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Glossary for single-cell RNA sequencing

Many fields of study use terms that are pretty much restricted to that field of study. This is also true for the field of single-cell RNA sequencing, which itself has different names: single-cell transcriptome sequencing, single-cell transcriptomics, and single-cell gene expression profiling. In this glossary, you can find common terminology from the single-cell RNA sequencing field.

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ERCC or spike-in

External RNA Control Consortium (ERCC) or spike-in controls are a set of nucleic acid fragments with a conventional sequence. They resemble natural eukaryotic mRNAs. Researchers add a known quantity of ERCCs to a sample to establish a baseline measurement. In this way, researchers use ERCCs to calibrate measurements and monitor technical variation.


In single-cell RNA studies, a library or sequencing library is a set of cDNA fragments prepared from the total RNA in a selected number of cells. In SORT-seq and VASA-seq, a library corresponds to the cDNA from all cells of one 384-well cell-capture plate. Sequencing four plates thus gives you four libraries.

In 10x Genomics Single Cell Gene Expression, a library corresponds to the cDNA from all cells in one 10x run, i.e. all cells loaded on one well in a 10x Genomics microfluidic chip. So, if you load eight wells on a 10x Genomics chip, you normally get eight libraries.

However, you can get more libraries per well if you combine gene expression analysis with other analyses in one 10x Genomics run. For example, in 10x Genomics Single Cell Immune Profiling, you can combine gene expression analysis with immune profiling and feature barcoding. So, if you load eight wells on a 10x Genomics chips, you can get up to 24 libraries.


See the entry on ERCC.

Unique Molecular Identifier (UMI)

UMIs are molecular barcodes used to add a unique tag to each RNA molecule in a sample. After PCR amplification, data scientists can trace back the distinct RNA molecules with their UMIs. UMIs are short DNA sequences with random bases. The number of distinct UMIs needs to exceed the number of unique RNA molecules, so the number of bases of a UMI is such that it serves that purpose—usually 4 to 12.

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