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Series GSE113074 Query DataSets for GSE113074
Status Public on Apr 28, 2018
Title The dynamics of gene expression in vertebrate embryogenesis at single cell resolution
Organism Xenopus tropicalis
Experiment type Expression profiling by high throughput sequencing
Summary Time series of single cell transcriptome measurements can reveal dynamic features of cell differentiation pathways. From measurements of whole frog embryos spanning zygotic genome activation through early organogenesis we derived a detailed catalog of cell states in vertebrate development and a map of differentiation across all lineages over time. The inferred map recapitulates most if not all developmental relationships, and associates new regulators and marker genes with each cell state. We find that many embryonic cell states appear earlier than previously appreciated. We also assess conflicting models of neural crest development. Incorporating a matched time series of zebrafish development from a companion paper, we reveal conserved and divergent features of vertebrate early developmental gene expression programs.
Overall design 136,966 single cell transcriptomes were profiled from whole Xenopus tropicalis embryos at ten timepoints during the first 24 hours of its embryonic development. The data includes 75 total single cell RNA sequencing libraries, collected in 2 replicate timeseries. 4 of the 75 libraries focussed on dissected neural plate border tissue. The counts data for all pass filter cells are available in a single matrix (see "Corrected_combined.annotated_counts.tsv.gz" and "Raw_combined.annotated_counts.tsv.gz"). Alternatively, raw FASTQ or unfiltered counts files are also available for each individual library.
Contributor(s) Briggs JA, Weinreb C, Wagner DE, Megason S, Peshkin L, Kirschner MW, Klein AM
Citation(s) 29700227
Submission date Apr 12, 2018
Last update date May 04, 2018
Contact name James Alexander Briggs
Organization name Harvard Medical School
Department Department of Systems Biology
Lab Kirschner / Klein labs
Street address 200 Longwood Avenue, Harvard Medical School
City Boston
State/province Massachusetts
ZIP/Postal code 02115
Country USA
Platforms (1)
GPL24884 Illumina NextSeq 500 (Xenopus tropicalis)
Samples (75)
GSM3095780 Stage 8 - scRNA-seq library 1
GSM3095781 Stage 8 - scRNA-seq library 2
GSM3095782 Stage 8 - scRNA-seq library 3
BioProject PRJNA449931
SRA SRP142544

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
GSE113074_Corrected_combined.annotated_counts.tsv.gz 3.9 Gb (ftp)(http) TSV
GSE113074_RAW.tar 447.4 Mb (http)(custom) TAR (of TSV)
GSE113074_Raw_combined.annotated_counts.tsv.gz 169.6 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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