Targeted scRNA-seq and AbSeq of human CAR-T cell infusion product from 24 cancer patients
type: Dataset
description: Backgroud information The 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 access Sequencing 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 code Processed 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
conditions of access: https://publications.europa.eu/resource/authority/access-right/NON_PUBLIC
conditions of access: info:eu-repo/semantics/restrictedAccess
creative work status: completed
  type: DefinedTerm
  in defined term set: http://publications.europa.eu/resource/authority/dataset-status
  term code: COMPLETED
creator: Claudio Mirabello
creator: Magnus Essand
  type: Person
  family name: Essand
  given name: Magnus
creator: Mohanraj Ramachandran
  type: Person
  family name: Ramachandran
  given name: Mohanraj
creator: Tina Sarén
  type: Person
  family name: Sarén
  given name: Tina
date modified: 2023-08-02
date published: 2023-08-02
funding: Cancer immunotherapy using next generation oncolytic viruses and CAR T cells
  type: Grant
  funder: Swedish Research Council
funding: ARMING CAR T CELLS AND SHAPING THE TUMOR MICROENVIRONMENT TO INCREASE THE EFFICACY OF CANCER IMMUNOTHERAPY
  type: Grant
  funder: Swedish Research Council
funding: Stockholms universitet, Wallenberg Advanced Bioinformatics Infrastructure, WABIBeviljat anslag: 68 miljoner kronor i fortsättningsanslag
  type: Grant
  funder: Knut and Alice Wallenberg Foundation
keywords: Medical and Health Sciences
  type: DefinedTerm
  term code: 3
keywords: Immunology
  type: DefinedTerm
  term code: 10605
keywords: Cancer and Oncology
  type: DefinedTerm
  term code: 30203
keywords: Cancer cell biology
keywords: Cancer genetics
keywords: Cancer therapy (excl. chemotherapy and radiation therapy)
keywords: Genetic immunology
keywords: Cellular immunology
publisher: Uppsala University
version: 0

PropertyValue
property ID: DOI
value: 10.17044/SCILIFELAB.20208764

Claudio Mirabello
type: Person
affiliation: Science for Life Laboratory
family name: Mirabello
given name: Claudio

Science for Life Laboratory
type: Organization

Swedish Research Council
type: Organization

Knut and Alice Wallenberg Foundation
type: Organization

Uppsala University
type: Organization