Return to search results Title: Enhancer chromatin signatures predict Smad2/3 binding in Xenopus

Summary

In this study we have examine the deposition of H3K4me1,H3K4Me3 and H3K27Ac and the Nodal transcription factor, Smad2/3, immediately following zygotic transcription and continuing through gastrulation.

Contributors: Julie Baker, Rakhi Gupta

Experiment Type: We profiled 4 histone modifications (H3K4Me3, H3K27Me3, H3K27AC, H3K4Me1) and one transcription factor smad2/3 (+ chromatin input) using ChIP-Seq, and expression profiles (3' RNA-Seq) for Xenopus tropicalis embryos stage8, stage9 and stage10.5. Furthermore, we have profile two histone modifications (H3K4Me1 and H3K27Ac) in absance of nodal signaling in stage9 Xenopus tropicalis embryos using ChIP-seq and 3-seq

Experiment Reagents: SB431542.

Article: XB-ART-49423, PubMed

Source: NCBI GEO, Xenbase Download

Sample	View		GSMs	Assay Type
input WE - NF10.5 GSM1350504  ChIP-Seq [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 10.5      H3K27ac WE - NF10.5 GSM1350516  ChIP-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 10.5 Acetylated H3f3a Ab20    H3K27me2me3 WE - NF10.5 GSM1350519  ChIP-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 10.5 h3f3a Ab28    H3K4me1 WE - NF10.5 GSM1350513  ChIP-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 10.5 methyl-H3f3a Ab13    H3K4me3 WE - NF10.5 GSM1350510  ChIP-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 10.5 Methyl H3f3a Ab19    Smad2/3 WE - NF10.5 GSM1350507  ChIP-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 10.5 Smad2 Ab9 input WE - NF8 GSM1350502  ChIP-Seq [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 8      H3K27ac WE - NF8 GSM1350514  ChIP-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 8 Acetylated H3f3a Ab20    H3K27me2me3 WE - NF8 GSM1350517  ChIP-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 8 h3f3a Ab28    H3K4me1 WE - NF8 GSM1350511  ChIP-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 8 methyl-H3f3a Ab13    H3K4me3 WE - NF8 GSM1350508  ChIP-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 8 Methyl H3f3a Ab19    Smad2/3 WE - NF8 GSM1350505  ChIP-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 8 Smad2 Ab9 input WE - NF9 GSM1350503  ChIP-Seq [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 9      H3K27ac WE + SB431542 - NF9 GSM1350520  ChIP-Seq Xtr   [-] [+] Background: Xtr.Outbred Manipulations: Manipulation Type Reagent Target Gene Stage Treatment Area chemical SB431542 NF stage 4 (8-cell) whole organism Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 9 Acetylated H3f3a Ab20    H3K27ac WE - NF9 GSM1350515  ChIP-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 9 Acetylated H3f3a Ab20    H3K27me2me3 WE - NF9 GSM1350518  ChIP-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 9 h3f3a Ab28    H3K4me1 WE + SB431542 - NF9 GSM1350521  ChIP-Seq Xtr   [-] [+] Background: Xtr.Outbred Manipulations: Manipulation Type Reagent Target Gene Stage Treatment Area chemical SB431542 NF stage 4 (8-cell) whole organism Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 9 methyl-H3f3a Ab13    H3K4me1 WE - NF9 GSM1350512  ChIP-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 9 methyl-H3f3a Ab13    H3K4me3 WE - NF9 GSM1350509  ChIP-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 9 Methyl H3f3a Ab19    Smad2/3 WE - NF9 GSM1350506  ChIP-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 9 Smad2 Ab9 WE - NF9 GSM1350523  RNA-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 9      WE + SB431542 - NF9 DEG GSM1350525  RNA-Seq Xtr   [-] [+] Background: Xtr.Outbred Manipulations: Manipulation Type Reagent Target Gene Stage Treatment Area chemical SB431542 NF stage 4 (8-cell) whole organism Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 9   WE - NF10.5 GSM1350524  RNA-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 10.5   WE - NF8 GSM1350522  RNA-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 8

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