Here we present a new methodology called single-cell TCRseq (scTCRseq) for the identification and assembly of full-length rearranged V(D)J T-cell receptor sequences from paired-end single-cell RNA sequencing reads. The method allows accurate identification of the V(D)J rearrangements for each...
In the case of dual V-gene usage, the V gene with highest number of clones (if obtained from cloning) or with highest number of reads (if obtained from high-throughput sequencing) was used for analysis. In some cases of dual V-gene usage in clonally expanded population, we carried out ...
参考文献 Ma K Y, He C, Wendel B S, et al. Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification:[J]. Frontiers in Immunology, 2018, 9. 关注康测科技,获取更多信息! 地址:武汉市东湖...
21 All sequencing was done using the Illumina MiSeq platform, performed at the Norwegian Sequencing Center. All TCR sequence data were deposited in the European Genome-Phenome Archive (accession number EGAS00001003897). TCR repertoire analysis Obtained reads from the Illumina sequencing was processed ...
to quantify the number of UMIs per cell by dividing the total number of UMIs (obtained from Illumina sequencing) by the number of cells\({{UMI}}_{c}\frac{\mathop{\sum }\nolimits_{i=1}^{n}{x}_{i}}{c}\). We then used this factor to normalize the UMI counts per clone and ...
VDJmatch accepts TCR clonotype table(s) as an input and relies onVDJtoolsframework to parse the output of commonly used immune repertoire sequencing (RepSeq) processing tools. Seeformatsection of VDJtools docs for the list of supported formats. Note that VDJmatch can be used withmetadatasemantics...
151 bp sequencing was performed on a NextSeq2000 (Illumina). Alternatively, mRNA sequencing was performed at Macrogen (Seoul, Korea) using a TruSeq Stranded mRNA kit (Illumina) and sequencing 2 × 101 bp on a Novaseq (Illumina) to 2 × 101 bp 50E6 reads....
Confirmation that these cells are genuine iNKT precursors is provided by the analysis of the sequencing reads that are mapped to the TCRα locus (Supplementary Fig 3). We detected statistically significant differential expression (FDR < 0.1) of 238 genes between the two genoty...
As Illumina sequencing is particularly error-prone in the reverse read, and that reads can be phased (i.e. they do not always begin with the next nucleotide that follows the sequencing primer) our protocol uses known spacer sequences to border the random barcode bases, so that we can ...
The lack of an IFNγ response in TCRα transgenics after boosting correlated with selection of a single shared Vβ2 partner chain, as demonstrated by TCR sequencing and by spectratyping using V gene specific primers (Figure 3D, E). All the CD4+CD69+ cells expressed the same TCRβ chain...