图1. TCR/BCR结构(图来自10X) TCR/BCR都含有三个互补决定区(CDR1、CDR2和CDR3),其中CDR1和CDR2由V区编码,结构相对保守,负责识别MHC;CDR3位于V(D)J重组的连接处,是最具多样性的区域,决定了抗原识别的特异性。这三个CDR区共同形成抗原结合位点,参与抗原识别和结合。 图2. TCR/BCR结构[1] 免疫组库指机...
Zhang等人描述了一种名为ICON (IntegrativeCOntext-specific Normalization) 的数据标准化方法,该方法通过消除背景噪声从10xGenomics pMHC结合数据集中识别可靠的TCR-pMHC相互作用。通过评估取自四名健康供体并在44个dextramers中测试的CD8+T细胞的结合谱,他们将15,821个已测序的T细胞中的89%与成对的αβ链连接到其抗原...
TCR-seq数据分析的主要目的就是统计各区域基因的出现频率,即geneUsage。这个时候就轮到今天的主角上场了——immunarch是一个R包,可以用来对很多软件的TCR-seq数据如mixcr、10X等做后续的数据分析。该R包含有丰富的处理函数以及多样性的数据展示类型,用起来也是相当方便,那话不多说来看一下如何使用该R包。 代码 insta...
单细胞测序数据,包括但不限于10x基因组学方案 RNA-Seq或任何其他类型的片段/霰弹枪数据,这些数据可能只包含目标序列的一小部分 以及包含TCR或BCR的任何其他类型的测序数据 Installation / Download Requirements Any OS with Java support (Linux, Windows, Mac OS X, etc..) Java 1.8 or higher 几种安装方式 Us...
其中，经典的免疫组库分析软件MiXCR[1]可以通过调用rnaseq-cdr3模块来实现免疫组库分析。此外，哈佛大学刘小乐团队专门开发了对应的分析工具TRUST4[2]，该软件可以兼容bulk RNA-seq、10x单细胞RNA-seq以及smart-seq2的数据分析。TRUST4的基本思想是：1）对含有V，J和C基因的候选reads进行de novo组装得到一致性...
10X Amplification Mix, and 10 µM Partial Read 1 primer. The resulting PCR product was purified without fragmentation using SPRIselect beads and quantified with a Qubit 1X dsDNA HS Assay Kit (Thermo Fisher Scientific). Sample index PCR was performed using primers from the 10X Genomics Dual...
We performed 10X Visium spatial transcriptomics on 9 primary and recurrent glioblastoma with both 3'-sequencing and SPTCR-seq. For SPTCR-seq, we target enriched T cell receptor sequences by capturing by hybridization followed by Oxford-Nanopore long-read sequencing. The on-target rate was above ...
(ATLAS-seq) double-positive cells were selected using each method for 10X Genomics single-cell sequencing. Input: unstimulated T cells from the same donor PBMCs. Gating strategies are demonstrated in supplementary information (Input: Fig.S4A, Dextramer: Fig.S4B, ATLAS-seq: Fig.S4C).BAverage ...
Each lot of this antibody is quality control tested byimmunofluorescent staining with flow cytometric analysisand the oligomer sequence is confirmed by sequencing. TotalSeq?-A antibodies are compatible with 10x Genomics Single Cell Gene ExpressionSolutions. ...
reagents are designed to profile protein levels at a single cell level following an optimized protocol similar to the CITE-seq workflow. A compatible single cell device (e.g.10x Genomics Chromium System and Reagents) and sequencer (e.g. Illumina analyzers) are required. Please contacttechnical su...