标签归档：v

0.4w/v% Trypan Blue Solution 0.4w/v%台盼蓝溶液

发表于由

0.4w/v% Trypan Blue Solution

0.4w/v%台盼蓝溶液

品牌：FUJIFILM Wako
CAS No.：
储存条件：室温
纯度：–
产品编号

(生产商编号)

 等级 规格 运输包装 零售价(RMB) 库存情况 参考值

207-17081

 for Cell Staining 100mL –

0.4w/v% Trypan Blue Solution 0.4w/v%台盼蓝溶液

 – –


* 干冰运输、大包装及大批量的产品需酌情添加运输费用


* 零售价、促销产品折扣、运输费用、库存情况、产品及包装规格可能因各种原因有所变动，恕不另行通知，确切详情请联系上海金畔生物科技有限公司。

Next FFPE DNA 修复模块 v2 |NEB酶试剂 New England Biolabs

发表于由

上海金畔生物科技有限公司代理New England Biolabs（NEB）酶试剂全线产品，欢迎访问官网了解更多产品信息和订购。

产品信息

NEBNext FFPE DNA 修复模块 v2 包含经过优化的酶和缓冲液，可在二代测序流程中以精简的方式修复 FFPE DNA。

NEBNext FFPE DNA 修复模块 v2 在初代 NEBNext FFPE DNA 修复混合液基础上提升了性能：

  • 更高的 FFPE DNA 修复效率
  • 更精简的 NGS 文库制备流程
  • 更便捷的反应缓冲液，包含高效 FFPE DNA 修复和下游末端修复以及 dA 加尾所需的所有缓冲液成分。
  • 修复后使用热敏蛋白酶 Proteinase K 处理，无需纯化即可进行文库制备。

表 1：FFPE DNA 损伤类型以及 NEBNext FFPE DNA 修复模块 v2 的修复能力

FFPE 损伤类型 可被 FFPE DNA 修复模块 v2 修复
胞嘧啶脱氨成尿嘧啶 是
切刻和缺口 是
氧化碱基 是
3´ 末端封闭 是
DNA 片段化 否
DNA-蛋白交联 否
图 1：NEBNext FFPE DNA 修复模块 v2 与 NEBNext Ultra™ II DNA 文库制备试剂盒实验流程

Next FFPE DNA 修复模块 v2 |

图 2：经 NEBNext FFPE DNA 修复模块 v2 修复的各种质量的 FFPE DNA 样本，都可进行稳定的文库制备。

Next FFPE DNA 修复模块 v2 |

25 ng 不同质量和组织来源的 FFPE DNA 样本经 Covaris® 超声打断后制备文库。经过 NEBNext FFPE DNA 修复模块 v2 修复后，再使用 NEBNext Ultra II DNA 文库制备试剂盒（NEB #E7645）制备文库，进行 9 个 PCR 循环。使用 Agilent® HS D1000 TapeStation® 定量文库。取决于起始 DNA 的质量和损伤类型，NEBNext FFPE DNA 修复模块 v2 不同程度地提高 FFPE 文库的产量。误差条表示每个文库样本两次重复的标准偏差。
图 3：NEBNext FFPE DNA 修复模块 v2 可配合使用 NEBNext 发夹结构接头和 Unique 双端 Index 引物 UMI 接头修复 5 至 250 ng 起始 FFPE DNA，而后进行稳定的文库制备。

Next FFPE DNA 修复模块 v2 |

使用三种不同质量的 5、50、或 250 ng 正常肝脏 FFPE DNA 样本制备文库，并比较使用和不使用 NEBNext FFPE DNA 修复模块 v2 修复的文库制备效果。NEBNext Ultra II DNA 文库制备试剂盒（NEB #E7645）与（a）NEBNext 发夹结构接头配合使用，针对 5、50、和 250 ng 的起始量分别进行 11、8、和 6 个 PCR 扩增循环；与（b）NEBNext Unique 双端 Index 引物 UMI DNA 接头（NEB #E7395）配合使用，针对 5、50、和 250 ng 的起始量分别进行 11、8、和 6 个 PCR 循环。所有文库均使用 Agilent HS D1000 Tapestation 进行定量，并绘制了 2 个文库（5 ng 和 50 ng）和 1 个重复（250 ng）的平均产量。误差条表示 5 ng 和 50 ng 文库重复样本的标准偏差。NEBNext FFPE DNA 修复模块 v2 适用于 5 至 250 ng 的起始 FFPE DNA 和不同的 NEBNext 接头。
图 4：NEBNext FFPE DNA 修复模块 v2 改善了文库质量指标，包括比对率、正确配对的 Reads 和嵌合 Reads

