Jun 1, 2020 · To overcome these limitations, we introduce targeted Perturb-seq (TAP-seq), a sensitive, inexpensive and platform-independent method focusing single-cell RNA-seq coverage on genes of...

Here we provide a step-by-step protocol for targeted single-cell RNA-seq and targeted Perturb-seq, as reported in the linked publication Schraivogel et al. Nat Meth 2020. The protocol describes cell preparation using flow cytometry, single-cell droplet formation with 10X Genomics, and tar...

Feb 1, 2024 · In TAP-seq the sequencing library is first enriched for transcripts of interest (e.g., 100–1000 specific transcripts), which provides a balance between multidimensional phenotyping and cost, as it can reduce the reads-per-cell requirements by up to 50-fold.

An R-package to design PCR primers for TAP-seq published in Nature Methods, 2020. TAPseq is available through Bioconductor.

Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using Primer3. Potential off-targets can be estimated with BLAST.

To overcome these limitations, we introduce targeted Perturb-seq (TAP-seq), a sensitive, inexpensive and platform-independent method focusing single-cell RNA-seq coverage on genes of interest, thereby increasing the sensitivity and scale of genetic screens by orders of magnitude.

Oct 29, 2024 · TAPseq implements TsIO and TsIOList objects, which store Primer3 input and output for TAP-seq primer design in R’s S4 class system. They serve as the users interface to Primer3 during primer design.

With TAP-seq, it’s possible to analyse genes that are only transcribed into a very small number of mRNA molecules, and to detect subtle changes amounting to an increase or decrease of only one mRNA molecule per cell.

Here we overcome these limitations by introducing a protocol for targeted Perturb-seq (TAP-seq) (Figure 1). The method has been established primarily as a readout for pooled CRISPR screens. However, TAP-seq is applicable to diverse single-cell applications in mammalian cell lines and primary mammalian cells, with or without CRISPR perturbations.

Design primers for targeted single-cell RNA-seq used by TAP-seq. Create sequence templates for target gene panels and design gene-specific primers using Primer3. Potential off-targets can be estimated with BLAST. Requires working installations of Primer3 and BLASTn.