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Tracheal to ciliated epithelium

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Series:IN_VITRO DIFFERENTIATION SERIES
Species:Mouse (Mus musculus)
Genomic View:Zenbu
Expression table:TET
Link to TET:FILE
Sample providers :Mitsuru Morimoto
Germ layer:endoderm
Primary cells or cell line:primary cells
Time span:120 hours
Number of time points:18


Overview

The vertebrate cilium is a sensory and mechanical organelle critical for a broad array of homeostatic mechanisms. Although such a biological importance of ciliogenesis is well investigated, molecular processes of ciliogenesis has been remained in mystery. Notch signaling plays a crucial role in alternative ciliated or secretory cell fate determination from bi-potential progenitor in developing lung epithelium. Using mouse tracheal epithelial primary culture cells (mTECs) that allow us to examine airway mucociliary epithelial cell differentiation from its progenitor cells in in vitro, we successfully established high-efficient ciliated cell induction culture system with pharmacological inhibition of Notch signaling. Taking advantage of this culture system, we harvested time-course samples from differentiating ciliated cells at 18 time points after the differentiation induction and harvested total RNA from these.

Sample description

The detailed protocol for the mTECs culture has been published by Vladar and Brody, 2013. mTECs are isolated from the tracheas removed from female mice between 12~20 weeks of age. mTECs were cultured on 12-well plates, 1.00 x 105 /well, containing Transwell permeable membrane supports (Corning). Within 5 days, the cells become confluent and differentiation was induced by removing serum and growth factors from the medium. For hyper induction of ciliated cells, 10 uM of gamma secretase “DAPT” was added into the medium. At the time points after differentiation induction, total RNA was extracted by lysing mTECs with QIAzol Lysis Reagent and purified by the miRNeasy kit (QIAGEN).

Quality control

Known marker genes: FoxJ1 [2] and Mcidas [3].
Figure 1: CAGE expression of marker genes in TPM.

References:
[1] Vladar EK and Brody SL, Analysis of ciliogenesis in primary culture mouse tracheal epithelial cells. Methods Enzymol. 2013;525:285-309.
[2] You Y, Huang T, Richer EJ, Schmidt JE, Zabner J, Borok Z, Brody SL. Role of f-box factor foxj1 in differentiation of ciliated airway epithelial cells. Am J Physiol Lung Cell Mol Physiol. 2004 Apr;286(4):L650-7. Epub 2003 Jun 20.
[3] Stubbs JL, Vladar EK, Axelrod JD, Kintner C. Multicilin promotes centriole assembly and ciliogenesis during multiciliate cell differentiation. Nat Cell Biol. 2012 Jan 8;14(2):140-7. doi: 10.1038/ncb2406.

Profiled time course samples

Only samples that passed quality controls (Arner et al. 2015) are shown here. The entire set of samples are downloadable from FANTOM5 human / mouse samples



