Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides that regulate gene expression and chromatin organization. With the development of RNA-Seq technologies, lncRNA research has expanded in cancer biology, epigenetics, and precision medicine.
Because many lncRNAs are low-abundance transcripts, library preparation quality is critical for accurate detection.
Key Applications
|
Application |
Description |
|
lncRNA discovery |
Identify novel regulatory RNAs |
|
Gene regulation studies |
Investigate RNA-mediated regulation |
|
Cancer research |
Identify disease-associated lncRNAs |
|
Biomarker identification |
Discover diagnostic markers |
Industry Challenges
|
Challenge |
Impact |
|
Low expression levels |
Difficult detection |
|
rRNA background |
Reduces sequencing efficiency |
|
Complex transcript structures |
Complicates annotation |
Yeasen lncRNA Library Prep Workflow
Yeasen provides optimized rRNA depletion-based library preparation workflows designed for high efficiency across diverse sample types, including human, mouse, and rat samples, plant tissues, and blood samples requiring globin depletion.
Example Case Study-Low-Quality Sample
Using Yeasen’s strand-specific lncRNA library preparation solution, high-quality libraries were successfully generated from low-input and partially degraded total RNA samples for long non-coding RNA profiling.
Results demonstrated:
- Effective removal of abundant rRNA background
- Strong strand specificity retention
- Stable detection of low-abundance lncRNA transcripts
- Consistent library complexity across degraded samples
- Reduced bias in transcript representation
Even under suboptimal RNA integrity conditions, the workflow maintained strong sensitivity and reproducibility, supporting reliable lncRNA discovery and differential expression analysis.
Case Study 1-Arabidopsis sample
lncRNA library preparation from the model plant Arabidopsis at various input amounts. The Hieff NGS™ Ultima Dual-mode RNA Library Prep Kit(CAT#12308) shows performance comparable to Supplier N* and slightly outperforms Supplier V* in terms of library yield and sequencing data metrics.
|
Exp. No. |
Input |
PCR Cycles |
Fragmentation |
Lib Yield (ng/μL) |
Clean Reads |
Raw Q30 (%) |
Clean GC (%) |
rRNA (%) |
Infer (%) |
Diff Chr (%) |
Gene (FPKM>1) |
Transcript (FPKM>1) |
Exon (%) |
|
Supplier N*** |
1 μg |
12 |
94℃ 10min |
7.64 |
9,102,183 |
92.30 |
45.51 |
0.83 |
99.0723 |
1.5208 |
16,305 |
21,926 |
98.3317 |
|
Supplier V*** |
85℃ 6min |
2.48 |
6,255,751 |
91.45 |
45.60 |
0.51 |
98.9404 |
2.0246 |
16,321 |
21,976 |
98.3050 |
||
|
YS-12308ES |
94℃ 7min |
6.90 |
7,440,032 |
92.99 |
45.45 |
1.33 |
98.1683 |
1.2951 |
16,544 |
22,144 |
98.2703 |
||
|
Supplier N*** |
100 ng |
14 |
94℃ 10min |
4.36 |
6,982,424 |
91.65 |
45.59 |
1.16 |
99.0001 |
0.1193 |
16,238 |
21,594 |
98.3670 |
|
Supplier V*** |
85℃ 6min |
2.90 |
5,553,079 |
91.53 |
45.69 |
0.65 |
98.9436 |
0.4505 |
16,386 |
21,780 |
98.3311 |
||
|
YS-12308ES |
94℃ 7min |
11.50 |
9,747,685 |
92.55 |
45.35 |
1.05 |
98.3953 |
0.1270 |
16,577 |
22,069 |
98.2759 |
||
|
Supplier N*** |
10 ng |
16 |
94℃ 10min |
2.23 |
9,066,858 |
91.09 |
46.44 |
1.13 |
99.1141 |
0.4906 |
15,994 |
20,217 |
69.0832 |
|
Supplier V*** |
85℃ 6min |
1.53 |
7,935,702 |
90.69 |
46.36 |
1.17 |
99.1540 |
0.8958 |
15,711 |
19,402 |
72.3912 |
||
|
YS-12308ES |
94℃ 7min |
5.20 |
6,766,839 |
91.15 |
44.85 |
0.97 |
98.8359 |
0.5547 |
16,409 |
21,363 |
35.9095 |
Case Study 2-FFPE sample
Libraries were prepared from 500 ng of various DV200 Human FFPE RNA inputs. Compared to supplier N*, the Hieff NGS™ Ultima Dual-mode RNA Library Prep Kit demonstrates higher library yield, superior data usability, lower rRNA contamination, and a higher exon ratio.
Key Experimental Tips
|
Factor |
Recommendation |
|
rRNA removal |
Ensure high depletion efficiency |
|
RNA input |
Use sufficient starting material |
|
RNA integrity |
Minimize degradation |
|
PCR cycles |
Optimize amplification steps |
When properly optimized, Total RNA-Seq provides a comprehensive view of transcriptome dynamics.
FAQ
Q1. Why is lncRNA-seq different from mRNA-seq?
Many long non-coding RNAs lack poly(A) tails, making poly(A) enrichment insufficient. lncRNA sequencing usually relies on rRNA depletion instead of poly(A) selection.
Q2. What types of transcripts can be detected with lncRNA-seq?
lncRNA-seq enables detection of both polyadenylated and non-polyadenylated transcripts, including regulatory lncRNAs, antisense RNAs, and intergenic transcripts.
Q3. Is RNA quality critical for lncRNA sequencing?
lncRNA-seq is generally more tolerant of partially degraded RNA because rRNA depletion does not depend on intact poly(A) tails.
Q4. What research applications benefit from lncRNA-seq?
Common applications include epigenetic regulation studies, cancer transcriptomics, RNA regulatory networks, and functional annotation of non-coding RNAs.
Related Product
|
Category |
Name |
Cat. No. |
Size |
|
|
RNA Lib Prep |
Dual-mode(Strand specific & Non Strand specific) |
12308ES24/96 |
24 T/96 T |
|
|
Premix version |
12340ES24/96 |
|||
|
12341ES24/96 |
||||
|
mRNA isolation |
Eukaryotic mRNA |
12629ES24/96 |
24 T/96 T |
|
|
rRNA depletion |
Human/Mouse/Rat |
Hieff NGS™ MaxUp Human/Mouse/Rat rRNA Depletion Kit(rRNA ITS/ETS) |
12257ES24/96 |
|
|
Hieff NGS™ MaxUp Human/Mouse/Rat rRNA Depletion Kit(rRNA ITS/ETS) 2.0 |
12726ES24/96 |
|||
|
Plant |
12254ES24/96 |
|||
|
Beads |
- |
12602ES03/08/56 |
1/5/60 mL |
|