Biotechnology Bulletin ›› 2025, Vol. 41 ›› Issue (2): 77-84.doi: 10.13560/j.cnki.biotech.bull.1985.2024-0783
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SUN Tong-yu1(
), RONG Fei-fei2, GAO Zhan2, MA Tao1(
)
Received:2024-08-14
Online:2025-02-26
Published:2025-02-28
Contact:
MA Tao
E-mail:1612541223@qq.com;matao@caas.cn
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 | [ |
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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