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Series GSE118024 Query DataSets for GSE118024
Status Public on Jun 04, 2019
Title Endodermal maternal transcription factors establish super enhancers during zygotic genome activation
Organism Xenopus tropicalis
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary We examined the combinatorial function of the Xenopus tropicalis maternal transcription factors Foxh1, Vegt and Otx1. The study involved combinatorial ectopic expression of vegt and otx1 RNA in the putative ectoderm; and combinatorial knock-down of vegt and otx1 in the putative endoderm both followed by transcriptomic analysis (RNA-seq). We performed chromatin immunoprecipitation combined with high throughput sequencing (ChIP-seq) to assess the chromatin association of Vegt and Otx1 prior to zygotic gene activation. In addition, we performed ChIP-seq on H3K4me1 on endoderm tissue to identify active regulatory regions in an unbiased manner.
 
Overall design Screen for animally and vegetally expressed transcription factors: In biological triplicates, the animal and vegetal blastomeres of 8-cell stage embryos were separated. Subsequently, RNA was harvested from both set of blastomeres and whole embryos at the same stage and prepared for RNA sequencing. Combinatorial ectopic expression experiment: In biological duplicates, titrating levels of vegt and otx1 RNA were combinatorially microinjected into 1-cell stage embryos. Animal caps (putative ectoderm) were microdissected at stage 9 (6 hpf) from uninjected and injected samples, and RNA was harvested at stage 10.5 (7 hpf) for RNA sequencing. Double morpholino experiment: In biological duplicates, Vegt and Otx1 morpholinos were injected in 1-cell stage embryos independently or together. Vegetal masses (putative endoderm) were microdissected at stage 9 (6 hpf) and RNA was harvested from uninjected and injected samples at stage 10.5 (7 hpf) for RNA sequencing. Vegt and Otx1 ChIP-seq analysis: Developmentally synchronized embryos were harvested at stage 8 (prior to zygotic gene activation) and fixed with formaldehyde in biological duplicates. Chromatin immunoprecipitation as performed using anti-Vegt or anti-Otx1 antibody and DNA was purified for sequencing. H3K4me1 ChIP-seq analysis: Developmentally synchronized embryos were harvested at stage 10.5 and fixed with formaldehyde in biological duplicates. The vegetal tissue was disssected from the fixed embryos, and ChIP-seq was performed using anti-H3K4me1 antibody.

Previously published Foxh1 ChIP-seq from GSE85273 was re-analyzed along with this study.

GSM2263590 and GSM2263598 used to generate:
GSE118024_foxh1_IDR_optimal_peaks.bed.gz

GSM2263598 used to generate:
GSE118024_otx1_IDR_optimal_peaks.bed.gz, GSE118024_vegt_IDR_optimal_peaks.bed.gz
 
Contributor(s) Paraiso KD, Cho KW
Citation(s) 31167141
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 GM126395 Mechanisms of Foxh1 pioneer factor action during mesendoderm development The Regents of the University of California Ken W.Y. Cho
R01 HD073179 Deciphering the gene regulatory network controlling vertebrate endodermal fates The Regents of the University of California Ken W.Y. Cho
T32 HD060555 Training Program in Systems Biology of Development The Regents of the University of California Arthur D Lander
Submission date Aug 02, 2018
Last update date Jul 16, 2019
Contact name Kitt D. Paraiso
E-mail(s) kparaiso@uci.edu
Phone 949-824-7950
Organization name University of California, Irvine
Department Department of Developmental and Cell Biology
Lab Ken W.Y. Cho
Street address 4410 Nat Sci II, University of California, Irvine
City Irvine
State/province CA
ZIP/Postal code 92697
Country USA
 
Platforms (2)
GPL21875 Illumina HiSeq 2500 (Xenopus tropicalis)
GPL23182 Illumina HiSeq 4000 (Xenopus tropicalis)
Samples (39)
GSM3317414 8-cell animal blastomeres replicate 1
GSM3317415 8-cell animal blastomeres replicate 2
GSM3317416 8-cell animal blastomeres replicate 3
Relations
BioProject PRJNA484112
SRA SRP156130

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
GSE118024_8cell_animal_vegetal_RNAseq_TPM.txt.gz 463.6 Kb (ftp)(http) TXT
GSE118024_8cell_animal_vegetal_RNAseq_readcounts.txt.gz 474.1 Kb (ftp)(http) TXT
GSE118024_H3K4me1-st10-vegetal-peaks.bed.gz 410.7 Kb (ftp)(http) BED
GSE118024_double_MO_vegt-otx1_TPM.txt.gz 507.4 Kb (ftp)(http) TXT
GSE118024_double_MO_vegt-otx1_readcounts.txt.gz 510.4 Kb (ftp)(http) TXT
GSE118024_ectopic_expression_vegt-otx1_TPM.txt.gz 848.0 Kb (ftp)(http) TXT
GSE118024_ectopic_expression_vegt-otx1_readcounts.txt.gz 928.0 Kb (ftp)(http) TXT
GSE118024_foxh1_IDR_optimal_peaks.bed.gz 760.1 Kb (ftp)(http) BED
GSE118024_otx1_IDR_optimal_peaks.bed.gz 106.8 Kb (ftp)(http) BED
GSE118024_vegt_IDR_optimal_peaks.bed.gz 420.5 Kb (ftp)(http) BED
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Raw data are available in SRA
Processed data are available on Series record

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