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GEO Series: GSE56242

Title: High-resolution analysis of gene activity during the Xenopus mid-blastula transition

Summary

The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss of synchronous cell divisions. Little is known about what triggers the activation of transcription or how newly expressed genes interact with each other. Here we use high-resolution expression profiling to identify three waves of gene activity: a post-fertilization wave involving polyadenylation of maternal transcripts; a broad wave of zygotic transcription detectable as early as the 7th cleavage and extending beyond the MBT at the 12th cleavage; and a shorter post-MBT wave of transcription that becomes apparent as development proceeds. Our studies have also allowed us to define a set of maternal genes whose mRNAs are deadenylated shortly after fertilization, and are likely to be degraded thereafter. Experimental analysis indicates that the polyadenylation of maternal transcripts is necessary for the establishment of proper levels of zygotic transcription at the MBT, and that genes activated in the second wave of expression, including Brachyury and Mixer, contribute to the regulation of genes expressed in the third. Together, our high-resolution time series and experimental studies have yielded a deeper understanding of the temporal organization of gene regulatory networks in the early


Contributors: Mike Gilchrist, Clara Collart, Nick Owens, Leena Bhaw-Rosun, Brook Cooper, Elena De Domenico, Ilya Patrushev, Abdul Sesay, James Smith, James Smith, Michael Gilchrist

Experiment Type: Time series polyA+ and RiboZero RNA sequencing of Xenopus Embryos covering 0-9.5 hours post fertilization

Article: Xenbase, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
WE - NF1 (0.0hpf) - Series1 GSM1357541  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
zygote NF stage 1  
WE - NF1 (0.0hpf) - Series3 GSM1357565  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
zygote NF stage 1  
WE - NF1 (0.0hpf) - Series3 rd GSM1357584  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
zygote NF stage 1  
WE - NF1 (0.5hpf) - Series1 GSM1357542  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 1  
WE - NF1 (0.5hpf) - Series3 GSM1357566  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 1  
WE - NF10 (7.0hpf) - Series2 GSM1357557  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10  
WE - NF10 (9.0hpf) - Series3 GSM1357583  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10  
WE - NF10.25 (7.5hpf) - Series2 GSM1357558  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.25  
WE - NF10.5 (8.0hpf) - Series2 GSM1357559  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5  
WE - NF10.5 (8.5hpf) - Series2 GSM1357560  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5  
WE - NF11 (9.0hpf) - Series2 GSM1357561  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11  
WE - NF11.5 (9.5hpf) - Series2 GSM1357562  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11.5  
WE - NF2 (1.0hpf) - Series1 GSM1357543  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 2 (2-cell)  
WE - NF2 (1.0hpf) - Series3 GSM1357567  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 2 (2-cell)  
WE - NF2 (1.0hpf) - Series3 rd GSM1357585  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 2 (2-cell)  
WE - NF2 (1.5hpf) - Series3 GSM1357568  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 2 (2-cell)  
WE - NF3 (1.5hpf) - Series1 GSM1357544  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 3 (4-cell)  
WE - NF4 (2.0hpf) - Series3 GSM1357569  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 4 (8-cell)  
WE - NF4 (2.0hpf) - Series3 rd GSM1357586  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 4 (8-cell)  
WE - NF5 (2.0hpf) - Series1 GSM1357545  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 5 (16-cell)  
WE - NF5 (2.5hpf) - Series3 GSM1357570  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 5 (16-cell)  
WE - NF6 (2.5hpf) - Series1 GSM1357546  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 6 (32-cell)  
WE - NF6 (2.5hpf) - Series2 GSM1357548  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 6 (32-cell)  
WE - NF6 (3.0hpf) - Series3 GSM1357571  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 6 (32-cell)  
WE - NF6 (3.0hpf) - Series3 rd GSM1357587  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 6 (32-cell)  
WE - NF6 (3.5hpf) - Series3 GSM1357572  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 6 (32-cell)  
WE - NF7 (3.0hpf) - Series1 GSM1357547  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 7  
WE - NF7 (3.0hpf) - Series2 GSM1357549  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 7  
WE - NF7 (3.5hpf) - Series2 GSM1357550  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 7  
WE - NF7 (4.0hpf) - Series3 GSM1357573  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 7  
WE - NF7 (4.0hpf) - Series3 rd GSM1357588  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 7  
WE - NF7 (4.5hpf) - Series3 GSM1357574  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 7  
WE - NF8 (4.0hpf) - Series2 GSM1357551  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8  
WE - NF8 (4.5hpf) - Series2 GSM1357552  GSM1357563  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8  
WE - NF8 (5.0hpf) - Series2 GSM1357553  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8  
WE - NF8 (5.0hpf) - Series3 GSM1357575  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8  
WE - NF8 (5.0hpf) - Series3 rd GSM1357589  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8  
WE - NF8 (5.5hpf) - Series3 GSM1357576  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8  
WE - NF8 (6.0hpf) - Series3 GSM1357577  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8  
WE - NF8 (6.0hpf) - Series3 rd GSM1357590  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8  
WE - NF8 (6.5hpf) - Series3 GSM1357578  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8  
WE - NF9 (5.5hpf) - Series2 GSM1357554  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
WE - NF9 (6.0hpf) - Series2 GSM1357555  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
WE - NF9 (6.5hpf) - Series2 GSM1357556  GSM1357564  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
WE - NF9 (7.0hpf) - Series3 GSM1357579  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
WE - NF9 (7.0hpf) - Series3 rd GSM1357591  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
WE - NF9 (7.5hpf) - Series3 GSM1357580  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
WE - NF9 (8.0hpf) - Series3 GSM1357581  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
WE - NF9 (8.0hpf) - Series3 rd GSM1357592  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
WE - NF9 (8.5hpf) - Series3 GSM1357582  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
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