Targeted scRNA-seq and AbSeq of human CAR-T cell infusion product from 24 cancer patients

Backgroud informationThe dataset contains single cell targeted RNA sequencing (RNAseq) and targeted antibody-oligonucleotide conjugates sequencing (Abseq) data from chimeric antigen receptor (CAR)-engineered T cells used to treat each individual cancer patients in a clinical study. The starting material was in all cases autologous T cells harvested from peripheral blood of patients. The data is collected from 24 participants of which 23 were adult patients with relapsed or refractory B cell lymphoma and one was a pediatric patient with relapsed B cell acute lymphoblastic leukemia. The data were generated as part of a study by Sarén et. al, Clinical Cancer Research (2023).Targeted RNA and protein single-cell libraries were generated using the BD Rhapsody™ platform (BD Biosciences). Cells were labeled with sample tags from the BD Human Immune Single-Cell Multiplexing Kit and BD Ab-seq Ab-Oligos and live cells were collected by flow cytometry. CAR-T cells were loaded on BD Rhapsody cartridge and mRNA captured with cell capture beads and used as template for cDNA synthesis. Four separate targeted libraries were produced and pooled for paired-end sequencing on NovaSeq 6000 S1 sequencer (Illumina) at the SNP&SEQ Technology Platform (Uppsala, Sweden).Terms of accessSequencing data generated during the current study are not publicly available due to the European General Data Protection Regulation (GDPR) to protect patients’ privacy but are available from the corresponding author on reasonable request (see contact info). The dataset is only to be used for research that is seeking to advance the understanding of CAR-T cell treatment of cancer.Ancillary datasets and codeProcessed RNAseq and AbSeq data, in the form of raw and normalized count matrices, are available on BioStudies (Accession: E-MTAB-12407).R code used to process the data is available on the study GitHub repository:https://github.com/magnessa/EudraCT_2016-004043-36

背景信息本数据集收录了针对单个细胞进行靶向RNA测序（RNAseq）及靶向抗体-寡核苷酸共轭物测序（Abseq）的数据，这些数据来源于嵌合抗原受体（CAR）工程化的T细胞，该T细胞用于治疗临床研究中每位癌症患者。在所有情况下，起始材料均为从患者外周血中采集的自体T细胞。数据收集自24位参与者，其中23位为复发或难治性B细胞淋巴瘤的成年患者，1位为复发B细胞急性淋巴细胞白血病的儿童患者。这些数据作为Sarén等人在《临床癌症研究》（2023年）发表的研究的一部分而生成。利用BD Rhapsody™平台（BD生物科学公司）生成了靶向RNA和蛋白质的单细胞库。细胞使用BD Human Immune Single-Cell Multiplexing Kit中的样本标签以及BD Ab-seq Ab-Oligos进行标记，并通过流式细胞术收集活细胞。CAR-T细胞装载于BD Rhapsody芯片上，使用细胞捕获珠捕获mRNA作为cDNA合成的模板。产生了四个单独的靶向库，并在位于瑞典乌普萨拉的SNP&SEQ技术平台上的NovaSeq 6000 S1测序仪上进行配对末端测序。靶向RNA和蛋白质的单细胞库的测序数据，以原始和归一化计数矩阵的形式，可在BioStudies（登录号：E-MTAB-12407）上获取。用于处理数据的R代码可在研究GitHub存储库中找到：https://github.com/magnessa/EudraCT_2016-004043-36。