I'm rather new to sequencing protocols and don't get the difference between different sample multiplexing approaches using in single-cell sequencing. I know you can add sample indices in the Illumina library construction step. Those allow running multiple samples together, right?
Then there's Article Cell Hashing with barcoded antibodies enables multiplexing a...
which allows multiplexing using the barcoded antibodies. In addition, https://github.com/statgen/demuxlet allows demultiplexing reads from multiple samples if sample genotypes are known. What I don't get is why can't just the Illumina indexing be used? What are the downsides?Thanks in advance!
A limited-cycle PCR step uses the adapters to amplify the insert DNA. The PCR step adds index adapter sequences on both ends of the DNA, which enables dual-indexed sequencing of pooled libraries on Illumina sequencing platforms.
Cell Hashing is a method that enables sample multiplexing and super-loading on single cell RNA-sequencing platforms, developed in the Technology Innovation lab at the New York Genome Center in collaboration with the Satija lab.
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