CITE-Seq
For phenotyping, this method has been shown to be as accurate as flow cytometry (a gold standard) by the groups that developed it.
[2] It is currently one of the main methods, along with REAP-Seq, to evaluate both gene expression and protein levels simultaneously in different species.
The method was established by the New York Genome Center in collaboration with the Satija lab.,[2] while a similar approach was earlier shown by AbVitro Inc.. Concurrent measurement of both protein and transcript levels opens up opportunities to use CITE-Seq in various biological areas, some of which were touched upon by the developers.
[3] All of the above are possible due to single-cell output of both protein and transcript data at the same time, also leading to novel information on protein-RNA correlation.
But in contrast to RNA data, due to higher amounts of protein in a cell, there is less dropout.
The applications of antibody-oligonucleotide conjugates have expanded beyond CITE-seq, and can be adapted for sample multiplexing as well as CRISPR screens.
Cell Hashing: New York Genome Center further adapted the use of their antibody-oligonucleotide conjugates to enable sample multiplexing for scRNA-seq.
Sequencing the antibody tags along with the cellular transcriptome helps identify a sample of origin for each analyzed cell.
[14] The ability of ECCITE-seq to detect sgRNA molecules and measure their effect on gene expression levels opens a prospect of applying this technique in CRISPR screens.
Previous efforts of coupling index-sorting measurements from single cell sorts with scRNA-seq were limited to running a small sample size and were not compatible with multiplexing and massive parallel high-throughput sequencing.
Lastly, CITE-seq can be adapted to detect small molecules, RNA interference, CRISPR, and other gene editing techniques.
[9] In terms of phenotyping, optimization of the assay and antibodies also presents a potential problem if proteins of interest are not included in the currently available panels.
[16] With the current protocol, there are many challenges that would arise during the permeabilization step, thus limiting the technique to surface markers.