Next FFPE DNA 修复模块 v2 |

使用或不使用 NEBNext FFPE DNA 修复模块 v2 处理三种不同质量的 50 ng 正常肝脏 FFPE DNA 样品后，采用 NEBNext Ultra II DNA 文库制备试剂盒（NEB #E7645）制备文库，每种样品（±修复处理）进行三次重复。在 Illumina NextSeq®500 上进行文库测序。向下抽样 100 万个双端 Reads，并使用 Bowtie2（v2.3.2）将 Reads 与 GRCh38 人类参考基因组（RefSeq 884148）进行比对。使用 MarkDuplicates（v1.56.0）和 Picard SAM/BAM alignment summary metrics（v1.56.0）分析比对到的 Reads。使用 NEBNext FFPE DNA 修复模块 v2 进行处理可提高比对率，并降低不正确配对和嵌合 Reads 的几率。
图 5：NEBNext FFPE DNA 修复模块 v2 可修复 FFPE DNA 样本中存在的大量胞嘧啶脱氨基损伤

Next FFPE DNA 修复模块 v2 |

使用或不使用 NEBNext FFPE DNA 修复模块 v2 处理 50 ng 两种不同的正常肝脏 FFPE DNA 样品后 (DIN 2.0 and DIN 1.8)，每种样品进行二个重复，然后采用 NEBNext Ultra II DNA 文库制备试剂盒（NEB #E7645）制备文库。在 Illumina NextSeq® 500 上进行文库测序。向下抽样 100 万个双端 Reads，并使用 Bowtie2（v2.3.2）将 Reads 与 GRCh38 人类参考基因组（RefSeq 884148）进行比对。使用 MarkDuplicates（v1.56.0）分析比对到的 Reads；并根据等式 MAX（（[C T] – [G A]）/（[NC]+[NG]），EXP（-10））用 Tasmanian（V0.1.3）分析 dCdT（CT）突变。（a）Read 1 和 Read 2 中的 CT 突变频率与 Read 位置（0 – 75 bp）的函数关系图。使用 NEBNext FFPE DNA 修复模块 v2 处理后，这些突变的丰度和位点偏差在两个不同 FFPE DNA 样本中有所减少。（b）Read 2 中识别出的突变量化为总频率。下图显示了每种条件下进行的两个重复。
图 6：NEBNext FFPE DNA 修复模块 v2 可修复 FFPE 和非 FFPE DNA 样本中的氧化损伤

Next FFPE DNA 修复模块 v2 |

A：以 25 ng 不同质量和组织来源的两种不同的正常 FFPE DNA 为样本制备文库，每种样品进行了两个重复，比较使用或未使用 NEBNext FFPE DNA 修复模块 v2 处理的文库效果。文库用 NEBNext Ultra II DNA 文库制备试剂盒（NEB #E7645）制备，在 Illumina NextSeq® 500 上进行测序。向下抽样 200 万个 Reads，并使用 Bowtie2（v2.3.2）比对 Reads 和 GRCh38 人类参考基因组。使用 MarkDuplicates（v1.56.0）和 Tasmanian（V0.1.3）分析比对到的 Reads。Read 1 显示了每个文库两个重复数据中的 dGdT（GT）突变频率。根据等式 MAX（（[G T] – [C A]）/（[NG]+[NC]），EXP（-10））计算 dGdT 突变。

B：以在水* 或 pH 8.0 的 Tris-EDTA 中 Covaris 超声打断的 100 ng 人类基因组 DNA 为起始样本，使用 NEBNext FFPE DNA 修复模块 v2 和 NEBNext Ultra II DNA 文库制备试剂盒（NEB #E7645）制备了两个文库，每个样本重复 2 次。使用 Illumina NextSeq 500 对文库进行测序，向下抽样 200 万个 Reads，并按如上所述分析 GT 突变频率。*注意：厂商（Covaris）产品说明书不推荐在水中超声打断 DNA，但可用此方法生成含氧化损伤的底物。

图 7：与使用 UDG 酶进行处理相比，用 NEBNext FFPE DNA 修复模块 v2 处理提高了文库产量

Next FFPE DNA 修复模块 v2 | 
选用 50 ng 不同组织来源和质量的 4 种不同的正常 FFPE DNA（DIN 2.0 的 FFPE #1-3 和 DIN 6.7 的 FFPE #4）制备文库，每个样本重复 2 次。在使用 NEBNext Ultra II DNA 文库制备试剂盒（NEB #E7645）制备文库之前，样品使用或未使用 NEBNext FFPE DNA 修复模块 v2 处理、或使用 UDG 酶（NEB #M0280）处理。虽然 UDG 酶可以消除起始 DNA 中的 dU 碱基，但 NEBNext FFPE DNA 修复模块 v2 可以完全修复这些损伤位点，提高最终文库产量（图 2、3、7）并完善指标（图 4）。
图 8：NEBNext FFPE DNA 修复模块 v2 减少了由胞嘧啶脱氨基引起的体细胞突变体识别中的假阳性

