CUTANA™ Tn5 Transposome
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CUTANA™ Tn5 Transposome for ATAC-seq is a highly active E. coli Tn5 transposase mutant, pre-charged with mosaic-end adapters and supplied ready for chromatin accessibility profiling by Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq). ATAC-seq was first described by Buenrostro et al. as a rapid method for mapping accessible chromatin by direct in vitro transposition of sequencing adapters into native chromatin [1]. The assay enables genome-wide analysis of open chromatin and regulatory element activity from low nuclei inputs.
The CUTANA™ Tn5 Transposome is compatible with workflows based on the Omni-ATAC protocol described by Corces et al. and detailed by Grandi et al., which improved ATAC-seq performance by reducing background and increasing signal-to-background across a broad range of sample types [2,3].
Key Advantages
- Pre-charged Tn5 Transposome supplied ready for ATAC-seq tagmentation
- Compatible with the Omni-ATAC protocol
- Recommended for chromatin accessibility profiling from isolated nuclei
Lot-validated with fresh nuclei
For a streamlined experience with validated reagents, see the CUTANA™ ATAC-seq Kit.
For full end-to-end support, see CUTANA™ ATAC-seq Services.
To place bulk orders, contact us. Keep learning by checking out our Tech Support Center.
Figure 1: CUTANA™ ATAC-seq generates reproducible data that outperforms ENCODE
ATAC-seq performed on K562 nuclei using CUTANA™ Tn5 Transposome, as part of the CUTANA™ ATAC-seq Kit, and analyzed with the CUTANA Cloud ATAC-seq pipeline. The assay yields reproducible data that meets or exceeds ENCODE reference data across users and days. Three experiments are shown (two users, three days) against ENCODE K562 ATAC-seq (GSE170214). (A) Genome browser tracks at high- (GAPDH, 15 kb), medium- (VAMP2, 11 kb), and low-expression (SLC12A5, 35 kb) loci, expression tiers set by RNA-seq (SRR4235541, SRR4235542), show sharp, concordant peaks at active loci and uniformly low signal at the inactive locus. (B) TSS enrichment (±2 kb, 23,235 genes) is sharp for every sample, with peak signal at or above ENCODE. (C) Called peaks, FRiP, and TSS enrichment (mean ± range, duplicate reactions) meet or exceed ENCODE across users and days.
Figure 2: CUTANA™ ATAC-seq generates robust results with as few as 1,000 nuclei
ATAC-seq performed on K562 nuclei using CUTANA™ Tn5 Transposome, as part of the CUTANA™ ATAC-seq Kit, generates high-quality data across an input titration from 50,000 down to 1,000 nuclei. Data was analyzed with the CUTANA Cloud ATAC-seq pipeline. (A) Genome browser tracks at high- (GAPDH, 15 kb), medium- (VAMP2, 11 kb), and low-expression (SLC12A5, 35 kb) loci, expression tiers set by RNA-seq (SRR4235541, SRR4235542), are highly concordant across 50k, 20k, 10k, 5k, and 1k nuclei, with minimal signal loss down to 1k. (B) TSS enrichment (±2 kb, 23,235 genes) remains strong at 50k, 10k, and 1k nuclei. (C) Signal at peaks called from the 50k condition (77,905 peaks, ±2 kb) is comparably robust at 1k nuclei, showing overall ATAC-seq signal is preserved at low input.
Figure 3: CUTANA™ Tn5 performance is comparable to a leading competitor enzyme
ATAC-seq performed on K562 nuclei using either CUTANA™ Tn5 Transposome or Competitor B Transposome, as part of the CUTANA™ ATAC-seq Kit, and was analyzed with the CUTANA Cloud ATAC-seq pipeline. The assay yields comparable high-quality data at 50k and 10k nuclei. (A) Genome browser tracks at high- (GAPDH, 15 kb), medium- (VAMP2, 11 kb), and low-expression (SLC12A5, 35 kb) loci, expression tiers set by RNA-seq (SRR4235541, SRR4235542), show comparable peak position and shape for both transposomes at both inputs. (B) TSS enrichment (±2 kb, 23,235 genes) is comparable between transposomes at 50k and 10k nuclei. (C) At a merged peak set from both transposomes at 50k nuclei (67,277 peaks, ±2 kb), signal is comparable, with the CUTANA™ Tn5 Transposome showing slightly higher overall signal.
Figure 4: ATAC-seq methods
ATAC-seq was performed on 50k native K562 nuclei using the CUTANA™ ATAC-seq Kit (EpiCypher 14-1121) and the CUTANA™ Nextera-Compatible CDI Primer Set 1 (EpiCypher 14-1190). Libraries were sequenced on an Illumina NextSeq2000 with paired-end sequencing (2×50 bp). Sequencing files were trimmed for adapter sequences with fastp and aligned to the hg38 reference genome using Bowtie2. Data were filtered to remove duplicates, multi-aligned reads, and ENCODE DAC Exclusion List regions.
Storage
Stable for six months at -80°C from date of receipt and up to 10 freeze/thaw cycles; aliquot if more are needed.
Formulation
50 mM HEPES-KOH pH 7.2, 100 mM NaCl, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton X-100, 50% glycerol.
Adapters
Tn5ME-A: 5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-3’
Tn5ME-B: 5’-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG-3’
Tn5ME-rev: 5’-[phos]CTGTCTCTTATACACATCT-3’
Application Notes
CUTANA™ Tn5 Transposome for ATAC-seq is compatible with the Omni-ATAC protocol described by Corces et al. and detailed by Grandi et al. [2,3]. For recommended reaction conditions, users should refer to the Omni-ATAC publications and associated protocol.
CUTANA™ Tn5 Transposome is available in multiple pack size options.
| Cat. No. (Pack Size) | # Standard ATAC-seq Reactions* |
|---|---|
| 15-1036-25uL (25 µL) | 10 |
| 15-1036-125uL (125 µL) | 50 |
| 15-1036-125uL (625 µL) | 250 |
*5 Units of CUTANA™ Tn5 Transposome, equivalent to 2.5 µL, is sufficient to optimally tagment 1,000–50,000 K562 nuclei at 37°C for 30 minutes in a 50 µL reaction. Because chromatin accessibility, nuclear integrity, and tagmentation efficiency can vary by cell type and sample preparation method, users may need to titrate CUTANA™ Tn5 Transposome to determine the optimal amount of enzyme for their cell type or sample of interest. See the EpiCypher Tech Support Center for guidance on optimizing tagmentation.
| Item | Cat. No. |
|---|---|
| CUTANA™ 8-strip tubes | 10-0009 |
| CUTANA™ Magnetic Separation Rack, 0.2 mL Tubes | 10-0008 |
| CUTANA™ Magnetic Separation Rack, 1.5 mL Tubes | 10-0012 |
| CUTANA™ DNA Purification Beads | 21-1407 |
| CUTANA™ Nextera-Compatible CDI Primers | 14-1190 |
| CUTANA™ Non-Hot Start 2X PCR Master Mix | 15-1018 |
| CUTANA™ 5% Digitonin | 21-1004 |
