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Series GSE85908 Query DataSets for GSE85908
Status Public on Jul 12, 2017
Title Single-cell alternative splicing analysis with Expedition reveals splicing dynamics during neuron differentiation
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Alternative splicing (AS) generates isoform diversity critical for cellular identity and homeostasis, yet characterization of this diversity in single cells remains limited. We developed Expedition, a computational framework to categorize and visualize the heterogeneity of AS from single-cell transcriptomes. Expedition consists of (i) outrigger, a de novo splice graph transversal algorithm to detect AS from single cell RNA-seq; (ii) anchor, a Bayesian approach to assign splicing modalities and (iii) bonvoyage, using non-negative matrix factorization to visualize modality changes. By applying Expedition to single iPSCs undergoing neuron differentiation, we discover that 25% of AS exons exhibit bimodality and are flanked by longer and more conserved introns harboring distinct cis-regulatory motifs. Bimodal exons are highly dynamic during cellular transitions, preserve translatability, enriched in recently emerged genes and have conserved AS in mammals. Applying Expedition ( in single cells redefines our estimates and understanding of AS in evolution and biology.
Overall design Analysis of alternative splicing changes across motor neuron differentiation
Contributor(s) Botvinnik OB, Song Y
Citation(s) 28673540
Submission date Aug 22, 2016
Last update date May 15, 2019
Contact name Gene Yeo
Organization name UCSD
Street address 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (214)
GSM2286986 NPC single cell 1
GSM2286987 NPC single cell 2
GSM2286988 NPC single cell 3
BioProject PRJNA339740
SRA SRP082522

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE85908_alternative_exons.bed.gz 962.1 Kb (ftp)(http) BED
GSE85908_cisbp_metadata.csv.gz 6.3 Kb (ftp)(http) CSV
GSE85908_cisbp_t_statistic.csv.gz 33.3 Kb (ftp)(http) CSV
GSE85908_constitutive_exons.bed.gz 70.6 Kb (ftp)(http) BED
GSE85908_expression.csv.gz 12.1 Mb (ftp)(http) CSV
GSE85908_expression_feature.csv.gz 1.3 Mb (ftp)(http) CSV
GSE85908_hg19_phastcons_placental_mammal.wig.gz 8.8 Gb (ftp)(http) WIG
GSE85908_kmer_zscores.csv.gz 926.8 Kb (ftp)(http) CSV
GSE85908_kmer_zscores_metadata.csv.gz 332 b (ftp)(http) CSV
GSE85908_mapping_stats.csv.gz 25.2 Kb (ftp)(http) CSV
GSE85908_metadata.csv.gz 919 b (ftp)(http) CSV
GSE85908_modalities_tidy.csv.gz 624.8 Kb (ftp)(http) CSV
GSE85908_splicing.csv.gz 1.4 Mb (ftp)(http) CSV
GSE85908_splicing_feature.csv.gz 2.7 Mb (ftp)(http) CSV
GSE85908_voyages.csv.gz 432.7 Kb (ftp)(http) CSV
GSE85908_waypoints.csv.gz 627.6 Kb (ftp)(http) CSV
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Processed data are available on Series record

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