Single-cell RNA-Seq Genome Browser (powered by GIVe)

The Single-cell RNA-Seq Genome Browser presents 49 new single-cell RNA-seq datasets (Biase et al., Genome Research, 24:1787-1796) along with mouse genome assembly GRCm38 (mm10) for comparative studies. Published RNA-seq datasets of Gan, H. et al. Dynamics of 5-hydroxymethylcytosine during mouse spermatogenesis. Nat Commun 4 [PUBMED] [ARTICLE] and Ramskold, D. et al. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotech 30, 777-782 [PUBMED] [ARTICLE] are also incorporated. To show these tracks, please scroll down the page and turn corresponding tracks (sperm and/or oocyte) on in "Single Cell Expression Profiling for Embryos group".

The interface and usage of Single-cell Genome Browser is similar to GIVe (Genomic Interaction Visualizer).

The height of the signals in every track is the number of reads stacked at the genomic position. The scale is set for each track to normalize the effect from different total numbers of reads for all samples. Therefore, in the browser, signals across cells at the same genomic region would be comparable by height in image. To see the total number of mapped reads, please click the button to the left of the track or click track name in track settings below.

For questions, please contact Xiaoyi Cao (x9cao at ucsd dot edu).