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Tracheal to ciliated epithelium: Difference between revisions

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{{Time_Course
{{TimeCourse
|collaborators=Boris Lenhard, Ana Pombo
|TCOverview=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.<br>
|description=ES embryonic stem cell series
|TCQuality_control=Known marker genes: FoxJ1 [2] and Mcidas [3].<br><html><img src='/resource_browser/images/TC_qc/1000px-Mouse_Tracheal_epithelial_cells.png' onclick='javascript:window.open("/resource_browser/images/TC_qc/1000px-Mouse_Tracheal_epithelial_cells.png", "imgwindow", "width=1000,height=500");' style='width:700px;cursor:pointer'/></html>Figure 1: CAGE expression of marker genes in TPM.<br><br>References:<br>[1] Vladar EK and Brody SL, Analysis of ciliogenesis in primary culture mouse tracheal epithelial cells. Methods Enzymol. 2013;525:285-309.<br>[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.<br>[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.<br>
|libraryids=CNhs14085,CNhs14086,CNhs14087,CNhs14088,CNhs14089,CNhs14090,CNhs14091,CNhs14092,CNhs14093,CNhs14094,CNhs14095,CNhs14097,CNhs14098,CNhs14099,CNhs14100,CNhs14101,CNhs14102,CNhs14103,CNhs14104,CNhs14105,CNhs14106,CNhs14107,CNhs14108,CNhs14109,CNhs14110,CNhs14111,CNhs14112,CNhs14113,CNhs14114,CNhs14115,CNhs14116,CNhs14117,CNhs14118,CNhs14119,CNhs14121,CNhs14122,CNhs14123,CNhs14124,CNhs14125,CNhs14126,CNhs14127
|TCSample_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).<br>
|Time_Course=
|category_treatment=Differentiation
|collaborators=Mitsuru Morimoto
|description=mouse_Tracheal_epithelial_cells
|germ_layer=endoderm
|libraryids=CNhs13739,CNhs13740,CNhs13741,CNhs13742,CNhs13743,CNhs13744,CNhs13745,CNhs13746,CNhs13747,CNhs13696,CNhs13748,CNhs13749,CNhs13750,CNhs13751,CNhs13752,CNhs13697,CNhs13753,CNhs13754,CNhs13755,CNhs13756,CNhs13757,CNhs13758,CNhs13759,CNhs13760,CNhs13762,CNhs13763,CNhs13764,CNhs13765,CNhs13766,CNhs13767,CNhs13768,CNhs13769,CNhs13770,CNhs13771,CNhs13772,CNhs13773,CNhs13774,CNhs13775,CNhs13776,CNhs13777,CNhs13778,CNhs13779,CNhs13780,CNhs13781,CNhs13782,CNhs13783,CNhs13784,CNhs13786,CNhs13787,CNhs13788,CNhs13789,CNhs13790,CNhs13791,CNhs13792
|number_time_points=18
|page_name=mouse_epithelial_cells
|page_name=mouse_epithelial_cells
|primary_cells=primary cells
|series=IN_VITRO DIFFERENTIATION SERIES
|series=IN_VITRO DIFFERENTIATION SERIES
|species=Mouse (Mus musculus)
|species=Mouse (Mus musculus)
|zenbu_config=https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config
|tet_config=https://fantom.gsc.riken.jp/5/suppl/tet/Epithelial_cells.tsv.gz
|tet_file=https://fantom.gsc.riken.jp/5/tet#!/search/?filename=mm9.cage_peak_phase1and2combined_tpm_ann_decoded.osc.txt.gz&file=1&c=1&c=360&c=361&c=362&c=363&c=364&c=365&c=366&c=367&c=368&c=369&c=370&c=371&c=372&c=373&c=374&c=375&c=376&c=377&c=378&c=379&c=380&c=381&c=382&c=383&c=384&c=385&c=386&c=387&c=388&c=389&c=390&c=391&c=392&c=393&c=394&c=395&c=396&c=397&c=398&c=399&c=400&c=401&c=402&c=403&c=404&c=405&c=406&c=407&c=408&c=409&c=410&c=411&c=412&c=413
|time_points=
|time_span=120 hours
|timepoint_design=Early focus
|tissue_cell_type=Lung epithelial cell
|zenbu_config=https://fantom.gsc.riken.jp/zenbu/gLyphs/#config=MSvP7mIyGhYqnD0eV4o1P
}}
}}

Latest revision as of 17:42, 14 March 2022

Series:IN_VITRO DIFFERENTIATION SERIES
Species:Mouse (Mus musculus)
Genomic View:Zenbu
Expression table:FILE
Link to TET:TET
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


