Massively parallel digital transcriptional profiling of single cells

Abstract

40Characterizing the transcriptome of individual cells is fundamental to understanding complex 41 biological systems. We describe a droplet-based system that enables 3' mRNA counting of up 56peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/065912 doi: bioRxiv preprint first posted online 84 RESULTS 86Droplet-based platform enables barcoding of tens of thousands of cells 88The scRNA-seq microfluidics platform builds on the GemCode ® technology, which has 89 been used for genome haplotyping, structural variant analysis and de novo assembly of a 90human genome [10][11][12] . The core of the technology is a Gel bead in Emulsion (GEM). GEM 91 peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/065912 doi: bioRxiv preprint first posted online 5 generation takes place in an 8-channel microfluidic chip that encapsulates single gel beads at ~80% fill rate (Fig. 1a-c). Each gel bead is functionalized with barcoded oligonucleotides that 93 consist of: i) sequencing adapters and primers, ii) a 14bp barcode drawn from ~750,000 94 designed sequences to index GEMs, iii) a 10bp randomer to index molecules (unique molecular 95 identifier, UMI), and iv) an anchored 30bp oligo-dT to prime poly-adenylated RNA transcripts 96 (Fig. 1d). Within each microfluidic channel, ~100,000 GEMs are formed per ~6-min run, 97encapsulating thousands of cells in GEMs. Cells are loaded at a limiting dilution to minimize co- 98occurrence of multiple cells in the same GEM. 100Cell lysis begins immediately after encapsulation. Gel beads automatically dissolve to 101 release their oligonucleotides for reverse transcription of poly-adenylated RNAs. Each cDNA 102 molecule contains a UMI and shared barcode per GEM, and ends with a template switching 103 oligo at the 3' end (Fig. 1e). Next, the emulsion is broken and barcoded cDNA is pooled for 104PCR amplification, using primers complementary to the switch oligos and sequencing adapters. Methods, Fig. 1f). Briefly, 98-nt of Read1s were aligned against the union of human (hg19) 123peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/065912 doi: bioRxiv preprint first posted online 6 Based on the distribution of total UMI counts for each barcode (Online Methods), we 124 estimated that 1,012 GEMs contained cells, of which 482 and 538 contained reads that mapped 125 primarily to the human and mouse transcriptome, respectively (and will be referred to as human 126 and mouse GEMs) (Fig. 2a). >83% of UMI counts were associated with cell barcodes, 127indicating low background of cell-free RNA. Eight cell-containing GEMs had a substantial 128 fraction of human and mouse UMI counts (the UMI count is >1% of each species' UMI...

Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics

“…We set out to obtain a comprehensive understanding of the cellular heterogeneity of the human placenta using large-scale dropletbased single-cell digital transcriptomic profiling (28) (Fig. 1A).…”

“…Liver-specific transcripts, such as ALB, are also readily detectable in the plasma (41). We, therefore, identified and filtered the cell signature genes of individual placental cell types in our dataset by reanalyzing peripheral blood mononucleated cells (PBMCs) single-cell transcriptomic profiles and the tissue transcriptome data of leukocytes and liver from public databases (28,42) (Fig. S3 A-E).…”

Detection of HPV E7 Transcription at Single-Cell Resolution in Epidermis

“…For the single-cell data, the cellranger pipeline v1.3.1 provided by 10X Genomics (mkfastq, count, aggr) (Zheng et al, 2017) was used to process the raw sequencing data using the default parameters, and adjusted to the expected number of cells per sample (3,000). Reads were aligned to a custom reference genome comprising the mouse (mm10) and the HPV16 genome (NC_001526) using the STAR aligner (Dobin et al, 2013) included in the cellranger pipeline.…”

“…The scRNA-seq data were generated using the Chromium Single Cell 3' RNA-sequencing method (10X Genomics) (Zheng et al, 2017), which includes unique molecular identifier barcodes, enabling the copy number of detected transcript molecules to be determined. We obtained high quality sequence data for 9,404 single cells, of which 3,959 and 5,445 cells were from K14E7 and C57BL/6 epidermis respectively.…”

CellView: Interactive exploration of high dimensional single cell RNA-seq data

“…To illustrate the utility and power of CellView, we generated and analyzed single cell transcriptome data from peripheral blood mononuclear cells (PBMCs) using the 10X Genomics Chromium 8 . As defined by the CellRanger 8 pipeline, this data consisted of 6,554 single cells sequenced to 90.1% saturation with, on average, 824 genes and 2,077 molecules detected per cell.…”