ArticleNucleic acids research2017
A cost effective 5΄ selective single cell transcriptome profiling approach with improved UMI design.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Environmental signals perceived by the brain abate pro-metastatic monocytes by dampening glucocorticoids receptor signaling.Cancer cell international · 2023Article
- Chemical capping improves template switching and enhances sequencing of small RNAs.Nucleic acids research · 2022Article
- Large-scale translatome profiling annotates the functional genome and reveals the key role of genic 3' untranslated regions in translatomic variation in plants.Plant communications · 2021Article
- μCB-seq: microfluidic cell barcoding and sequencing for high-resolution imaging and sequencing of single cells.Lab on a chip · 2020Article
- Decode-seq: a practical approach to improve differential gene expression analysis.Genome biology · 2020Article
- FB5P-seq: FACS-Based 5-Prime End Single-Cell RNA-seq for Integrative Analysis of Transcriptome and Antigen Receptor Repertoire in B and T Cells.Frontiers in immunology · 2020Article
- Non-templated addition and template switching by Moloney murine leukemia virus (MMLV)-based reverse transcriptases co-occur and compete with each other.The Journal of biological chemistry · 2019Article
- Single-cell transcriptome analysis of Physcomitrella leaf cells during reprogramming using microcapillary manipulation.Nucleic acids research · 2019Article
- NanoPARE: parallel analysis of RNA 5' ends from low-input RNA.Genome research · 2018Article
- The Human Cell Atlas: Technical approaches and challenges.Briefings in functional genomics · 2018Review
- CD4Frontiers in synaptic neuroscience · 2018Article
- Single molecule counting and assessment of random molecular tagging errors with transposable giga-scale error-correcting barcodes.BMC genomics · 2017Article
- International Standards for Genomes, Transcriptomes, and Metagenomes.Journal of biomolecular techniques : JBT · 2017Review
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7 authors.
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Abstract
Single cell RNA sequencing approaches are instrumental in studies of cell-to-cell variability. 5΄ selective transcriptome profiling approaches allow simultaneous definition of the transcription start size and have advantages over 3΄ selective approaches which just provide internal sequences close to the 3΄ end. The only currently existing 5΄ selective approach requires costly and labor intensive fragmentation and cell barcoding after cDNA amplification. We developed an optimized 5΄ selective workflow where all the cell indexing is done prior to fragmentation. With our protocol, cell indexing can be performed in the Fluidigm C1 microfluidic device, resulting in a significant reduction of cost and labor. We also designed optimized unique molecular identifiers that show less sequence bias and vulnerability towards sequencing errors resulting in an improved accuracy of molecule counting. We provide comprehensive experimental workflows for Illumina and Ion Proton sequencers that allow single cell sequencing in a cost range comparable to qPCR assays.
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