Next FFPE DNA 修复模块 v2 |

以 100 ng 四个不同质量和组织来源的 FFPE DNA 为起始样本，使用 NEBNext FFPE DNA 修复模块 v2 或 NEBNext FFPE DNA 修复混合液（NEB #M6630）、NEBNext Unique 双端 Index 引物 UMI 接头（NEB #E7395）、以及 NEBNext Ultra II DNA 文库制备试剂盒（NEB #E7645），进行 10 个 PCR 循环制备文库，每个样本重复 2 次。使用定制的 Cancer Hotspot 面板（Twist Bioscience®）捕获文库并用 Illumina NextSeq 2000 测序。所有 fastq 文件都向下抽样相同数量的 Reads（新鲜冰冻组织的 Reads 为 2 X 1800 万，FFPE 的 Reads 为 2 X 1300 万）。使用 fastp（版本 0.20.0）对双端 Reads 进行修剪，并使用 BWA mem（0.7.17）进行比对。使用 UMI 信息在 picard（2.20.6）中处理 Markduplicate。在 fgbio（0.8.1）中处理 UMI 信息，以获得共有序列 Reads。strelka2（2.9.10）程序的最终 bam 文件用于体细胞突变体识别，数据已用 UMI 矫正了重复序列。根据每种情况的替代类型绘制体细胞突变图。NEBNext FFPE DNA 修复 v2 模块可提高胞嘧啶脱氨基修复（CT/GA）效率，并有效修复氧化损伤（GT/CA）。

产品类别:
FFPE DNA Products,
Next Generation Sequencing Library Preparation Products

  • 试剂盒组成

    本产品提供以下试剂或组分：

    NEB # 名称 组分货号 储存温度 数量 浓度
    • E7360S     -20    
        NEBNext® FFPE DNA Repair Mix v2 E7361AVIAL -20 1 x 0.048 ml Not Applicable
        NEBNext® Thermolabile Proteinase K E7362AVIAL -20 1 x 0.048 ml Not Applicable
        NEBNext® FFPE DNA Repair Buffer v2 E7363AVIAL -20 1 x 0.168 ml Not Applicable
    • E7360L     -20    
        NEBNext® FFPE DNA Repair Mix v2 E7361AAVIAL -20 1 x 0.192 ml Not Applicable
        NEBNext® Thermolabile Proteinase K E7362AAVIAL -20 1 x 0.192 ml Not Applicable
        NEBNext® FFPE DNA Repair Buffer v2 E7363AAVIAL -20 1 x 0.672 ml Not Applicable

  • 特性和用法

    需要但不提供的材料

    • NEBNext Ultra II DNA 文库制备试剂盒（NEB #E7645S、#E7645L、#E7103S 、或 #E7103L）或其它
    • 80% 乙醇
    • 无核酶水
    • 0.1X TE（1 mM Tris-HCl pH 8.0，0.1 mM EDTA）
    • 无 DNase、无 RNase PCR 联管
    • DNA LoBind® 管（Eppendorf，#022431021）
    • SPRISelect®试剂盒（Beckman Coulter 公司，#B23317）或 AMPure® XP Beads（Beckman Coulter 公司，#A63881）
    • NEBNext 多样本接头引物试剂盒（www.neb.cn/oligos）
    • 磁力架/支架（NEB #S1515，Alpaqua® #A001322，或同等产品）
    • 热循环仪
    • Agilent Bioanalyzer® 或 TapeStation®，以及相关试剂和耗材
    • 接头稀释缓冲液 NEB #B1430S 或 NEBNext Unique 双端 Index 引物 UMI 接头稀释缓冲液，随 NEB #E7395S/L 提供

  • 相关产品

    相关产品

    • NEBNext® Ultra™ II DNA 文库制备试剂盒
    • NEBNext® Ultra™ II DNA 文库制备试剂盒（含纯化磁珠）

操作说明、说明书 & 用法

  • 操作说明

    1. Where can I find guidelines and protocols for using the NEBNext FFPE DNA Repair v2 Module (NEB #E7360)?

  • 说明书

    产品说明书包含产品使用的详细信息、产品配方和质控分析。

    • manualE7360

工具 & 资源

  • Web 工具

    • NEBNext Selector

FAQs & 问题解决指南

  • FAQs

    1. What is the difference between the NEBNext FFPE DNA Repair v2 Module (NEB #E7360) and the NEBNext FFPE DNA Repair Mix (NEB #M6630)?
    2. Will the FFPE DNA Repair v2 Module ligate my DNA fragments?
    3. Will treating my DNA with the FFPE DNA Repair v2 Module hurt my downstream reaction?
    4. Will the FFPE DNA Repair v2 Module blunt the ends of the DNA?
    5. Does the FFPE DNA Repair v2 Module insert random nucleotides into the sequence that it repairs?
    6. Does the FFPE DNA Repair v2 Module remove covalent modifications from DNA bases, such as biotin or digoxigenin?
    7. Does the FFPE DNA Repair v2 Mix repair DNA-protein crosslinks?
    8. Does the FFPE DNA Repair v2 Mix fix blocked 3′ ends?
    9. Can the FFPE DNA Repair v2 Mix repair damage in both single- and double-stranded DNA? Or, does it require double stranded DNA as a template?
    10. If I had a DNA template with mutation sites (i.e. 8-oxoguanine or deaminated cytosines) that are directly adjacent to each other on opposite strands would treatment with the FFPE DNA Repair v2 Mix cause a double strand nick/break?
    11. What gap lengths can be repaired with the FFPE DNA Repair v2 Mix?
    12. Can the FFPE DNA Repair v2 Module repair bisulfite-treated DNA?
    13. When working with fragmented DNA, will the ends be ligated together by the FFPE DNA Repair v2 Module?
    14. How are abasic sites repaired by the FFPE DNA Repair v2 Module?
    15. Can I use the FFPE DNA Repair v2 Module to repair other types of low quality DNA other than FFPE DNA?

