Human Lincode siRNA Library

siRNA screening tools to elucidate lncRNA function


An arrayed collection of siRNA reagents for RNAi screening, targeting human long noncoding RNA (lncRNA) from RefSeq v65 with NR accession numbers. Lincode siRNA reagents are specially modified to reduce off-targets for fewer false positives.
The Human Lincode NR lncRNA RefSeq v65 siRNA library targets long noncoding RNA (lncRNA) transcripts with NR accession number designation; both from lncRNA genes and within protein coding genes. The Lincode siRNA designs and modifications reduce off-target effects while maintaining high silencing potency for high-confidence screening results.

Highlights

  • Patented dual-strand modification pattern on all siRNAs to reduce off-targets
    • Sense strand is modified to prevent interaction with RISC and favor antisense strand uptake
    • Antisense strand seed region is modified to destabilize off-target activity and enhance target specificity
  • Available as SMARTpool siRNA reagents or a Set of 4 siRNAs in 96-well or 384-well plates

Gene Targets

This library targets 2022 unique human lncRNA genes and 1439 lncRNA transcripts that are associated with protein-coding gene records for a total of 3461 targets.

For a complete list of target genes in this siRNA Library, please email Technical Support, or call 1-800-235-9880. International customers, please call 303-604-9499 or your local Sales Representative. For pricing on this library or to request a custom library, please submit a Library Quote Request.

  
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Chart showing unaffected cell viability and reduced protein expression of BDNF-AS1 using 25 nM of siRNAs 1-4 and the siRNA SMARTpool.

Lincode siRNAs effectively knockdown target lncRNAs

Chart showing unaffected cell viability and reduced protein expression of BDNF-AS1 using 25 nM of siRNAs 1-4 and the siRNA SMARTpool.

Knockdown of BDNF-AS1 in hNDF cells by Lincode SMARTpool and four siRNAs. All siRNAs were used at 25 nM. LncRNA transcripts were detected with Solaris (sold under the Thermo Scientific brand) qPCR lncRNA Expression Assays and normalized to Non-targeting Control siRNA. Viability was assessed by resazurin assay.


Chart showing unaffected cell viability and high knockdown of CDKN2B-AS1 by siRNAs 1-4 and the SMARTpool.

Detection of effective lncRNA knockdown following application of Lincode siRNA

Chart showing unaffected cell viability and high knockdown of CDKN2B-AS1 by siRNAs 1-4 and the SMARTpool.

Knockdown of CDKN2B-AS1 in HeLa cells by Lincode SMARTpool and four siRNAs. All siRNAs were used at 25 nM. LncRNA transcripts were detected with Solaris (sold under the Thermo Scientific brand) qPCR lncRNA Expression Assays and normalized to Non-targeting Control siRNA. Viability was assessed by resazurin assay.


Scatterplot showing Cq values for BDNF-AS1, CDKN2B-AS1, FAS-AS1, FMR1-AS1, KCNQ1-ot1, NRON, MLK07, and PPIB in HeLa, HEK293T, or hNDF cells.

lncRNAs have highly variable expression

Scatterplot showing Cq values for BDNF-AS1, CDKN2B-AS1, FAS-AS1, FMR1-AS1, KCNQ1-ot1, NRON, MLK07, and PPIB in HeLa, HEK293T, or hNDF cells.

Expression analysis of nine lncRNAs varies widely across three human cell lines.

It is of vital importance to determine lncRNA expression in your cells prior to knockdown experiments. lncRNA expression can be expected to vary much more than is typically observed from protein-coding genes like Cyclophilin B (PPIB).

50 ng of total RNA was converted into cDNA using the Maxima First Strand cDNA Synthesis Kit (# K1641). PPIB was used as a reference for typical mRNA expression. Standard RT-PCR cycling conditions resulted in initial Cq values ranging from 22 (PPIB in 293T cells) to 36 (BDNF-AS1 in HeLa cells). lncRNA MLK7-AS1 expression was not detectable in any of the cell lines tested. Cell lines tested include HeLa, HEK293T, Human Neonatal Dermal Fibroblast (hNDF).


Chart showing unaffected cell viability over protein expression for BDNF-AS1 (<40% expression), BDNF (unaffected) and untreated cells (unaffected).

Lincode modifications enhance function and reduce off-targets

Chart showing unaffected cell viability over protein expression for BDNF-AS1 (<40% expression), BDNF (unaffected) and untreated cells (unaffected).

Lincode siRNA effectively knocks down BDNF-AS1 lncRNA, but not the protein-coding transcript BDNF that is antisense to the lncRNA target. This indicates strand specificity of Lincode siRNAs and effectiveness of ON TARGETplus modifications. siRNAs were applied at the indicated concentrations to hNDF cells. BDNF-AS1 and BDNF transcripts were detected with Solaris (sold under the Thermo Scientific brand) qPCR Expression Assays and normalized to Non-targeting control siRNA. Viability was assessed by resazurin assay and normalized to Untreated.


Cartoon showing Lincode siRNA modifications reducing seed-mediated off-targeting and inactivation of the passenger strand.

Sense strand activity is prevented by siRNA modifications

Cartoon showing Lincode siRNA modifications reducing seed-mediated off-targeting and inactivation of the passenger strand.

Lincode siRNAs are modified with a proprietary dual-strand modification that improves siRNA functionality. Additionally, off-targets are reduced due to:

  • Inactivation of passenger strand activity; driving preferential loading of the guide strand into RISC
  • Novel seed region modifications for disruption of microRNA-like off-targets