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SLAMseq - High-Throughput Metabolic Sequencing of RNA
SLAMseq is a high-sensitivity method for time-resolved measurement of newly synthesized and existing RNA in cultured cells. SLAMseq enables resolution of RNA synthesis and degradation kinetics. Lexogen offers a family of kits based on the new SLAMseq method: Thiol (SH)-Linked Alkylation for the Metabolic sequencing of RNA. SLAMseq enables the identification and quantification of newly synthesized (nascent) and existing RNA from the same sample in parallel, without the need for biochemical isolation. SLAMseq can be readily applied to living cell experiments. Combined with QuantSeq 3’ mRNA-Seq library preparation, SLAMseq provides a complete user friendly and high-throughput solution for analyzing transcriptome-wide RNA synthesis and turnover kinetics.
The SLAMseq kits portfolio includes Explorer and Kinetics Modules, which cover the entire metabolic RNA labeling experiment, from optimizing labeling conditions, to labeling of nascent or existing RNA and alkylation for downstream NGS library preparation.
Optimize 4-Thiouridine Labeling Conditions
The SLAMseq Explorer Kits facilitate the optimization of RNA labeling experiments using 4-Thiouridine (S4U). Assess cell viability and determine optimal concentrations for specific cell types and experimental durations using the SLAMseq Explorer Kit – Cell Viability Titration Module (Cat. No. 059).
Assess Nascent RNA Levels and RNA Synthesis Rates
Distinguish newly-synthesized (nascent) RNA from total RNA using the SLAMseq Kinetics Kit – Anabolic Kinetics Module (Cat. No. 061). Profile nascent RNA levels at specified time points for differential expression analyses, and perform time course S4U labeling experiments to map RNA synthesis dynamics for individual transcripts.
Measure Global S4U Uptake under Experimental Conditions
S4U incorporation rates may vary for different cell types and culture methods. The SLAMseq Explorer Kit – S4U Incorporation Module (Cat. No. 060) can be used to measure the efficiency of S4U incorporation into newly synthesized RNA.
Monitor RNA Degradation Rates
The SLAMseq Kinetics Kit – Catabolic Kinetics Module (Cat. No. 062) 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.
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.
Identify Direct Transcriptional Targets of Any Gene
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).
- Analyze transcriptome-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
- Use in combination with QuantSeq 3’ mRNA-Seq for cost-effective,
- high-throughput metabolic sequencing
- SLAMdunk - automated and user-friendly SLAMseq-QuantSeq data analysis
- pipeline on the BlueBee genomics analysis platform