Recent advances in single-cell RNA-sequencing (scRNA-seq) 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 non-computational immunologist. To facilitate datasets reuse, researchers at the Ben-Gurion University of the Negev created the JingleBells repository for immune-related scRNA-seq datasets ready for analysis and visualization of reads at the single-cell level. To this end, the researchers 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. They 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.
Cd34 read-level data reveal isoform preference and cell-specific mutations
Visualization of the reads that are aligned to the mouse gene Cd34 from scRNA-seq reads of hematopoietic stem cells. Shown are the total number of reads that are aligned to each genomic position [(A), top, grey bars. Numbers on the left state the scale of read numbers.], the reads that are aligned to the region [(B), middle, colored lines], and the known transcripts from the National Center for Biotechnology Information Reference Sequence Database (RefSeq, https://www.ncbi.nlm.nih.gov/refseq/) of the gene [(C), bottom, blue schematics]. Exon numbers are marked. Reads from different cells are separated by a gray line and by different colors. The thin blue line connects the junction spanning reads. The black box marks the reads from one cell that is mutated. The genomic region displayed is chr1:194,958,200–194,961,500. Data are from GSE61533 (19). Read visualization was done by IGV (www.broadinstitute.org/igv/).
Availability – JingleBells is freely available on the web at http://jinglebells.bgu.ac.il/. The data files are stored on Google Drive (https://drive.google.com/open?id=0BxSFjdiDhUI1amNoSks0SmpMdE0), but do not require a Google log in