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GEO Series: GSE130448

Title: Mucociliary epidermis RNA-seq data from comparison of controls and DN-tp63 morpholino knockdown in Xenopus animal cap explants.

Summary

This study was conducted to investigate the effects of DN-tp63 loss-of-function on mucociliary basal stem cells in Xenopus laevis. Uninjected control embryos and DN-tp63 morpholino oligonucleotide injected embryos were used to generate animal cap explants at embryonic stage 8. Explants were grown into mucociliary organoids and collected at embryonic stages 10.5, 16-19, and 24-25 for total RNA extraction.


Contributors: Peter Walentek

Experiment Type: The experiment was conducted in three biological replicates (embryos were derived from three different females and fertilizations). Control samples remained uninjected, DN-tp63 morphant samples were injected with morpholino oligonucleotides targeting the start condon of DN-tp63 and resulted in protein knockdown (loss-of-function). Sequencing was performed in two seperate paired-end runs to increase sequencing dpth, with each run containing all samples.

Experiment Reagents: tp63 MO3.

Phenotypes:
Xla Wt + tp63 MO + animal cap explant + animal cap explant NF19 (RNA-Seq (RNA))

Article: XB-ART-56304, PubMed

Source: NCBI GEO, Xenbase Download

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
animal cap explant - NF10.5 GSM3738794  GSM3738800  GSM3738806  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
explant   NF stage 8 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 10.5  
   animal cap explant + tp63 MO - NF10.5 DEG GSM3738797  GSM3738803  GSM3738809  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection tp63 MO3 tp63 (Xla) NF stage 4 (8-cell) animal hemisphere
explant   NF stage 8 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 10.5  
animal cap explant - NF19 GSM3738795  GSM3738807  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
explant   NF stage 8 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 19  
   animal cap explant + tp63 MO - NF19 DEG GSM3738798  GSM3738810  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection tp63 MO3 tp63 (Xla) NF stage 4 (8-cell) animal hemisphere
explant   NF stage 8 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 19  
animal cap explant - NF25 GSM3738796  GSM3738808  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
explant   NF stage 8 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 25  
   animal cap explant + tp63 MO - NF25 DEG GSM3738799  GSM3738811  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection tp63 MO3 tp63 (Xla) NF stage 4 (8-cell) animal hemisphere
explant   NF stage 8 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 25  
animal cap explant - NF16 GSM3738801  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
explant   NF stage 8 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 16  
   animal cap explant + tp63 MO - NF16 DEG GSM3738804  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection tp63 MO3 tp63 (Xla) NF stage 4 (8-cell) animal hemisphere
explant   NF stage 8 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 16  
animal cap explant - NF24 GSM3738802  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
explant   NF stage 8 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 24  
   animal cap explant + tp63 MO - NF24 DEG GSM3738805  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection tp63 MO3 tp63 (Xla) NF stage 4 (8-cell) animal hemisphere
explant   NF stage 8 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 24  
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Xtr   
Xla 

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