Details

Autor(en) / Beteiligte

• Schraivogel, Daniel
• Gschwind, Andreas R
• Milbank, Jennifer H
• Leonce, Daniel R
• Jakob, Petra
• Mathur, Lukas
• Korbel, Jan O
• Merten, Christoph A
• Velten, Lars
• Steinmetz, Lars M

Titel

Targeted Perturb-seq enables genome-scale genetic screens in single cells

Ist Teil von

• Nature methods, 2020-06, Vol.17 (6), p.629

Ort / Verlag

United States

Erscheinungsjahr

2020

Link zum Volltext

Quelle

MEDLINE

Beschreibungen/Notizen

• The transcriptome contains rich information on molecular, cellular and organismal phenotypes. However, experimental and statistical limitations constrain sensitivity and throughput of genetic screening with single-cell transcriptomics readout. 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. TAP-seq permits routine analysis of thousands of CRISPR-mediated perturbations within a single experiment, detects weak effects and lowly expressed genes, and decreases sequencing requirements by up to 50-fold. We apply TAP-seq to generate perturbation-based enhancer-target gene maps for 1,778 enhancers within 2.5% of the human genome. We thereby show that enhancer-target association is jointly determined by three-dimensional contact frequency and epigenetic states, allowing accurate prediction of enhancer targets throughout the genome. In addition, we demonstrate that TAP-seq can identify cell subtypes with only 100 sequencing reads per cell.