Next® rRNA Depletion Kit v2 (Human/Mouse/Rat) with RNA Sample Purification Beads |NEB酶试剂 New England Biolabs

发表于由

上海金畔生物科技有限公司代理New England Biolabs（NEB）酶试剂全线产品，欢迎访问官网了解更多产品信息和订购。

产品信息

Highly expressed transcripts with minimal biological interest, such as ribosomal RNA (rRNA) can dominate readouts, masking detection of more informative low-abundance transcripts. This second-generation NEBNext rRNA Depletion Kit is has been further optimized to incorporate reagent, probe and protocol improvements to the RNaseH-based workflow, resulting in superior depletion performance. 

  • The efficiency of this workflow, and close spacing of probes, enables effective depletion from both low- and high-quality RNA, with a broad range of input amounts from human, mouse and rat samples.
  • The rRNA-depleted RNA can be used in RNA-seq, random-primed cDNA synthesis, or other RNA analysis methods. 
  • The NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) depletes cytoplasmic (5S, 5.8S, 18S, 28S, human ITS, ETS) and mitochondrial (12S, 16S) rRNA.
  • The kit is also available without RNAClean® beads.     
Figure 1: The NEBNext rRNA Depletion Kit v2 enriches for RNAs of interest across a wide range of total RNA inputs in human, mouse and rat

Next® rRNA Depletion Kit v2 (Human/Mouse/Rat) with RNA Sample Purification Beads |

Universal human, mouse and rat reference total RNA (1 µg, 100 ng and 10 ng) was depleted of rRNA using the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat). RNA-seq libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina followed by paired-end sequencing (2 x 75 bp). 10 Million reads were sampled (seqtk) from each library and reads were identified as ribosomal using mirabait (6 or more shared 25-mers) with rRNA sequences for human baits (5S, 5.8S, 12S, 16S, 18S, 28S, ETS/ITS) or mouse/rat baits (5S, 5.8S, 12S, 16S, 18S, 28S). Levels of rRNA remaining were calculated by dividing matched reads by the total number of reads passing instrument quality filtering. The data represents an average of 3 replicates. The NEBNext rRNA Depletion Kit v2 is efficient at depleting rRNA across species and input amounts.
Figure 2: Treatment with the NEBNext rRNA Depletion Kit v2 does not affect the abundances of non-targeted transcripts

Next® rRNA Depletion Kit v2 (Human/Mouse/Rat) with RNA Sample Purification Beads |

Universal human, mouse and rat reference total RNA (1 µg) was depleted of rRNA using the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat). RNA-seq libraries were prepared from untreated and depleted RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina followed by paired-end sequencing (2 x 75bp). 10 million reads were sampled (seqtk) for depleted libraries and 100 million reads for undepleted libraries. GENCODE v27 transcript abundances were estimated using Salmon. Read Counts and R2 values for the linear fit are shown. Transcript expression is consistent after depletion across species.
Figure 3: Transcript expression correlation is preserved across a wide range of inputs

Next® rRNA Depletion Kit v2 (Human/Mouse/Rat) with RNA Sample Purification Beads |

Universal human, mouse and rat reference total RNA (1 µg) was depleted of rRNA using the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat). RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina followed by paired-end sequencing (2 x 75bp). GENCODE v27 transcript abundances were estimated using Salmon. Read Counts and R2 values for the linear fit are shown. Transcript expression correlation is consistent regardless of input amount.
Figure 4: The NEBNext rRNA Depletion Kit v2 efficiently depletes rRNA from degraded FFPE total RNA while preserving transcript abundances

Next® rRNA Depletion Kit v2 (Human/Mouse/Rat) with RNA Sample Purification Beads |

