Even larger numbers of barcode combinations can be achieved by performing experiments in 384-well plates or through additional rounds of barcoding (Fig. transcriptomic analysis of additional similarly complex multicellular systems. One Sentence Summary: Here we use SPLiT-seq, a scalable method for APX-115 single-cell or single-nucleus sequencing, to profile 156,049 solitary nuclei from your developing mouse mind and spinal cord. Intro Over three hundred years have approved since Leeuwenhoek 1st explained living cells, yet we still do not have a complete catalogue of cell types or their functions. Recently, transcriptomic profiling of individual cells has emerged as an essential tool for characterizing cellular diversity (1C3). Solitary cell RNA-seq (scRNA-seq) methods APX-115 have profiled tens of thousands of individual cells (4C6), exposing fresh insights about cell types within both healthy (7C14) and diseased cells (15C18). Regrettably, since these methods require cell sorters, custom microfluidics, or microwells, throughput is still limited and experiments are expensive. We expose SPLiT-seq, a low-cost, scRNA-seq method that enables transcriptional profiling of hundreds of thousands of fixed cells or nuclei in one experiment. SPLiT-seq does not require partitioning solitary cells into individual compartments (droplets, microwells or wells), but relies on the cells themselves as compartments. The entire workflow before sequencing consists just of pipetting methods and no complex tools are essential. In SPLiT-seq, individual transcriptomes are distinctively labeled by moving a suspension of formaldehyde fixed cells or nuclei through four rounds of combinatorial barcoding. In the 1st round of barcoding, cells are distributed into a 96-well plate and CDH5 cDNA is definitely generated with an APX-115 in-cell reverse transcription (RT) reaction using well-specific barcoded primers. Each well can contain a different biological sample C therefore enabling multiplexing of up to 96 samples in one experiment. After APX-115 this step, cells from all wells are pooled and redistributed into a fresh 96-well plate, where an in-cell ligation reaction appends a second well-specific barcode to the cDNA. The third-round barcode, which also contains a unique molecular identifier (UMI), is definitely then appended with another round of pooling, splitting, and ligation. After three rounds of barcoding, the cells are pooled, split into sublibraries, and sequencing barcodes are launched by PCR. This final step provides a fourth barcode, while also making it possible to sequence different numbers of cells in each sublibrary. After sequencing, each transcriptome is definitely assembled by combining reads containing the same four-barcode combination (Fig. 1A, Fig. S1A). Open in a separate windowpane Fig. 1 Overview of SPLiT-seq.(A) Labeling transcriptomes with APX-115 split-pool barcoding. In each split-pool round, fixed cells or nuclei are randomly distributed into wells and transcripts are labeled with well-specific barcodes. Barcoded RT primers are used in the first round. Second and third round barcodes are appended to cDNA through ligation. A fourth barcode is definitely added to cDNA molecules by PCR during sequencing library preparation. The bottom scheme shows the final barcoded cDNA molecule. (B) Varieties mixing experiment with a library prepared from 1,758 whole cells. Human being UBCs are blue, mouse UBCs are reddish, and mixed-species UBCs are gray. The estimated barcode collision rate is definitely 0.2%, whereas varieties purity is >99%. (C) UMI counts from mixing experiments performed with new and freezing (stored at ?80C for 2 weeks) cells and nuclei. Median human being UMI counts for new cells: 15,365; freezing cells: 15,078; nuclei: 12,113; freezing nuclei: 13,636. (D) Measured gene manifestation by SPLiT-seq is definitely highly correlated between freezing cells and cells processed immediately (Pearson-r: 0.987). Frozen and new cells were processed in two different SPLiT-seq experiments. Four rounds of combinatorial barcoding can yield 21,233,664 barcode mixtures (three rounds of barcoding in 96-well plates followed by a fourth round with 24 PCR reactions) – plenty of to distinctively label over 1 million cells. Actually larger numbers of barcode mixtures can be achieved by performing experiments in 384-well plates or through additional rounds of barcoding (Fig. S1B). In addition, by carrying out the first step inside a 384-well plate, up to 384 different biological samples could be combined in one experiment. SPLiT-seq validation To test SPLiT-seqs.