Abstract
High-throughput single-cell RNA-seq methods assign limited unique molecular identifier (UMI) counts as gene expression values to single cells from shallow sequence reads and detect limited gene counts. We thus developed a high-throughput single-cell RNA-seq method, Quartz-Seq2, to overcome these issues. Our improvements in several of the reaction steps of Quartz-Seq2 allow us to effectively convert initial reads to UMI counts (at a rate of 30%–50%). To demonstrate the power of Quartz-Seq2, we analyzed transcriptomes from a cell population of in vitro embryonic stem cells and an in vivo stromal vascular fraction with a limited number of sequence reads.
Footnotes
Yohei Sasagawa: youhei.sasagawa{at}riken.jp
Hiroki Danno: hiroki.danno{at}riken.jp, redgrapefruit{at}mac.com
Hitomi Takada: htakada{at}bs.naist.jp
Masashi Ebisawa: masashi.ebisawa{at}riken.jp
Tetsutaro Hayashi: tetsutaro.hayashi{at}riken.jp
Akira Kurisaki: akikuri{at}bs.naist.jp
Itoshi Nikaido: itoshi.nikaido{at}riken.jp
List of abbreviations
- UMI
- unique molecular identifier
- PCR
- polymerase chain reaction
- SCC
- Spearman’s rank correlation coefficient
- CV
- coefficient of variation
- ES cell
- embryonic stem cell
- PrE cell
- primitive endoderm cell
- SVF
- stromal vascular fraction
- RT
- reverse-transcription
- Dex
- dexamethasone
- PCA
- principal component analysis
- MSC
- mesenchymal stem cell
- TdT
- terminal deoxynucleotidyl transferase
- GO
- Gene Ontology
- FDR
- false discovery rate
- t-SNE
- t-distributed stochastic neighbor embedding
- nt
- nucleotide
- bp
- base pair
- SSC
- side scatter