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. 2018 Dec 24;19:960. doi: 10.1186/s12864-018-5249-x

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© The Author(s) 2018

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 1 — Schematic of Bio-Rad ddSEQ/Illumina reads’ structure (Top) In BioRad ddSEQ, barcoded beads capture mRNA molecules through hybridization with mRNA poly-A tails. Each single DNA strand is characterized by the following structure: a phase block (PB), three barcode blocks (BC1, BC2, BC3) interlinked by two different linkers (L1 and L2), and one UMI flanked by two trinucleotides (ACG and GAC). (Middle) Read 1 (R1) contains molecular tags while Read 2 (R2) contains the information of the mRNA sequence (R1 and R2 are not in scale). (Bottom) Separation of cDNA from the beads can occur at different nucleotides within the PB, thus making the position of the two linkers variable