Tracheal to ciliated epithelium: Difference between revisions
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|series=IN_VITRO DIFFERENTIATION SERIES | |series=IN_VITRO DIFFERENTIATION SERIES | ||
|species=Mouse (Mus musculus) | |species=Mouse (Mus musculus) | ||
|tet_config= | |tet_config=https://fantom.gsc.riken.jp/5/suppl/tet/Epithelial_cells.tsv.gz | ||
|tet_file= | |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_points= | ||
|time_span=120 hours | |time_span=120 hours | ||
|timepoint_design=Early focus | |timepoint_design=Early focus | ||
|tissue_cell_type=Lung epithelial cell | |tissue_cell_type=Lung epithelial cell | ||
|zenbu_config= | |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.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
| 13367-143G1 | 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 |
