CITE-Seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) is a method for performing RNA sequencing along with gaining quantitative and qualitative information on surface proteins with available antibodies on a single cell level. [1]

May 2, 2017 · Here, we present a biochemical method, based on the selective enrichment and identification of adapter-tagged DNA ends by sequencing (SITE-Seq). SITE-Seq can be used to identify off-target cleavage sites within a genomic DNA sample.

May 1, 2017 · Here, we developed a biochemical method (SITE-Seq), using Cas9 programmed with single-guide RNAs (sgRNAs), to identify the sequence of cut sites within genomic DNA. Cells edited with the same...

To reduce such cost, scientists developed SITE-seq, a method that adds a selective biotinylation reaction on the cleaved genomic sites and leverages streptavidin pulldown to enrich these sites before sequencing (Cameron et al., 2017). SITE-seq reduces the background noise of Digenome-seq and requires much less sequencing coverage (∼0.62–2. ...

SITE-Seq Improves Digenome-seq Methodology With Selective Target Enrichment. SITE-Seq is an unbiased, in vitro detection technique for nuclease-induced DSBs (Cameron et al., 2017). SITE-Seq involves the in vitro digestion of genomic DNA with CRISPR/Cas9, similar to Digenome-seq. Following 3′ adenylation, DSBs are ligated with biotinylated ...

To resolve these issues, we have developed a biochemical method that uses the selective enrichment and identification of tagged genomic DNA ends by sequencing (SITE-Seq) to identify Cas9 cleavage sites in purified genomic DNA.

Feb 9, 2015 · Digested genome sequencing (Digenome-seq) is a highly sensitive, easy-to-carry-out, cell-free method for experimentally identifying genome-wide off-target sites of programmable nucleases and...

We propose a new coding scheme for coding sequence pairs and design a new model called CRISPR-IP for predicting off-target activity. Our coding scheme distinguishes regions with different functions in the sequence pairs through the function channel.

Mar 2, 2023 · Our site-profiling strategy exhibited broad site coverage, while the site-seq and site-link strategies assured the orthogonality and site specificity for introducing lysine acylations and their photoaffinity analogues into unperturbed chromatin.

Jul 2, 2024 · In the present study, we developed Tracking-seq (tracking RPA-bound single-stranded DNA by sequencing), a universal off-target detection assay that aims to track common DNA damage repair...