Sample Name Time point Donor/Replica
13367-143G1 Tracheal epithelial cells, differentiation to ciliated epithelial cells 000hr biol_rep1
13368-143G2 Tracheal epithelial cells, differentiation to ciliated epithelial cells 000hr biol_rep2
13369-143G3 Tracheal epithelial cells, differentiation to ciliated epithelial cells 000hr biol_rep3
13370-143G4 Tracheal epithelial cells, differentiation to ciliated epithelial cells 004hr biol_rep1
13371-143G5 Tracheal epithelial cells, differentiation to ciliated epithelial cells 004hr biol_rep2
13372-143G6 Tracheal epithelial cells, differentiation to ciliated epithelial cells 004hr biol_rep3
13373-143G7 Tracheal epithelial cells, differentiation to ciliated epithelial cells 008hr biol_rep1
13374-143G8 Tracheal epithelial cells, differentiation to ciliated epithelial cells 008hr biol_rep2
13375-143G9 Tracheal epithelial cells, differentiation to ciliated epithelial cells 008hr biol_rep3
13376-143H1 Tracheal epithelial cells, differentiation to ciliated epithelial cells 012hr biol_rep1
13377-143H2 Tracheal epithelial cells, differentiation to ciliated epithelial cells 012hr biol_rep2
13378-143H3 Tracheal epithelial cells, differentiation to ciliated epithelial cells 012hr biol_rep3
13379-143H4 Tracheal epithelial cells, differentiation to ciliated epithelial cells 016hr biol_rep1
13380-143H5 Tracheal epithelial cells, differentiation to ciliated epithelial cells 016hr biol_rep2
13381-143H6 Tracheal epithelial cells, differentiation to ciliated epithelial cells 016hr biol_rep3
13382-143H7 Tracheal epithelial cells, differentiation to ciliated epithelial cells 020hr biol_rep1
13383-143H8 Tracheal epithelial cells, differentiation to ciliated epithelial cells 020hr biol_rep2
13384-143H9 Tracheal epithelial cells, differentiation to ciliated epithelial cells 020hr biol_rep3
13385-143I1 Tracheal epithelial cells, differentiation to ciliated epithelial cells 024hr biol_rep1
13386-143I2 Tracheal epithelial cells, differentiation to ciliated epithelial cells 024hr biol_rep2
13387-143I3 Tracheal epithelial cells, differentiation to ciliated epithelial cells 024hr biol_rep3
13388-143I4 Tracheal epithelial cells, differentiation to ciliated epithelial cells 030hr biol_rep1
13389-143I5 Tracheal epithelial cells, differentiation to ciliated epithelial cells 030hr biol_rep2
13390-143I6 Tracheal epithelial cells, differentiation to ciliated epithelial cells 030hr biol_rep3
13391-143I7 Tracheal epithelial cells, differentiation to ciliated epithelial cells 036hr biol_rep1
13392-143I8 Tracheal epithelial cells, differentiation to ciliated epithelial cells 036hr biol_rep2
13393-143I9 Tracheal epithelial cells, differentiation to ciliated epithelial cells 036hr biol_rep3
13394-144A1 Tracheal epithelial cells, differentiation to ciliated epithelial cells 042hr biol_rep1
13395-144A2 Tracheal epithelial cells, differentiation to ciliated epithelial cells 042hr biol_rep2
13396-144A3 Tracheal epithelial cells, differentiation to ciliated epithelial cells 042hr biol_rep3
13397-144A4 Tracheal epithelial cells, differentiation to ciliated epithelial cells 048hr biol_rep1
13398-144A5 Tracheal epithelial cells, differentiation to ciliated epithelial cells 048hr biol_rep2
13399-144A6 Tracheal epithelial cells, differentiation to ciliated epithelial cells 048hr biol_rep3
13400-144A7 Tracheal epithelial cells, differentiation to ciliated epithelial cells 054hr biol_rep1
13401-144A8 Tracheal epithelial cells, differentiation to ciliated epithelial cells 054hr biol_rep2
13402-144A9 Tracheal epithelial cells, differentiation to ciliated epithelial cells 054hr biol_rep3
13403-144B1 Tracheal epithelial cells, differentiation to ciliated epithelial cells 060hr biol_rep1
13404-144B2 Tracheal epithelial cells, differentiation to ciliated epithelial cells 060hr biol_rep2
13405-144B3 Tracheal epithelial cells, differentiation to ciliated epithelial cells 060hr biol_rep3
13406-144B4 Tracheal epithelial cells, differentiation to ciliated epithelial cells 066hr biol_rep1
13407-144B5 Tracheal epithelial cells, differentiation to ciliated epithelial cells 066hr biol_rep2
13408-144B6 Tracheal epithelial cells, differentiation to ciliated epithelial cells 066hr biol_rep3
13409-144B7 Tracheal epithelial cells, differentiation to ciliated epithelial cells 072hr biol_rep1
13410-144B8 Tracheal epithelial cells, differentiation to ciliated epithelial cells 072hr biol_rep2
13411-144B9 Tracheal epithelial cells, differentiation to ciliated epithelial cells 072hr biol_rep3
13412-144C1 Tracheal epithelial cells, differentiation to ciliated epithelial cells 084hr biol_rep1
13413-144C2 Tracheal epithelial cells, differentiation to ciliated epithelial cells 084hr biol_rep2
13414-144C3 Tracheal epithelial cells, differentiation to ciliated epithelial cells 084hr biol_rep3
13415-144C4 Tracheal epithelial cells, differentiation to ciliated epithelial cells 096hr biol_rep1
13416-144C5 Tracheal epithelial cells, differentiation to ciliated epithelial cells 096hr biol_rep2
13417-144C6 Tracheal epithelial cells, differentiation to ciliated epithelial cells 096hr biol_rep3
13418-144C7 Tracheal epithelial cells, differentiation to ciliated epithelial cells 120hr biol_rep1
13419-144C8 Tracheal epithelial cells, differentiation to ciliated epithelial cells 120hr biol_rep2
13420-144C9 Tracheal epithelial cells, differentiation to ciliated epithelial cells 120hr biol_rep3