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Epithelial to mesenchymal

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Series:IN_VITRO DIFFERENTIATION SERIES
Species:Human (Homo sapiens)
Genomic View:Zenbu
Expression table:TET
Link to TET:FILE
Sample providers :Soichi Ogishima
Germ layer:mesoderm
Primary cells or cell line:cell line
Time span:60 hours
Number of time points:21

Overview

Epithelial\u2013mesenchymal transition (EMT) is a process of transition from epithelial cells to mesenchymal cells characterized by loss of cell adhesion and polarity, repression of E-cadherin expression, gain of cell motility and nvasive properties. EMT is essential for numerous developmental processes including mesoderm formation and neural tube formation. EMT is also essential for wound healing, organ fibrosis and initiation of metastasis for cancer progression. During the process of epithelial to mesenchymal transition, epithelial cells transforms to mesenchymal cells, and change their shapes. Mesenchymal cells get to gather and form focus. To clarify the transcriptional networks regulating EMT, we obtained time-course sample of human ARPE-19 epithelial to mesenchymal transition. After preculture for 7 days on 10cm dishes and cell seeding and cell culture for 5 days on 6-well glass bottom plate, we induced epithelial to mesenchymal transition on human ARPE-19 cells by TT-mixture of TNF\u03b1 and TGF\u03b22. Triplication for RNA extraction and 1 for imaging. We sampled total RNA of human ARPE-19 cells along with time-course of epithelial to mesenchymal transition.

Sample description

ARPE-19 cells were cultured in Dulbecco\u2019s Modified Eagle\u2019s Medium/Nutrient Mixture F-12 medium (Sigma-Aldrich) with 10% fetal bovine serum in a CO2 incubator at 37 ーC. After 5 days of preculture, cells were treated with human recombinant TGF-\u03b22 and human recombinant TNF-\u03b1 and continuously incubated in serum free medium at 37 ーC to induce EMT. At 21 different time points (0 min, 15 min, 30 min, 45 min, 60 min, 80 min, 100 min, 2 hr, 2.5 hr, 3 hr, 3.5 hr, 4 hr, 5 hr, 6 hr, 7 hr, 8 hr, 12 hr, 16 hr, 24 hr, 42 hr and 60 hr), cells were dissolved in lysis reagent and collected. For the samples of 0 min, cells were treated with PBS without TGF-\u03b22 and TNF-\u03b1. Using miRNeasy Mini Kit (QIAGEN), total RNA was extracted from each cell lysate according to a manufacturer\u2019s protocol.