Human adult normal liver tissue FFPE Total RNA, RIN 2.3 (100 ng and 10 ng) was depleted of rRNA using the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) (A, B, C) or the TruSeq® Stranded Total RNA Gold kit (A). RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina® followed by paired-end sequencing (2 x 75 bp). 20 Million reads were sampled (seqtk) from depleted libraries and 200 million reads from undepleted libraries. (A) Reads were identified as ribosomal using mirabait (6 or more shared 25-mers) with rRNA sequences for 5S, 5.8S, 12S, 16S, 18S, 28S and ETS/ITS as baits. Levels of rRNA remaining were calculated by dividing matched reads by the total number of reads passing instrument quality filtering. The data represents an average of 3 replicates and error bars indicate standard error. (B) and (C) GENCODE v27 transcript abundances were estimated using Salmon. Read Counts and R2 values for the linear fit are shown. The NEBNext kit provides superior depletion of rRNA from FFPE (degraded) samples and offers the flexibility of lower total RNA input amounts. Transcript expression correlation is consistent after treatment and regardless of input amount.
Figure 5: The NEBNext rRNA Depletion Kit v2 depletes both mature and pre-rRNA from human total RNA

Next® rRNA Depletion Kit v2 (Human/Mouse/Rat) with RNA Sample Purification Beads |

Human universal reference total RNA (1 µg) was depleted of rRNA using the original NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB #E6310) and the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) (NEB #E7400). RNA-seq libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina followed by paired-end sequencing (2 x 75 bp). 10 Million reads were sampled (seqtk) from each library. Reads were identified as ribosomal using mirabait (6 or more shared 25-mers) with rRNA sequences for 5S, 5.8S 12S, 16S, 18S, 28S and ETS/ITS as baits. Levels of rRNA remaining were calculated by dividing matched reads by the total number of reads passing instrument quality filtering. The data represents an average of 3 replicates. NEBNext rRNA Depletion Kit v2 provide superior depletion of rRNA.
Figure 6: Workflow

Next® rRNA Depletion Kit v2 (Human/Mouse/Rat) with RNA Sample Purification Beads |

产品类别:
RNA Depletion & mRNA Enrichment Products,
RNA Library Prep for Illumina,
Next Generation Sequencing Library Preparation Products

  • 试剂盒组成

    本产品提供以下试剂或组分：

    NEB # 名称 组分货号 储存温度 数量 浓度
    • E7405S     Multi-temperature    
        NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) E7400S -20    
        NEBNext® DNase I E7753-2VIAL -20 1 x 0.015 ml 20,000 units/ml
        NEBNext® Thermostable RNase H E7752-2VIAL -20 1 x 0.012 ml 5,000 units/ml
        NEBNext v2 rRNA Depletion Solution E7401-2VIAL -20 1 x 0.012 ml Not Applicable
        RNase H Reaction Buffer E6312-2VIAL -20 1 x 0.012 ml Not Applicable
        DNase I Reaction Buffer E6315-2VIAL -20 1 x 0.03 ml Not Applicable
        Nuclease-free Water E6317-2VIAL -20 1 x 0.4 ml Not Applicable
        NEBNext Probe Hybridization Buffer E6314-2VIAL -20 1 x 0.012 ml Not Applicable
        NEBNext® RNA Sample Purification Beads E6351S 4    
        NEBNext® RNA Sample Purification Beads E6351SVIAL 4 1 x 0.66 ml Not Applicable
    • E7405L     Multi-temperature    
        NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) E7400L -20    
        NEBNext® DNase I E7753-3VIAL -20 1 x 0.06 ml 20,000 units/ml
        NEBNext® Thermostable RNase H E7752-3VIAL -20 1 x 0.048 ml 5,000 units/ml
        NEBNext v2 rRNA Depletion Solution E7401-3VIAL -20 1 x 0.048 ml Not Applicable
        RNase H Reaction Buffer E6312-3VIAL -20 1 x 0.048 ml Not Applicable
        DNase I Reaction Buffer E6315-3VIAL -20 1 x 0.12 ml Not Applicable
        Nuclease-free Water E6317-3VIAL -20 1 x 1.5 ml Not Applicable
        NEBNext Probe Hybridization Buffer E6314-3VIAL -20 1 x 0.048 ml Not Applicable
        NEBNext® RNA Sample Purification Beads E6351L 4    
        NEBNext® RNA Sample Purification Beads E6351LVIAL 4 1 x 2.64 ml Not Applicable
    • E7405X     Multi-temperature    
        NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) E7400X -20    
        NEBNext® DNase I E7753-4VIAL -20 1 x 0.24 ml 20,000 units/ml
        NEBNext® Thermostable RNase H E7752-4VIAL -20 1 x 0.192 ml 5,000 units/ml
        NEBNext v2 rRNA Depletion Solution E7401-4VIAL -20 1 x 0.192 ml Not Applicable
        RNase H Reaction Buffer E6312-4VIAL -20 1 x 0.192 ml Not Applicable
        DNase I Reaction Buffer E6315-4VIAL -20 1 x 0.48 ml Not Applicable
        Nuclease-free Water E6317-4VIAL -20 1 x 6 ml Not Applicable
        NEBNext Probe Hybridization Buffer E6314-4VIAL -20 1 x 0.192 ml Not Applicable
        NEBNext® RNA Sample Purification Beads E6351X 4    
        NEBNext® RNA Sample Purification Beads E6351XVIAL 4 1 x 10.6 ml Not Applicable