13367-143G1Tracheal epithelial cells, differentiation to ciliated epithelial cells000hrbiol_rep1
13368-143G2Tracheal epithelial cells, differentiation to ciliated epithelial cells000hrbiol_rep2
13369-143G3Tracheal epithelial cells, differentiation to ciliated epithelial cells000hrbiol_rep3
13370-143G4Tracheal epithelial cells, differentiation to ciliated epithelial cells004hrbiol_rep1
13371-143G5Tracheal epithelial cells, differentiation to ciliated epithelial cells004hrbiol_rep2
13372-143G6Tracheal epithelial cells, differentiation to ciliated epithelial cells004hrbiol_rep3
13373-143G7Tracheal epithelial cells, differentiation to ciliated epithelial cells008hrbiol_rep1
13374-143G8Tracheal epithelial cells, differentiation to ciliated epithelial cells008hrbiol_rep2
13375-143G9Tracheal epithelial cells, differentiation to ciliated epithelial cells008hrbiol_rep3
13376-143H1Tracheal epithelial cells, differentiation to ciliated epithelial cells012hrbiol_rep1
13377-143H2Tracheal epithelial cells, differentiation to ciliated epithelial cells012hrbiol_rep2
13378-143H3Tracheal epithelial cells, differentiation to ciliated epithelial cells012hrbiol_rep3
13379-143H4Tracheal epithelial cells, differentiation to ciliated epithelial cells016hrbiol_rep1
13380-143H5Tracheal epithelial cells, differentiation to ciliated epithelial cells016hrbiol_rep2
13381-143H6Tracheal epithelial cells, differentiation to ciliated epithelial cells016hrbiol_rep3
13382-143H7Tracheal epithelial cells, differentiation to ciliated epithelial cells020hrbiol_rep1
13383-143H8Tracheal epithelial cells, differentiation to ciliated epithelial cells020hrbiol_rep2
13384-143H9Tracheal epithelial cells, differentiation to ciliated epithelial cells020hrbiol_rep3
13385-143I1Tracheal epithelial cells, differentiation to ciliated epithelial cells024hrbiol_rep1
13386-143I2Tracheal epithelial cells, differentiation to ciliated epithelial cells024hrbiol_rep2
13387-143I3Tracheal epithelial cells, differentiation to ciliated epithelial cells024hrbiol_rep3
13388-143I4Tracheal epithelial cells, differentiation to ciliated epithelial cells030hrbiol_rep1
13389-143I5Tracheal epithelial cells, differentiation to ciliated epithelial cells030hrbiol_rep2
13390-143I6Tracheal epithelial cells, differentiation to ciliated epithelial cells030hrbiol_rep3
13391-143I7Tracheal epithelial cells, differentiation to ciliated epithelial cells036hrbiol_rep1
13392-143I8Tracheal epithelial cells, differentiation to ciliated epithelial cells036hrbiol_rep2
13393-143I9Tracheal epithelial cells, differentiation to ciliated epithelial cells036hrbiol_rep3
13394-144A1Tracheal epithelial cells, differentiation to ciliated epithelial cells042hrbiol_rep1
13395-144A2Tracheal epithelial cells, differentiation to ciliated epithelial cells042hrbiol_rep2
13396-144A3Tracheal epithelial cells, differentiation to ciliated epithelial cells042hrbiol_rep3
13397-144A4Tracheal epithelial cells, differentiation to ciliated epithelial cells048hrbiol_rep1
13398-144A5Tracheal epithelial cells, differentiation to ciliated epithelial cells048hrbiol_rep2
13399-144A6Tracheal epithelial cells, differentiation to ciliated epithelial cells048hrbiol_rep3
13400-144A7Tracheal epithelial cells, differentiation to ciliated epithelial cells054hrbiol_rep1
13401-144A8Tracheal epithelial cells, differentiation to ciliated epithelial cells054hrbiol_rep2
13402-144A9Tracheal epithelial cells, differentiation to ciliated epithelial cells054hrbiol_rep3
13403-144B1Tracheal epithelial cells, differentiation to ciliated epithelial cells060hrbiol_rep1
13404-144B2Tracheal epithelial cells, differentiation to ciliated epithelial cells060hrbiol_rep2
13405-144B3Tracheal epithelial cells, differentiation to ciliated epithelial cells060hrbiol_rep3
13406-144B4Tracheal epithelial cells, differentiation to ciliated epithelial cells066hrbiol_rep1
13407-144B5Tracheal epithelial cells, differentiation to ciliated epithelial cells066hrbiol_rep2
13408-144B6Tracheal epithelial cells, differentiation to ciliated epithelial cells066hrbiol_rep3
13409-144B7Tracheal epithelial cells, differentiation to ciliated epithelial cells072hrbiol_rep1
13410-144B8Tracheal epithelial cells, differentiation to ciliated epithelial cells072hrbiol_rep2
13411-144B9Tracheal epithelial cells, differentiation to ciliated epithelial cells072hrbiol_rep3
13412-144C1Tracheal epithelial cells, differentiation to ciliated epithelial cells084hrbiol_rep1
13413-144C2Tracheal epithelial cells, differentiation to ciliated epithelial cells084hrbiol_rep2
13414-144C3Tracheal epithelial cells, differentiation to ciliated epithelial cells084hrbiol_rep3
13415-144C4Tracheal epithelial cells, differentiation to ciliated epithelial cells096hrbiol_rep1
13416-144C5Tracheal epithelial cells, differentiation to ciliated epithelial cells096hrbiol_rep2
13417-144C6Tracheal epithelial cells, differentiation to ciliated epithelial cells096hrbiol_rep3
13418-144C7Tracheal epithelial cells, differentiation to ciliated epithelial cells120hrbiol_rep1
13419-144C8Tracheal epithelial cells, differentiation to ciliated epithelial cells120hrbiol_rep2
13420-144C9Tracheal epithelial cells, differentiation to ciliated epithelial cells120hrbiol_rep3
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