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GEO Series: GSE89271

Title: RNAseq and ChIPseq profiling of Foxn4 and Foxj1 in multiciliated cells

Summary

Foxn4 and Foxj1 are expressed in multiciliated cells. Here, we dissect their role with knockdowns using two different technologies (morpholinos and CRISPR) and examine Foxn4 genomic binding sites in wild-type tissue and tissue converted entirely into multiciliated cells.


Contributors: Ian Quigley, Chris Kintner

Experiment Type: To examine Foxn4 and Foxj1's effect on multiciliated cells, we knocked them down in tissue where we also overexpressed an inducible form of multicilin (also known as mcidas; Stubbs et al., 2012). After injecting, we isolated ectoderm surgically and, when injected with multicilin, induced at mid-stage 11. We then harvested RNA or chromatin at 9 hours after induction, roughly corresponding to stage 18 and performed poly-a+ RNAseq (Illumina Truseq v2) or ChIPseq. We then aligned reads to X. laevis gene models (Mayball version, Chung and Kwon et al. 2014) or the genome (v7.1) and determined differential expression or binding targets. To determine differential expression, we compared RNAseq reads from ectoderm isolated from embryos injected with multicilin alone, as reported in Ma et al. 2014 (PMID: 24934224, NCBI GEO:GSE59309) with samples here injected with multicilin and Foxn4 or Foxj1 perturbations.

Experiment Reagents: dexamethasone, foxn4 MO1, Tg(foxn4-GFP-GR),

Article: XB-ART-52793, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
input animal cap - NF18 GSM2363464  GSM2363465  GSM2363466  GSM2363467  GSM2363468  GSM2363469  ChIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 18  
   foxn4 animal cap + mcidas - NF18 GSM2363463  ChIP-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(foxn4-GFP-GR) foxn4.L NF stage 2 (2-cell) blastomere
mRNA injection Tg(mcidas-GR) NF stage 2 (2-cell) blastomere
explant   NF stage 10.5 animal cap
chemical dexamethasone NF stage 11.5 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 18 GFP Ab5
   foxn4 animal cap - NF18 GSM2363462  ChIP-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(foxn4-GFP-GR) foxn4.L NF stage 2 (2-cell) blastomere
explant   NF stage 10.5 animal cap
chemical dexamethasone NF stage 11.5 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 18 GFP Ab5
animal cap + mcidas + foxj1 CRISPR - NF18 GSM2363456  GSM2363457  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
CRISPR foxj1.L NF stage 2 (2-cell) animal blastomere
mRNA injection Tg(mcidas-GR) mcidas.L NF stage 3 (4-cell) animal blastomere
explant   NF stage 10.5 animal cap
chemical dexamethasone NF stage 11.5 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 18  
animal cap + mcidas + foxn4 CRISPR - NF18 GSM2363458  GSM2363459  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
CRISPR foxn4.L NF stage 2 (2-cell) animal blastomere
mRNA injection Tg(mcidas-GR) NF stage 3 (4-cell) animal blastomere
explant   NF stage 10.5 animal cap
chemical dexamethasone NF stage 11.5 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 18  
animal cap + mcidas + foxn4 MO - NF18 GSM2363460  GSM2363461  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection foxn4 MO1 foxn4 NF stage 2 (2-cell) animal blastomere
mRNA injection Tg(mcidas-GR) NF stage 3 (4-cell) animal blastomere
explant   NF stage 10.5 animal cap
chemical dexamethasone NF stage 11.5 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 18  
animal cap + mcidas - NF18 GSM2364660  GSM2364661  GSM2364662  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(mcidas-GR) NF stage 2 (2-cell) blastomere
explant   NF stage 10.5 animal cap
chemical dexamethasone NF stage 11.5 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 18  
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Xtr   
Xla 

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