  • 特性和用法

    需要但不提供的材料

    • Pipettes
    • Magnetic rack (NEB #S1515), magnetic plate (Alpaqua. cat. #A001322) or equivalent
    • 80% Ethanol (freshly prepared)
    • Thin wall 200 μl PCR tubes and 1.5 ml tubes
    • Microcentrifuge
    • Vortex mixer
    • Thermocycler
    • Bioanalyzer., TapeStation. (Agilent Technologies, Inc.) or similar instrument and consumables

  • 优势和特性

    Features

    • Superior depletion of rRNA from human, mouse and rat RNA
    • Depletion of cytoplasmic (5S, 5.8S, 18S, 28S, human ITS, ETS) and mitochondrial (12S and 16S) rRNA
    • Compatible with a broad range of input amounts: 10 ng – 1 µg
    • Suitable for low-quality or high-quality RNA
    • Fast workflow: 2 hours, with less than 10 minutes hands-on time

  • 相关产品

    相关产品

    • e7760-nebnext-ultra-ii-directional-rna-library-prep-kit-for-illumina
    • e7765-nebnext-ultra-ii-directional-rna-library-prep-with-sample-purification-beads
    • E7750 NEBNext Globin and rRNA Depletion Kit Human Mouse Rat
    • E7755 NEBNext Globin and rRNA Depletion Kit Human Mouse Rat with RNA Sample Purification Beads
    • E7850 NEBNext rRNA Depletion Kit Bacteria
    • E7860 NEBNext rRNA Depletion Kit Bacteria with RNA Sample Purification Beads
    • e7490-nebnext-polya-mrna-magnetic-isolation-module

操作说明、说明书 & 用法

  • 操作说明

    1. Where can I find protocols for using NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) with NEBNext Ultra II RNA Library Prep (NEB #E7400 & #E7405)?

  • 说明书

    产品说明书包含产品使用的详细信息、产品配方和质控分析。

    • manualE7400_E7405

工具 & 资源

  • Web 工具

    • NEBNext Selector

FAQs & 问题解决指南

  • FAQs

    1. What is the difference between the NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) and the original NEBNext® rRNA Depletion Kit (Human/Mouse/Rat)?
    2. Which species are compatible with the NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) for? Will it work for other species?
    3. Which rRNA subunits are depleted with the NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat)?
    4. Can I use this product with degraded RNA or fragmented RNA?
    5. What total RNA input should I use?
    6. Why must the RNA be free of DNA?
    7. What is the percentage of rRNA remaining after depletion?
    8. How can I determine if the rRNA depletion was efficient?
    9. Does the NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) work for ribosomal footprinting or profiling applications?
    10. To remove ribosomal RNA from total RNA, should I use the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) or the NEBNext rRNA Depletion Kit v2 (Human, Mouse, Rat)?
    11. Can I use more than one type of NEBNext Depletion Solution in the NEBNext RNA depletion workflow?
    12. Can the enriched RNA resulting from the NEBNext depletion kit be used in long read sequencing applications?

Next® rRNA Depletion Kit v2 (Human/Mouse/Rat) |NEB酶试剂 New England Biolabs

发表于由

上海金畔生物科技有限公司代理New England Biolabs（NEB）酶试剂全线产品，欢迎访问官网了解更多产品信息和订购。

产品信息

Next® rRNA Depletion Kit v2 (Human/Mouse/Rat) |

Highly expressed transcripts with minimal biological interest, such as ribosomal RNA (rRNA) can dominate readouts, masking detection of more informative low-abundance transcripts. This second-generation NEBNext rRNA Depletion Kit is has been further optimized to incorporate reagent, probe and protocol improvements to the RNaseH-based workflow, resulting in superior depletion performance. 

  • The efficiency of this workflow, and close spacing of probes, enables effective depletion from both low- and high-quality RNA, with a broad range of input amounts from human, mouse and rat samples.
  • The rRNA-depleted RNA can be used in RNA-seq, random-primed cDNA synthesis, or other RNA analysis methods. 
  • The NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) depletes cytoplasmic (5S, 5.8S, 18S, 28S, human ITS, ETS) and mitochondrial (12S, 16S) rRNA.
  • The kit is also available with RNAClean® beads.
Figure 1: The NEBNext rRNA Depletion Kit v2 enriches for RNAs of interest across a wide range of total RNA inputs in human, mouse and rat

