Bioinformatics Terms Explanation
CITE-seq: Cellular Indexing of Transcriptomes and Epitopes by Sequencing, it 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]. It provides an additional layer of information for the same cell by combining both proteomics and transcriptomics data.
High variable genes (HVGs): The expression levels of these genes vary greatly between different cells, which are normally considered as the key for identifying the cells.
Multi-modal/Multi-modality: Multi-modality here refers to the captured multi-type sequencing data from the same targets in dataset. For example, the RNA sequencing data and ADT data in single cell provided by CITE-seq dataset.
Sequencing data/Sequencing: In genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succinctly summarizes much of the atomic-level structure of the sequenced molecule [2].
SHARE-seq: Simultaneous high-throughput ATAC and RNA expression with sequencing, it is a highly scalable approach for measurement of chromatin accessibility and gene expression in the same single cell, applicable to different tissues [3]. It provides information combining data of both chromatin Accessibility and transcriptomics.
TEA-seq: An more advanced technology that measure the Transcriptomic state (scRNA-seq), cell surface Epitopes, and chromatin Accessibility (scATAC-seq) from single cells in parallel [4]. It provides chromatin Accessibility, proteomics and transcriptomics data at the same time.
Reference:
[1] Mercatelli, Daniele; Balboni, Nicola; De Giorgio, Francesca; Aleo, Emanuela; Garone, Caterina; Giorgi, Fedrico M. (2021-05-06). “The Transcriptome of SH-SY5Y at Single-Cell Resolution: A CITE-Seq Data Analysis Workflow”. Methods and Protocols. 4 (2): 28. doi:10.3390/mps4020028. ISSN 2409-9279. PMC 8163004. PMID 34066513.
[2] Sequencing, Wikipedia. https://en.wikipedia.org/wiki/Sequencing
[3] Ma S, Zhang B, LaFave LM, Earl AS, Chiang Z, Hu Y, Ding J, Brack A, Kartha VK, Tay T, Law T, Lareau C, Hsu YC, Regev A, Buenrostro JD. Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin. Cell. 2020 Nov 12;183(4):1103-1116.e20. doi: 10.1016/j.cell.2020.09.056. Epub 2020 Oct 23. PMID: 33098772; PMCID: PMC7669735.
[4] Swanson, E., Lord, C., Reading, J., Heubeck, A. T., Genge, P. C., Thomson, Z., … & Skene, P. J. (2021). Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq. Elife, 10, e63632.