SLAMseq Metabolic RNA labelling - Lexogen

Reagents & Kits

SLAMseq Metabolic RNA labelling 

SLAMseq Metabolic Labelling kits enable time-resolved measurement of newly synthesized and existing RNA in cultured cells.
This family of kits uses the fast and reliable thiol (SH)-Linked Alkylation for Metabolic Labelling method. This enables identification and quantification of newly synthesized and existing RNA and the monitoring of RNA synthesis and degradation kinetics from the same sample in parallel, without the need for biochemical isolation, meaning that SLAMseq can be readily applied to living cell experiments

The SLAMseq kits portfolio includes Explorer and Kinetics Modules, which cover the entire metabolic RNA labelling experiment, from optimizing labelling conditions, to labelling of newly synthesized or existing RNA and alkylation for downstream NGS library prep.

Combining SLAMseq with QuantSeq 3’ mRNA-seq or QuantSeq Flex Targeted RNA-Seq kits provides a complete user-friendly solution for high throughput metabolic RNA-seq experiments.
Total RNA from SLAMseq experiments can be used directly in the QuantSeq protocol. Simply isolate total RNA, alkylate with iodoacetamide, prepare libraries and sequence. 

•    Analyse transcriptomics-wide kinetics of RNA synthesis and turnover
•    Measure nascent RNA expression and transcript stability
•    Enhance the temporal resolution of differential expression
•    Identify primary and secondary transcriptional targets
•    No pull-down or biochemical isolation required
•    Combine with QuantSeq 3’ mRNA-seq for cost-effective high throughput metabolic sequencing
•    Automated and user-friendly SLAMseq-QuantSeq data analysis pipeline available via the Bluebee® Genomics Analysis platform (SLAMdunk)

Identify direct transcriptional targets of any gene

Combining SLAMseq with protein modulators or drug treatments enables distinction between primary and secondary target responses. Use SLAMseq to dissect the underlying biological processes of signalling pathways and characterize drug-target responses on the transcriptional level (Muhar, M et al., 2018)

Monitor RNA degradation Rates
The Catabolic Kinetics module can be used to measure transcript degradation rates. Cells are first grown in S4U-containing medium for a specified time period to label existing RNA. S4U is then replaced by unmodified uridine (U) and RNA is sampled. RNA degradation rates are calculated from the decrease in S4U-labeled RNA over time.

figure 1: S4U labeling followed by drug treatment and early-stage sampling (time points t1-t2) measures mRNA stability changes to map sequential drug responses

Analyze Transcriptome-wide Expression Dynamics
SLAMseq resolves transcript expression dynamics on a transcriptome-wide scale. Individual transcript RNA synthesis and degradation rates can be measured directly.

figure 2: S4U labeling kinetics experiment reveal individual RNA synthesis and degradation rates

Assess Nascent RNA levels and RNA synthesis rates
Distinguish newly synthesized (nascent) RNA from total RNA using the Anabolic Kinetics Module. Profile nascent RNA levels and perform time course 4SU labelling experiments to map RNA synthesis dynamics for individual transcripts.


figure 3: Read coverage of the Sox2 3'UTR from a SLAMseq experiment. Nascent RNA (green) is labeled and decreased over time, despite stable total RNA levels (blue)



Cat. n°


Reaction Size



SLAMseq Explorer Kit - Cell Viability Titration Module

24 preps

- Asses S4U toxicity in Target Cell Lines

- Optimize S4U labelling concentrations


SLAMseq Explorer Kit - S4U Incorporation Module

24 preps

- Measure S4U uptake and incorporation rates using HPLC Analysis


SLAMseq Kinetics Kit - Anabolic Kinetics Module

24 preps

- Label newly transcribed RNA with S4U

- Measure nascent RNA expression

- Analyse RNA degradation kinetics


SLAMseq Kinetics Kit - Catabolic Kinetics Module

24 preps

- Label existing RNA with S4U

- Asses Transcript stability

- Analyse RNA degradation kinetics


SLAMdunk Data Analysis for SLAMseq integrated on Bluebee®

0-2 GB



SLAMdunk Data Analysis for SLAMseq integrated on Bluebee®

0-6 GB



SLAMdunk Data Analysis for SLAMseq integrated on Bluebee®

0-12 GB



SLAMdunk Data Analysis for SLAMseq integrated on Bluebee®

0-25 GB





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