Jingle bells: A repository of immune-related single-cell RNA-sequencing datasets

Hadas Ner-Gaon, Ariel Melchior, Nili Golan, Yael Ben-Haim, Tal Shay

Research output: Contribution to journalArticlepeer-review

Abstract

Recent advances in single-cellRNA-sequencing (scRNAseq) technology increase the understanding of immune differentiation and activation processes, as well as the heterogeneity of immune cell types. Although the number of available immune-related scRNA-seq datasets increases rapidly, their large size and various formats render them hard for the wider immunology community to use, and read-level data are practically inaccessible to the noncomputational immunologist. To facilitate datasets reuse, we created the JingleBells repository for immune-related scRNA-seq datasets ready for analysis and visualization of reads at the single-cell level (http://jinglebells.bgu.ac.il/). To this end, we collected the raw data of publicly available immune-related scRNA-seq datasets, aligned the reads to the relevant genome, and saved aligned reads in a uniform format, annotated for cell of origin. We also added scripts and a step-by-step tutorial for visualizing each dataset at the single-cell level, through the commonly used Integrated Genome Viewer (www. broadinstitute.org/igv/). The uniform scRNA-seq format used in JingleBells can facilitate reuse of scRNA-seq data by computational biologists. It also enables immunologists who are interested in a specific gene to visualize the reads aligned to this gene to estimate cell-specific preferences for splicing, mutation load, or alleles. Thus JingleBells is a resource that will extend the usefulness of scRNA-seq datasets outside the programming aficionado realm.

Original languageAmerican English
Pages (from-to)3375-3379
Number of pages5
JournalJournal of Immunology
Volume198
Issue number9
DOIs
StatePublished - 1 May 2017

All Science Journal Classification (ASJC) codes

  • Immunology and Allergy
  • Immunology

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