Hieff NGSTM MaxUp Human rRNA Depletion Kit (rRNA & ITS/ETS)

Details:

Description

Hieff NGSTM MaxUp Human rRNA Depletion Kit (rRNA & ITS/ETS) is designed to remove rRNA and 45S ITS/ETS from human, mouse and rat total RNA based on RNase H-based workflow and to retain mRNA and other non-coding RNA. This kit is suitable for both intact and partially degraded RNA samples (e.g., FFPE RNA). Since degraded FFPE samples usually contain a higher proportion of ITS/ETS than fresh tissue samples, this kit adds probes in the Human 45S ITS/ETS region, and ITS removal can significantly increase the proportion of valid data in raw data.

Features

  • Strong specificity: specifically remove rRNA and ITS/ETS from human samples, especially for FFPE samples
  • High compatibility of template starting amount: applicable to 100 ng~1μg sample
  • High removal effect: for rRNA, ITS and ETS in human\mouse and rat samples, the removal effect is more than 95%
  • Stable quality: strict batch performance and stability quality control

Applications

  • Gene Expression Research
  • Alternative splicing analysis
  • Detection and discovery of non coding RNA
  • dentification of selective polyadenylation sites
  • Fusion gene detection

Specifications

Depletion Technology RNase H
Sample Type Total RNA of human, mouse and rat
Final Product Type mRNA and other non coding RNAs
No. of Reactions 24/96 Preps
Starting Material Amount 100 ng~1 μg total RNA
Target Remove rRNA and 45S ITS/ETS form human total RNA

Components

Components No. Name 12257ES24 (24T) 12257ES96 (96T)
12257-A Hybridization Buffer 72 μL 288 μL
12257-B Probe Mix (rRNA & ITS/ETS) 48 μL 192 μL
12257-C RNase H Buffer 72 μL 288 μL
12257-D RNase H 48 μL 192 μL
12257-E DNase I Buffer 660 μL 2×1320 μL
12257-F DNase I 60 μL 240 μL

Shipping and Storage

All the components are shipped with dry ice and can be stored at -15℃ ~ -25℃ for one year.

Figures

  • rRNA removal specificity

For conventional samples, rRNA and ITS/EST can be removed by more than 98%, while for FFPE samples with integrity of about 50%, rRNA and ITS/EST can be removed by more than 95%. At the same time, FFPE with poor integrity can also be removed effectively.

Table 1. rRNA Removal specificity effect

RNA quality Removal scheme Input rRNA (%) ITS/ETS (%) Mapping (%)
293T RNA;  RIN=10 remove rRNA 1μg 0.19 4.6 98.28
remove rRNA and ITS/ETS 1μg 0.15 0.04 98.79
FFPE RNA;  DV200 =90% remove rRNA 500ng 0.23 4.75 95.35
remove rRNA and ITS/ETS 500ng 0.21 0.02 95.42
FFPE RNA;  DV200 =50% remove rRNA 500ng 1.4 16.28 95.57
remove rRNA and ITS/ETS 500ng 0.56 0.11 95.51
FFPE RNA;  DV200 =20% remove rRNA 1μg 0.35 67.61 58.4
remove rRNA and ITS/ETS 1μg 0.79 0.84 60.35

Note: Different human RNA samples were used to remove rRNA or rRNA and ITS/ETS, and to construct libraries with RNA library Prep kit after ITS/ETS. The proportions of rRNA and ITS/ETS in offline data were analyzed by sequencing.

  • Sequencing data performance

Table 2. Sequencing data performance

Sample DV200 Kit Clean Q20 (%) Clean Q30 (%) Clean GC (%) rRNA (%) ITS/ETS (%) unique(%)
1 24% YEASEN Cat#12257 96.75 92.68 57.05 4.58 2.42 96.90
2 40% 96.56 92.42 55.31 1.93 0.63 96.45
3 53% 97.4 93.52 45.19 0.23 0.01 98.08
4 76% 97.67 93.78 51.28 0.44 0.01 93.63
Citations & References:

[1] Tian S, Zhang B, He Y, et al. CRISPR-iPAS: a novel dCAS13-based method for alternative polyadenylation interference. Nucleic Acids Res. 2022;50(5):e26. doi:10.1093/nar/gkac108(IF:16.971)

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