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GEO Series: GSE76342

Title: RNAseq profiling of multiciliated cells

Summary

To determine what genes are upregulated in multiciliated cells, we manipulated Xenopus laevis ectoderm to either make more or fewer of this cell type with multiple approaches across multiple timepoints. By finding differentially expressed genes in common across all comparisons in which multiciliated cell number changed, we obtained a robust, but conservative, core group of multiciliated cell genes.


Contributors: Ian Quigley, Chris Kintner

Experiment Type: We suppressed multiciliated cell development by activating the notch pathway with an injected mRNA encoding the intracellular domain of notch (icd) or by injecting an mRNA encoding a dominant-negative form of multicilin (dnmcidas). Conversely, we promoted multiciliated cell differentiation by blocking notch signaling with a DNA-binding mutant of Suppressor of Hairless (dbm), or by overexpressing an inducible form of multicilin (mcidas). We also coinjected these constructs in a way aimed at causing the greatest change in multiciliated cells and reducing background transcriptional programs not associated with these cells: for example, we coinjected icd with mcidas, in order to reduce other cell types specified by notch. After injecting, we isolated ectoderm surgically and, when injected with multicilin, induced at mid-stage 11. We then harvested RNA at 3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18 and performed poly-a+ RNAseq (Illumina Truseq v2). We then aligned reads to X. laevis gene models (Mayball version, Chung and Kwon et al. 2014) and took the intersection of genes differentially expressed between all comparisons in which the multiciliated cell number dramatically changed (icd vs. icd + mcidas, icd vs. dbm, dbm vs. dbm + dnmcidas) to obtain a core list of multiciliated cell genes.

Experiment Reagents: dexamethasone, Tg(CAnotch1), Tg(DNmcidas),

Article: Xenbase, PubMed

Source: NCBI GEO, Xenbase FTP

Samples:
Sample View GSMs Assay Type
animal cap - NF18 GSM1981773  GSM1981774  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF18  
   animal cap + CAnotch1 + foxi1 - NF18 DEG GSM1981779  GSM1981780  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(CAnotch1) notch1.L NF2 animal blastomere
mRNA injection Tg(foxi1-GR) foxi1.L NF2 blastomere
explant     NF9 animal cap
chemical dexamethasone   NF11.5 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF18  
   animal cap + CAnotch1 + mcidas - NF18 DEG GSM1981761  GSM1981762  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(CAnotch1) notch1.L NF2 animal blastomere
mRNA injection Tg(mcidas-GR)   NF2 blastomere
explant     NF9 animal cap
chemical dexamethasone   NF11.5 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF18  
   animal cap + CAnotch1 - NF18 DEG GSM1981749  GSM1981750  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(CAnotch1) notch1.L NF2 animal blastomere
explant     NF9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF18  
   animal cap + DNrbpj + DNmcidas - NF18 DEG GSM1981767  GSM1981768  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(DNrbpj) rbpj.L NF2 animal blastomere
mRNA injection Tg(DNmcidas)   NF2 blastomere
explant     NF9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF18  
   animal cap + DNrbpj - NF18 DEG GSM1981755  GSM1981756  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(DNrbpj) rbpj.L NF2 animal blastomere
explant     NF9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF18  
animal cap - NF13 GSM1981769  GSM1981770  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF13  
   animal cap + CAnotch1 + foxi1 - NF13 DEG GSM1981775  GSM1981776  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(CAnotch1) notch1.L NF2 animal blastomere
mRNA injection Tg(foxi1-GR) foxi1.L NF2 blastomere
explant     NF9 animal cap
chemical dexamethasone   NF11.5 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF13  
   animal cap + CAnotch1 + mcidas - NF13 DEG GSM1981757  GSM1981758  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(CAnotch1) notch1.L NF2 animal blastomere
mRNA injection Tg(mcidas-GR)   NF2 blastomere
explant     NF9 animal cap
chemical dexamethasone   NF11.5 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF13  
   animal cap + CAnotch1 - NF13 DEG GSM1981745  GSM1981746  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(CAnotch1) notch1.L NF2 animal blastomere
explant     NF9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF13  
   animal cap + DNrbpj + DNmcidas - NF13 DEG GSM1981763  GSM1981764  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(DNrbpj) rbpj.L NF2 animal blastomere
mRNA injection Tg(DNmcidas)   NF2 blastomere
explant     NF9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF13  
   animal cap + DNrbpj - NF13 DEG GSM1981751  GSM1981752  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(DNrbpj) rbpj.L NF2 animal blastomere
explant     NF9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF13  
animal cap - NF16 GSM1981771  GSM1981772  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF16  
   animal cap + CAnotch1 + foxi1 - NF16 DEG GSM1981777  GSM1981778  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(CAnotch1) notch1.L NF2 animal blastomere
mRNA injection Tg(foxi1-GR) foxi1.L NF2 blastomere
explant     NF9 animal cap
chemical dexamethasone   NF11.5 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF16  
   animal cap + CAnotch1 + mcidas - NF16 DEG GSM1981759  GSM1981760  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(CAnotch1) notch1.L NF2 animal blastomere
mRNA injection Tg(mcidas-GR)   NF2 blastomere
explant     NF9 animal cap
chemical dexamethasone   NF11.5 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF16  
   animal cap + CAnotch1 - NF16 DEG GSM1981747  GSM1981748  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(CAnotch1) notch1.L NF2 animal blastomere
explant     NF9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF16  
   animal cap + DNrbpj + DNmcidas - NF16 DEG GSM1981765  GSM1981766  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(DNrbpj) rbpj.L NF2 animal blastomere
mRNA injection Tg(DNmcidas)   NF2 blastomere
explant     NF9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF16  
   animal cap + DNrbpj - NF16 DEG GSM1981753  GSM1981754  RNA-Seq
Background: Xla.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection Tg(DNrbpj) rbpj.L NF2 animal blastomere
explant     NF9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF16  
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