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GEO Series: GSE78176

Title: Histone modification and transcription factor ChIPseq of Xenopus laevis epithelial progenitors

Summary

To determine the positions of promoters and enhancers in developing Xenopus laevis epithelial progenitors, we performed ChIPseq on the histone modifications H3K4me3 and H3K27ac. We also performed ChIPseq on the transcription factors foxj1 (in the presence or absence of rfx2), myb (in the presence or absence of multicilin), and rad21.


Contributors: Ian Quigley, Chris Kintner

Experiment Type: Some embryos were harvested as wild-types; in other experiments, we injected embryos with mRNAs encoding FLAG-foxj1 (with and without rfx2 morpholino) or GFP-myb (with and without an inducible form of multicilin (mcidas-HGR)). We then isolated epithelial progenitors surgically and, when injected with multicilin, induced at mid-stage 11. We then harvested chromatin at 9 hours after induction (roughly stage 18) and performed ChIPseq using antibodies against endogenous targets (H3K4me3, H3K27ac, rad21) or protein tags (FLAG, GFP). We then sequenced these libraries, aligned the reads to the X. laevis genome (version 9.1) with bwa mem and called peaks with HOMER, using input as background.

Experiment Reagents: dexamethasone, rfx2 MO1, Tg(foxj1-FLAG),

Article: XB-ART-53709, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
input animal cap - NF18 - 9hr GSM2068810  GSM2068811  ChIP-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
explant   NF stage 9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 18  
   H3K27ac animal cap - NF18 - 9hr GSM2068804  ChIP-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
explant   NF stage 9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 18 Acetylated H3f3a Ab20
   H3K4me3 animal cap - NF18 GSM2068802  ChIP-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
explant   NF stage 9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 18 Methyl H3f3a Ab19
input animal cap - NF18 GSM2068812  ChIP-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(foxj1-FLAG) foxj1.L NF stage 2 (2-cell) animal blastomere
explant   NF stage 9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 18  
   foxj1 animal cap + rfx2 MO - NF18 GSM2068809  ChIP-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(foxj1-FLAG) foxj1.L NF stage 2 (2-cell) animal blastomere
morpholino injection rfx2 MO1 rfx2.L rfx2.S NF stage 2 (2-cell) animal blastomere
explant   NF stage 9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 18 FLAG Ab3
   foxj1 animal cap - NF18 GSM2068808  ChIP-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(foxj1-FLAG) foxj1.L NF stage 2 (2-cell) animal blastomere
explant   NF stage 9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 18 FLAG Ab3
input animal cap - NF18 GSM2068814  ChIP-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(myb-GFP) myb.L NF stage 2 (2-cell) animal blastomere
explant   NF stage 9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 18  
   myb animal cap - NF18 GSM2068806  ChIP-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(myb-GFP) myb.L NF stage 2 (2-cell) animal blastomere
explant   NF stage 9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 18 GFP Ab5
input animal cap - NF18 - 3hr GSM2068813  ChIP-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
explant   NF stage 9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 18  
   H3K27ac animal cap - NF18 - 3hr GSM2068803  ChIP-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
explant   NF stage 9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 18 Acetylated H3f3a Ab20
   Rad21 animal cap - NF18 GSM2068805  ChIP-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
explant   NF stage 9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 18 Rad21 Ab1
input animal cap + mcidas - NF18 GSM2068815  ChIP-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(myb-GFP) myb.L NF stage 2 (2-cell) animal blastomere
mRNA injection Tg(mcidas-GR) NF stage 2 (2-cell) animal blastomere
explant   NF stage 9 animal cap
chemical dexamethasone NF stage 11.5 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 18  
   myb animal cap + mcidas - NF18 GSM2068807  ChIP-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(myb-GFP) myb.L NF stage 2 (2-cell) animal blastomere
mRNA injection Tg(mcidas-GR) NF stage 2 (2-cell) animal blastomere
explant   NF stage 9 animal cap
chemical dexamethasone NF stage 11.5 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 18 GFP Ab5
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