TY - JOUR
T1 - Jingle bells
T2 - A repository of immune-related single-cell RNA-sequencing datasets
AU - Ner-Gaon, Hadas
AU - Melchior, Ariel
AU - Golan, Nili
AU - Ben-Haim, Yael
AU - Shay, Tal
N1 - Publisher Copyright: Copyright © 2017 by The American Association of Immunologists, Inc.
PY - 2017/5/1
Y1 - 2017/5/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85018474650&partnerID=8YFLogxK
U2 - https://doi.org/10.4049/jimmunol.1700272
DO - https://doi.org/10.4049/jimmunol.1700272
M3 - Article
C2 - 28416714
SN - 0022-1767
VL - 198
SP - 3375
EP - 3379
JO - Journal of Immunology
JF - Journal of Immunology
IS - 9
ER -