GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE145619 Query DataSets for GSE145619
Status Public on Dec 18, 2020
Title Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates
Organism Xenopus tropicalis
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary We applied chromatin accessibility and single cell transcriptome analyses to explore the emergence of heterogeneity and underlying gene-regulatory mechanisms during early gastrulation in Xenopus. TF activity was inferred by integrating chromatin accessibility and single cell transcriptomics. Our results show that combinatorial activity of zygotically expressed transcription factors acts on maternally-regulated accessible chromatin to induce organizer gene expression.
Overall design ATAC-seq on Xenopus embryos (stage 9, 10.5, 12 and 16) and gastrula stage embryo explants (Animal cap and Dorsal marginal zone). RNA-seq on animal caps overexpressed with Foxb1, Foxb1 + Eomes, Eomes, Irx3, Irx3 + Otx2 and Lhx8 mRNA. ScRNA-seq on Animal cap and Dorsal marginal zone explants. scATAC-seq was performed on stage 10.5 Xenopus embryos.
Contributor(s) Bright AR, van Genesen S, Li Q, Grasso A, Veenstra GJ
Citation(s) 33555045
Submission date Feb 20, 2020
Last update date Mar 02, 2021
Contact name Ann Rose Bright
Organization name RIMLS
Department Department of Molecular Biology
Street address Geert Grooteplein Zuid 30
City Nijmegen
ZIP/Postal code 6525 GA
Country Netherlands
Platforms (2)
GPL21875 Illumina HiSeq 2500 (Xenopus tropicalis)
GPL24884 Illumina NextSeq 500 (Xenopus tropicalis)
Samples (132)
GSM4322283 Stage9_Rep1_ATAC-Seq
GSM4322284 Stage9_Rep2_ATAC-Seq
GSM4322285 Stage10.5_Rep1_ATAC-Seq
BioProject PRJNA607864
SRA SRP250335

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 267.4 Kb (ftp)(http) TAB 231.0 Kb (ftp)(http) TAB 235.8 Kb (ftp)(http) TAB 193.7 Kb (ftp)(http) TAB
GSE145619_RAW.tar 16.9 Mb (http)(custom) TAR (of BED, TAB)
GSE145619_fragments_v2_CoVar1.0.tsv.gz 203.7 Mb (ftp)(http) TSV
GSE145619_fragments_v2_CoVar1.0.tsv.gz.tbi.gz 295.6 Kb (ftp)(http) TBI
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap