Reference mRNA databases | [ |
2019 | 无 | Illumina HiSeq 2500 | Cutadapt v1.16/STAR v.21 | miRDeep2/oasis | miRDeep2 | DESeq2 | N | miRBase | [ |
2020 | 差速离心法 | Illumina | N | miRDeep2/srna-tools-cli | miRDeep2/miREvo | DESeq | miRanda | miRBase20.0 | [ |
2020 | 蔗糖密度 梯度离心 | Illumina HiSeq2500 | Btrim | N | N | DESeq2 | miRTarBase | miRBase v21/RNAcentral | [ |
2021 | 差速离心 | Illumina HiSeq | sRNAbench | sRNAbench | N | ANOVA | N | miRBase v22 | [ |
2022 | 血浆/血清外泌体提纯方法(试剂盒) | Illumina HiSeq 4000 SR | miRdeep2/sRNAbench | miRdeep2/sRNAbench | N | DESeq2 | TargetScan | N | [ |
2023 | 碘二醇密度 梯度离心 | Illumina Hiseq 4000 SR | miRdeep2 | miRdeep2 | N | DESeq2 | TargetScan | N | [ |
2023 | 蔗糖密度 梯度离心 | Illumina NextSeq 500 system | N | N | miRPara | N | N | miRBase v20 | [ |
2023 | 差速离心 | Illumina HiSeq 4000 | Cutadapt | miRDeep2 | miRDeep2 | DESeq2 | Tarbase v8/Diana mirPath v3 | miRBase v.22 | [ |
2024 | 无 | N | N | N | N | DESeq2 | TargetScan v8.0 | N | [ |
2024 | 差速离心 | Illumina NextSeq 500 | N | Feature Count | N | DESeq2 | MiRWalk 3.0 | miRBase v.22 | [ |
2024 | 差速离心 | DNBSEQ | N | N | N | N | TargetScan\miRTarbase\miRDB | N | [ |
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