bioRxivMicrobiologyPreprint
Designing and implementing programmable depletion in sequencing libraries with DASHit
D. Dynerman, A. Lyden, J. Quan, S. Caldera, A. McGeever, B. Dimitrov, R. King, G. Cirola, M. Tan, R. Sit, M. van den Berge, H. A. M. Kerstjens, A. Faiz, S. Christenson, C. Langelier, J. DeRisi, E. D. Crawford
Abstract
Since Next-Generation Sequencing produces reads uniformly subsampled from an input library, highly abundant sequences may mask interesting low abundance sequences. The DASH (Depleting Abundant Sequences by Hybridization) technique takes advantage of the programmability of CRISPR/Cas9 to deplete unwanted high-abundance sequences. Because desired depletion targets vary by sample type, here we describe DASHit, software that outputs an optimal DASH target set given a sequencing dataset, an updated DASH protocol, and show depletion results with DASHit-designed targets for three different species.
- organism: human
- organism: mouse
- organism: rat
- assay: bulk RNA-seq
- research focus: cell type annotation
- research focus: clustering
- research focus: differential expression
- research focus: variant calling
- approach: experimental assay
- approach: wet-lab / biochemical assay
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