![]() ![]() For a detailed discussion, check the text boxes from our review: From Tissues to Cell Types and Back: Single-Cell Gene Expression Analysis of Tissue Architectureīarcoded RT primers and library PCR with barcoded primersīarcoded RT primers and gel bead barcodes The basic chemistry is very similar, the main differences among those scRNA-seq methods are summarised in the table below. Slide-seq / Slide-seqV2 / Slide-DNA-seq.10x Chromium Single Cell Multiome ATAC + Gene Expression.Chromatin accessibility and protein-DNA interactions.10x Chromium Single Cell 3’ V2 and V3 GE.10x Chromium Single Cell 3’ V3 FeatureBarcoding.CEL-seq family (including CEL-seq and CEL-seq2).Quartz-seq family (including Quartz-seq and Quartz-seq2).STRT-seq family (including STRT-seq, STRT-seq-C1 and STRT-seq-2i).SMART-seq family (including SMART-seq, SMART-seq2 and SMART-seq3).All methods listed below use iSeq 100, MiniSeq (Standard), NextSeq, HiSeq X, HiSeq 3000/4000 and NovaSeq 6000 (v1.5) as examples, because this configuration is more frequently used nowadays. iSeq 100, MiniSeq, NextSeq, HiSeq X, HiSeq 3000/4000 and NovaSeq 6000 (v1.5) use the top strand as template (Reverse Complement Workflow), which is why the index sequences are reverse-complementary to the primer sequences in those machines. According to the Index Sequencing Guide from Illumina, Miseq, Hiseq2000/2500, MiniSeq (Rapid) and NovaSeq 6000 (v1.0) use the bottom strand as template (Forward Strand Workflow), which is why the index sequences are the same as the primer sequences in those machines. IMPORTANT: In a dual-index library, how index2 (i5) is sequenced differs from machines to machines.That is why the index sequences are reverse complementary to the primer sequences. Index1 (i7) is always sequenced using the bottom strand as template, regardless of the Illumina machine in use.How to use?Ĭlick the following links to view the methods. For the machine-readable format of the library structure, check seqspec. For the computational preprocessing pipelines for each method, please see this accompanying ReadTheDocs documentation. The HTML pages listed below contain step-by-step procedures of how the libraries are generated experimentally. If you are not familiar with the Illumina sequencing libraries, click here to check some general information about Illumina library structures and the nature of library preparation. Make sure you understand the basic configuration of the Illumina libraries, because most single cell sequencing methods are developed to be sequenced on the Illumina platforms. Scg_lib_structs Single Cell Genomics Library StructureĬollections of library structure and sequence of popular single cell genomic methods (mainly scRNA-seq). ![]()
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