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High-Throughput Kinetic RNA Sequencing

SLAMseq Catabolic Kinetic RNA-Seq

SLAMseq Catabolic RNA-Seq labels newly synthesized (nascent) transcripts in cell culture experiments and detects the decreasing signal of nascent RNA as they are being degraded.

Precise time-resolved analysis of RNA degradation and turnover

SLAMseq offers a straightforward and easy approach to track signal reduction over time for precise and time-resolved measurements of RNA decay in response to stimuli. Compared to conventional methods, SLAMseq delivers higher resolution and allows to study treatment effects and their sequence within cellular processes. SLAMseq Catabolic RNA-Seq is ideal for transcript stability and mRNA half-life measurements, to decipher cell-signaling pathways, or during drug discovery and development processes, and target identification & validation or biomarker discovery.


SLAMseq delivers precise measurements for global RNA decay rates in living cells and allows to distinguish primary and secondary effects of treatments.

The Catabolic Kinetics Module uses a longer initial S4U labeling duration to enable RNA metabo­lism to reach an approximate steady-state level. The exchange of S4U for unlabeled uridine in cell media stops the labeling at t0 (chase) and samples are collected over time (tx up to 24 hours) following addition of unlabeled uridine. Existing RNA is therefore labeled with S4U, while nascent RNA synthesized after the uridine chase is unlabeled. The experiment is thus ideal to monitor RNA degradation rates (Fig. 1).

Figure 1 | 4SU labeling to saturation followed by a uridine chase allows to interrogate RNA degradation over time.

The SLAMseq Kinetics Kit – Catabolic Kinetics Module is ideal 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 (+Uridine) and RNA is sampled. RNA degradation rates are calculated from the decrease in S4U-labeled RNA over time (Fig. 2). For cost-efficient RNA-Seq analysis of degradation rates convenient bundles of SLAMseq Catabolic Kinetic 3’ mRNA-Seq with QuantSeq FWD V2 are available.

Figure 2 | Catabolic kinetics labeling experiment time course. Initial steady-state labeling of RNA is achieved by incubating cells in S4U-containing media for an extended time period, up to 24 hours. The expulsion of S4U from the cells reduces the intracellular S4U concentration back to zero after unlabeled uridine (+Uridine) is added. Only the RNA synthesized before t0 will be labeled with S4U and levels will decrease as transcripts are degraded over time. Time course measurements taken after unlabeled uridine is added determine fast (solid black line) and slow (solid gray line) degradation rates. S4U levels for individual transcripts are measured by counting sequenc¬ing reads with T > C conversions.

SLAMseq resolves transcript expression dynamics on a transcriptome-wide scale. Individual transcript RNA degradation rates can be measured directly. RNA degradation rates are depending on gene regulation processes, such as blockers, enhancer, cofactors, and are transcript specific.

Figure 3 | S4U labeling kinetics experiments reveal individual RNA degradation rates of four gene loci.

Combining SLAMseq with protein modulators, or drug treatments distinguishes direct (primary) and indirect (secondary) target responses. Use SLAMseq to dissect signaling pathways underlying biological processes and characterize drug-target responses on the transcriptional level (Muhar, M et al., 2018).

Figure 4 | S4U labeling followed by drug treatment and early-stage sampling (time points: t1 – t2) measures mRNA stability changes to map sequential drug responses.

Find more information about SLAMseq data analysis here or contact us at


SLAMseq Catabolic Kinetic RNA-Seq allows to detect RNA degradation rates over time in cell culture experiments in response to a stimuli, e.g., a fast-acting compound or drug candidate. Optimal concentration of labeling reagent must be determined during exploring phase to avoid cell toxicity.

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Cultured cells are grown in 4-Thiouridine (S4U) for up to 24 h to allow S4U nucleotides to be incorporated into newly synthesized RNA until saturation is reached. Optimal concentration of S4U must be determined during exploring phase to avoid cell toxicity.

Cells are treated for >30 min with fast-acting compound or drug. The incubation duration depends on the compound and cell type. Negative controls need to be applied.

Cells are supplied with fresh media containing Uridine to perform a chase experiment to assess RNA decay over time.

Cells are sampled at a given timepoint(s) and RNA is extracted under reducing conditions. The isolated total RNA contains both existing (labeled) and newly synthesized (unlabeled) RNA for catabolic kinetics experiments.

Total RNA (1 - 5 µg) is mixed with iodoacetamide (IAA), which modifies the 4-thiol group of S4U-containing nucleotides via the addition of a carboxyamidomethyl group. The RNA is purified by ethanol precipitation prior to proceeding to library preparation.

Total RNA is reverse-transcribed to cDNA. For labeled RNA transcripts, reverse transcriptase incorporates a G instead of an A at positions where reduced *S4U-modified nucleotides are encountered.
Second-strand cDNA synthesis is then performed to generate a double-stranded SLAMseq RNA-Seq library.

PCR is used to amplify the SLAMseq RNA-Seq library and to add indices and full adapter sequences for next-generation sequencing. Sequencing reads with T>C mutations distinguish labeled from unlabeled transcripts, which are read-out during data analysis.


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Ordering Information

Cat. №Product Name
062.24SLAMseq Kinetics Kit - Catabolic Kinetics Module, 24 preps
230.24SLAMseq Catabolic Kinetic 3’ mRNA-Seq with QuantSeq FWD V2, 24 preps

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