|NextSeq 550 System||4 to 6 samples per run (based on a minimum of 100,000 reads per cell)||read 1: 68 bp, read 2: 75 bp|
|HiSeq 2500 System||Rapid run: 4-5 samples per lane; high output v4: 4 samples per lane (based on a minimum of 100,000 reads per cell)||read 1: 68 bp, read 2: 75 bp|
|SureCell WTA 3′ Library Prep Kit for the ddSEQ System||TruSeq RNA Library Prep Kit v2||Illumina Stranded mRNA Prep||Illumina RNA Prep with Enrichment|
|Assay Time||11-12 hours||~10.5 hours||6.5小时||＜9小时|
|Content Specifications||Captures the coding transcriptome (3' enriched), with strand-specific information||Captures the coding transcriptome (without strand information)||捕获编码转录组（带链信息）||与Illumina Exome Panel一起使用时可捕获编码转录组|
|Description||Enables single-cell RNA-Seq studies using a droplet generator that isolates ~1200 cells per cartridge, and a simple library prep process.||A simple, cost-effective research solution for analysis of the coding transcriptome.||简单、经济的编码转录组分析解决方案，可提供精确的链信息||一种可重现且经济的解决方案，可使用多种类型的样本和起始材料来检测和发现目标转录本，包括福尔马林固定石蜡包埋（FFPE）组织和其他低质量样本|
|Hands-On Time||4-5 hours||~4.5 hours||＜3小时||＜2小时|
|Input Quantity||~45,000 cells per cartridge (required input)||0.1 - 1 ug total RNA or 10 - 400 ng previously isolated mRNA (from species with polyA tails)||25-1000 ng标准质量的总RNA||10 ng新鲜/冷冻样本来源的总RNA，或20 ng FFPE样本来源的总RNA|
|Mechanism of Action||Oligo dT capture, single cell||Oligo-dT beads capture polyA tails||PolyA捕获，连接接头和标签||连接磁珠的转座酶|
|Method||mRNA Sequencing||mRNA Sequencing||mRNA Sequencing||mRNA Sequencing, 靶向RNA测序, 靶向富集|
|Multiplexing||1-24||Up to 24-plex per lane||多达384个唯一双标签序列（UDI）||多达384个唯一双标签序列（UDI）|
|Specialized Sample Types||Single Cells, 不兼容FFPE||不兼容FFPE||Low-Input Samples, Not FFPE-Compatible||Blood, FFPE Tissue, Low-Input Samples|
|Species Category||人类, 小鼠||Bovine, Mammalian, 人类, 大鼠, 小鼠||Bovine, Mammalian, 人类, 大鼠, 小鼠||Virus, 人类|
Mouse cell lines (A20, NIH3T3) and human cell lines (HEK, BJ) were processed using the SureCell WTA 3′Library Prep Kit. Consistently high numbers of detected genes demonstrates that recovery of transcripts is not limited by cell size.
A. BaseSpace-generated plots of the number of unique molecular identifiers (UMI), i.e. transcripts, assigned to the mouse/mm10 (red) and human/hg19 (blue) genomes for each cell barcode. Unique transcripts mapping to both mouse and human (purple) represent cell doublets. B. Cumulated fraction of unique transcripts assigned to cell barcodes (linear scale). The inflection point (red line) determines the number of barcoded cells detected in the sequencing run.
A. PCA clustering of 1384 single cells sorted from a 1:1 ratio mixture of HEK 293 and NIH 3T3 cells, sequenced and analyzed with the BaseSpace SureCell Single-Cell RNA App. B. Cell populations cluster based on expression of the human (hg19) RPL13 gene.
A. Analysis in the BaseSpace SureCell Single-Cell RNA App using the t-SNE algorithm of a mixture of NIH 3T3 and HEK 293 cells identifies a distinct subpopulation of cells. B. Cells color coded by gene expression of hg19 RPL 13 confirms the identity of the subpopulation as human.
Analysis of cell cycle state using the BaseSpace SureCell Single-Cell RNA App is based on unique transcript counts of genes associated with each phase of the cell cycle, normalized by the total count for each cell. Expression is centered by the median and scaled by the median absolute deviation for each cell cycle.