Next® rRNA Depletion Kit v2 (Human/Mouse/Rat) |

Universal human, mouse and rat reference total RNA (1 µg, 100 ng and 10 ng) was depleted of rRNA using the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat). RNA-seq libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina followed by paired-end sequencing (2 x 75 bp). 10 Million reads were sampled (seqtk) from each library and reads were identified as ribosomal using mirabait (6 or more shared 25-mers) with rRNA sequences for human baits (5S, 5.8S, 12S, 16S, 18S, 28S, ETS/ITS) or mouse/rat baits (5S, 5.8S, 12S, 16S, 18S, 28S). Levels of rRNA remaining were calculated by dividing matched reads by the total number of reads passing instrument quality filtering. The data represents an average of 3 replicates. The NEBNext rRNA Depletion Kit v2 is efficient at depleting rRNA across species and input amounts.
Figure 2: Treatment with the NEBNext rRNA Depletion Kit v2 does not affect the abundances of non-targeted transcripts

Next® rRNA Depletion Kit v2 (Human/Mouse/Rat) |

Universal human, mouse and rat reference total RNA (1 µg) was depleted of rRNA using the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat). RNA-seq libraries were prepared from untreated and depleted RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina followed by paired-end sequencing (2 x 75bp). 10 million reads were sampled (seqtk) for depleted libraries and 100 million reads for undepleted libraries. GENCODE v27 transcript abundances were estimated using Salmon. Read Counts and R2 values for the linear fit are shown. Transcript expression is consistent after depletion across species.
Figure 3: Transcript expression correlation is preserved across a wide range of inputs

Next® rRNA Depletion Kit v2 (Human/Mouse/Rat) |

Universal human, mouse and rat reference total RNA (1 µg) was depleted of rRNA using the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat). RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina followed by paired-end sequencing (2 x 75bp). GENCODE v27 transcript abundances were estimated using Salmon. Read Counts and R2 values for the linear fit are shown. Transcript expression correlation is consistent regardless of input amount.
Figure 4: The NEBNext rRNA Depletion Kit v2 efficiently depletes rRNA from degraded FFPE total RNA while preserving transcript abundances

Next® rRNA Depletion Kit v2 (Human/Mouse/Rat) |

Human adult normal liver tissue FFPE Total RNA, RIN 2.3 (100 ng and 10 ng) was depleted of rRNA using the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) (A, B, C) or the TruSeq® Stranded Total RNA Gold kit (A). RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina® followed by paired-end sequencing (2 x 75 bp). 20 Million reads were sampled (seqtk) from depleted libraries and 200 million reads from undepleted libraries. (A) Reads were identified as ribosomal using mirabait (6 or more shared 25-mers) with rRNA sequences for 5S, 5.8S, 12S, 16S, 18S, 28S and ETS/ITS as baits. Levels of rRNA remaining were calculated by dividing matched reads by the total number of reads passing instrument quality filtering. The data represents an average of 3 replicates and error bars indicate standard error. (B) and (C) GENCODE v27 transcript abundances were estimated using Salmon. Read Counts and R2 values for the linear fit are shown. The NEBNext kit provides superior depletion of rRNA from FFPE (degraded) samples and offers the flexibility of lower total RNA input amounts. Transcript expression correlation is consistent after treatment and regardless of input amount.
Figure 5: The NEBNext rRNA Depletion Kit v2 depletes both mature and pre-rRNA from human total RNA

Next® rRNA Depletion Kit v2 (Human/Mouse/Rat) |

Human universal reference total RNA (1 µg) was depleted of rRNA using the original NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB #E6310) and the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) (NEB #E7400). RNA-seq libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina followed by paired-end sequencing (2 x 75 bp). 10 Million reads were sampled (seqtk) from each library. Reads were identified as ribosomal using mirabait (6 or more shared 25-mers) with rRNA sequences for 5S, 5.8S 12S, 16S, 18S, 28S and ETS/ITS as baits. Levels of rRNA remaining were calculated by dividing matched reads by the total number of reads passing instrument quality filtering. The data represents an average of 3 replicates. NEBNext rRNA Depletion Kit v2 provide superior depletion of rRNA.
Figure 6: Workflow

