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Journal ArticleDOI

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

Simone Picelli, +9 more
- 01 Nov 2013 - 
- Vol. 10, Iss: 11, pp 1096-1098
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TLDR
Smart-seq2 with improved reverse transcription, template switching and preamplification to increase both yield and length of cDNA libraries generated from individual cells to improve detection, coverage, bias and accuracy.
Abstract: 
Single-cell gene expression analyses hold promise for characterizing cellular heterogeneity, but current methods compromise on either the coverage, the sensitivity or the throughput. Here, we introduce Smart-seq2 with improved reverse transcription, template switching and preamplification to increase both yield and length of cDNA libraries generated from individual cells. Smart-seq2 transcriptome libraries have improved detection, coverage, bias and accuracy compared to Smart-seq libraries and are generated with off-the-shelf reagents at lower cost.

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Citations
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Journal ArticleDOI

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

Evan Z. Macosko, +26 more
- 21 May 2015 - 
TL;DR: Drop-seq will accelerate biological discovery by enabling routine transcriptional profiling at single-cell resolution by separating them into nanoliter-sized aqueous droplets, associating a different barcode with each cell's RNAs, and sequencing them all together.

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

Evan Z. Macosko, +26 more
TL;DR: Drop-seq as discussed by the authors analyzes mRNA transcripts from thousands of individual cells simultaneously while remembering transcripts' cell of origin, and identifies 39 transcriptionally distinct cell populations, creating a molecular atlas of gene expression for known retinal cell classes and novel candidate cell subtypes.
Journal ArticleDOI

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

Itay Tirosh, +45 more
- 08 Apr 2016 - 
TL;DR: The cellular ecosystem of tumors is begin to unravel and how single-cell genomics offers insights with implications for both targeted and immune therapies is unraveled.
Journal ArticleDOI

Full-length RNA-seq from single cells using Smart-seq2

Simone Picelli, +5 more
- 01 Jan 2014 - 
TL;DR: In this article, the authors presented a detailed protocol for Smart-seq2 that allows the generation of full-length cDNA and sequencing libraries by using standard reagents, and the entire protocol takes ∼2 d from cell picking to having a final library ready for sequencing; sequencing will require an additional 1-3 d depending on the strategy and sequencer.
Journal ArticleDOI

RNA velocity of single cells

Gioele La Manno, +31 more
- 08 Aug 2018 - 
TL;DR: It is shown that RNA velocity—the time derivative of the gene expression state—can be directly estimated by distinguishing between unspliced and spliced mRNAs in common single-cell RNA sequencing protocols, and expected to greatly aid the analysis of developmental lineages and cellular dynamics, particularly in humans.
References
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Journal ArticleDOI

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin, +8 more
- 01 Jan 2013 - 
TL;DR: The Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure outperforms other aligners by a factor of >50 in mapping speed.
Journal ArticleDOI

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Cole Trapnell, +9 more
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TL;DR: The results suggest that Cufflinks can illuminate the substantial regulatory flexibility and complexity in even this well-studied model of muscle development and that it can improve transcriptome-based genome annotation.
Journal ArticleDOI

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Daehwan Kim, +8 more
- 25 Apr 2013 - 
TL;DR: TopHat2 is described, which incorporates many significant enhancements to TopHat, and combines the ability to identify novel splice sites with direct mapping to known transcripts, producing sensitive and accurate alignments, even for highly repetitive genomes or in the presence of pseudogenes.
Journal ArticleDOI

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Fuchou Tang, +11 more
- 06 Apr 2009 - 
TL;DR: A single-cell digital gene expression profiling assay with only a single mouse blastomere is described, which detected the expression of 75% more genes than microarray techniques and identified 1,753 previously unknown splice junctions called by at least 5 reads.
Journal ArticleDOI

RSeQC: quality control of RNA-seq experiments

Liguo Wang, +2 more
- 15 Aug 2012 - 
TL;DR: The RSeQC package is developed to comprehensively evaluate different aspects of RNA-seq experiments, such as sequence quality, GC bias, polymerase chain reaction bias, nucleotide composition bias, sequencing depth, strand specificity, coverage uniformity and read distribution over the genome structure.
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Full-length RNA-seq from single cells using Smart-seq2

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STAR: ultrafast universal RNA-seq aligner

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