Next® rRNA Depletion Kit v2 (Human/Mouse/Rat) |

产品类别:
RNA Depletion & mRNA Enrichment Products,
RNA Library Prep for Illumina

  • 试剂盒组成

    本产品提供以下试剂或组分：

    NEB # 名称 组分货号 储存温度 数量 浓度
    • E7400S     -20    
        NEBNext® DNase I E7753-2VIAL -20 1 x 0.015 ml 20,000 units/ml
        NEBNext® Thermostable RNase H E7752-2VIAL -20 1 x 0.012 ml 5,000 units/ml
        NEBNext v2 rRNA Depletion Solution E7401-2VIAL -20 1 x 0.012 ml Not Applicable
        RNase H Reaction Buffer E6312-2VIAL -20 1 x 0.012 ml Not Applicable
        DNase I Reaction Buffer E6315-2VIAL -20 1 x 0.03 ml Not Applicable
        Nuclease-free Water E6317-2VIAL -20 1 x 0.4 ml Not Applicable
        NEBNext Probe Hybridization Buffer E6314-2VIAL -20 1 x 0.012 ml Not Applicable
    • E7400L     -20    
        NEBNext® DNase I E7753-3VIAL -20 1 x 0.06 ml 20,000 units/ml
        NEBNext® Thermostable RNase H E7752-3VIAL -20 1 x 0.048 ml 5,000 units/ml
        NEBNext v2 rRNA Depletion Solution E7401-3VIAL -20 1 x 0.048 ml Not Applicable
        RNase H Reaction Buffer E6312-3VIAL -20 1 x 0.048 ml Not Applicable
        DNase I Reaction Buffer E6315-3VIAL -20 1 x 0.12 ml Not Applicable
        Nuclease-free Water E6317-3VIAL -20 1 x 1.5 ml Not Applicable
        NEBNext Probe Hybridization Buffer E6314-3VIAL -20 1 x 0.048 ml Not Applicable
    • E7400X     -20    
        NEBNext® DNase I E7753-4VIAL -20 1 x 0.24 ml 20,000 units/ml
        NEBNext® Thermostable RNase H E7752-4VIAL -20 1 x 0.192 ml 5,000 units/ml
        NEBNext v2 rRNA Depletion Solution E7401-4VIAL -20 1 x 0.192 ml Not Applicable
        RNase H Reaction Buffer E6312-4VIAL -20 1 x 0.192 ml Not Applicable
        DNase I Reaction Buffer E6315-4VIAL -20 1 x 0.48 ml Not Applicable
        Nuclease-free Water E6317-4VIAL -20 1 x 6 ml Not Applicable
        NEBNext Probe Hybridization Buffer E6314-4VIAL -20 1 x 0.192 ml Not Applicable

  • 特性和用法

    需要但不提供的材料

    • Pipettes
    • Magnetic rack (NEB #S1515), magnetic plate (Alpaqua. cat. #A001322) or equivalent
    • 80% Ethanol (freshly prepared)
    • Thin wall 200 μl PCR tubes and 1.5 ml tubes
    • Microcentrifuge
    • Vortex mixer
    • Thermocycler
    • Bioanalyzer., TapeStation. (Agilent Technologies, Inc.) or similar instrument and consumables
    • Agencourt. RNAClean. XP Beads (Beckman Coulter, Inc. #A63987)

  • 优势和特性

    Features

    • Superior depletion of rRNA from human, mouse and rat RNA
    • Depletion of cytoplasmic (5S, 5.8S, 18S, 28S, human ITS, ETS) and mitochondrial (12S and 16S) rRNA
    • Compatible with a broad range of input amounts: 10 ng – 1 µg
    • Suitable for low-quality or high-quality RNA
    • Fast workflow: 2 hours, with less than 10 minutes hands-on time

  • 相关产品

    相关产品

    • e7760-nebnext-ultra-ii-directional-rna-library-prep-kit-for-illumina
    • e7765-nebnext-ultra-ii-directional-rna-library-prep-with-sample-purification-beads
    • E7750 NEBNext Globin and rRNA Depletion Kit Human Mouse Rat
    • E7755 NEBNext Globin and rRNA Depletion Kit Human Mouse Rat with RNA Sample Purification Beads
    • E7850 NEBNext rRNA Depletion Kit Bacteria
    • e7490-nebnext-polya-mrna-magnetic-isolation-module

操作说明、说明书 & 用法

  • 操作说明

    1. Where can I find protocols for using NEBNext® RNA Library Prep reagents?

  • 说明书

    产品说明书包含产品使用的详细信息、产品配方和质控分析。

    • manualE7400_E7405

工具 & 资源

  • Web 工具

    • NEBNext Selector

FAQs & 问题解决指南

  • FAQs

    1. What is the difference between the NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) and the original NEBNext® rRNA Depletion Kit (Human/Mouse/Rat)?
    2. Which species are compatible with the NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) for? Will it work for other species?
    3. Which rRNA subunits are depleted with the NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat)?
    4. Can I use this product with degraded RNA or fragmented RNA?
    5. What total RNA input should I use?
    6. Why must the RNA be free of DNA?
    7. What is the expected RNA yield recovered after rRNA depletion?
    8. What is the percentage of rRNA remaining after depletion?
    9. How can I determine if the rRNA depletion was efficient?
    10. Does the NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) work for ribosomal footprinting or profiling applications?
    11. Can I use Agencourt® AMPure® XP Magnetic Beads instead of NEBNext® RNA Sample Purification Beads (RNAClean® XP Magnetic Beads)?
    12. Can I use purification methods other than NEBNext® RNA Sample Purification Beads/Agencourt® RNAClean® XP Magnetic Beads?
    13. To remove ribosomal RNA from total RNA, should I use the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) or the NEBNext rRNA Depletion Kit v2 (Human, Mouse, Rat)?
    14. Can I use more than one type of NEBNext Depletion Solution in the NEBNext RNA depletion workflow?
    15. Can the enriched RNA resulting from the NEBNext depletion kit be used in long read sequencing applications?