Figure 1: Sample protocol


Figure 2: Cell morphology

Quality control


Figure 3: 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




Sample Name Time point Donor/Replica
13625-146H7 ARPE-19 EMT induced with TGF-beta and TNF-alpha 00hr00min biol_rep1
13626-146H8 ARPE-19 EMT induced with TGF-beta and TNF-alpha 00hr00min biol_rep2
13627-146H9 ARPE-19 EMT induced with TGF-beta and TNF-alpha 00hr00min biol_rep3
13628-146I1 ARPE-19 EMT induced with TGF-beta and TNF-alpha 00hr15min biol_rep1
13629-146I2 ARPE-19 EMT induced with TGF-beta and TNF-alpha 00hr15min biol_rep2
13630-146I3 ARPE-19 EMT induced with TGF-beta and TNF-alpha 00hr15min biol_rep3
13631-146I4 ARPE-19 EMT induced with TGF-beta and TNF-alpha 00hr30min biol_rep1
13632-146I5 ARPE-19 EMT induced with TGF-beta and TNF-alpha 00hr30min biol_rep2
13633-146I6 ARPE-19 EMT induced with TGF-beta and TNF-alpha 00hr30min biol_rep3
13634-146I7 ARPE-19 EMT induced with TGF-beta and TNF-alpha 00hr45min biol_rep1
13635-146I8 ARPE-19 EMT induced with TGF-beta and TNF-alpha 00hr45min biol_rep2
13636-146I9 ARPE-19 EMT induced with TGF-beta and TNF-alpha 00hr45min biol_rep3
13637-147A1 ARPE-19 EMT induced with TGF-beta and TNF-alpha 01hr00min biol_rep1
13638-147A2 ARPE-19 EMT induced with TGF-beta and TNF-alpha 01hr00min biol_rep2
13639-147A3 ARPE-19 EMT induced with TGF-beta and TNF-alpha 01hr00min biol_rep3
13640-147A4 ARPE-19 EMT induced with TGF-beta and TNF-alpha 01hr20min biol_rep1
13641-147A5 ARPE-19 EMT induced with TGF-beta and TNF-alpha 01hr20min biol_rep2
13642-147A6 ARPE-19 EMT induced with TGF-beta and TNF-alpha 01hr20min biol_rep3
13643-147A7 ARPE-19 EMT induced with TGF-beta and TNF-alpha 01hr40min biol_rep1
13644-147A8 ARPE-19 EMT induced with TGF-beta and TNF-alpha 01hr40min biol_rep2
13645-147A9 ARPE-19 EMT induced with TGF-beta and TNF-alpha 01hr40min biol_rep3
13646-147B1 ARPE-19 EMT induced with TGF-beta and TNF-alpha 02hr00min biol_rep1
13647-147B2 ARPE-19 EMT induced with TGF-beta and TNF-alpha 02hr00min biol_rep2
13648-147B3 ARPE-19 EMT induced with TGF-beta and TNF-alpha 02hr00min biol_rep3
13649-147B4 ARPE-19 EMT induced with TGF-beta and TNF-alpha 02hr30min biol_rep1
13650-147B5 ARPE-19 EMT induced with TGF-beta and TNF-alpha 02hr30min biol_rep2
13651-147B6 ARPE-19 EMT induced with TGF-beta and TNF-alpha 02hr30min biol_rep3
13652-147B7 ARPE-19 EMT induced with TGF-beta and TNF-alpha 03hr00min biol_rep1
13653-147B8 ARPE-19 EMT induced with TGF-beta and TNF-alpha 03hr00min biol_rep2
13654-147B9 ARPE-19 EMT induced with TGF-beta and TNF-alpha 03hr00min biol_rep3
13655-147C1 ARPE-19 EMT induced with TGF-beta and TNF-alpha 03hr30min biol_rep1
13656-147C2 ARPE-19 EMT induced with TGF-beta and TNF-alpha 03hr30min biol_rep2
13657-147C3 ARPE-19 EMT induced with TGF-beta and TNF-alpha 03hr30min biol_rep3
13658-147C4 ARPE-19 EMT induced with TGF-beta and TNF-alpha 04hr00min biol_rep1
13659-147C5 ARPE-19 EMT induced with TGF-beta and TNF-alpha 04hr00min biol_rep2
13660-147C6 ARPE-19 EMT induced with TGF-beta and TNF-alpha 04hr00min biol_rep3
13661-147C7 ARPE-19 EMT induced with TGF-beta and TNF-alpha 05hr00min biol_rep1
13662-147C8 ARPE-19 EMT induced with TGF-beta and TNF-alpha 05hr00min biol_rep2
13663-147C9 ARPE-19 EMT induced with TGF-beta and TNF-alpha 05hr00min biol_rep3
13664-147D1 ARPE-19 EMT induced with TGF-beta and TNF-alpha 06hr00min biol_rep1
13666-147D3 ARPE-19 EMT induced with TGF-beta and TNF-alpha 06hr00min biol_rep3
13667-147D4 ARPE-19 EMT induced with TGF-beta and TNF-alpha 07hr00min biol_rep1
13668-147D5 ARPE-19 EMT induced with TGF-beta and TNF-alpha 07hr00min biol_rep2
13669-147D6 ARPE-19 EMT induced with TGF-beta and TNF-alpha 07hr00min biol_rep3
13670-147D7 ARPE-19 EMT induced with TGF-beta and TNF-alpha 08hr00min biol_rep1
13671-147D8 ARPE-19 EMT induced with TGF-beta and TNF-alpha 08hr00min biol_rep2
13672-147D9 ARPE-19 EMT induced with TGF-beta and TNF-alpha 08hr00min biol_rep3
13674-147E2 ARPE-19 EMT induced with TGF-beta and TNF-alpha 12hr00min biol_rep2
13675-147E3 ARPE-19 EMT induced with TGF-beta and TNF-alpha 12hr00min biol_rep3
13676-147E4 ARPE-19 EMT induced with TGF-beta and TNF-alpha 16hr00min biol_rep1
13677-147E5 ARPE-19 EMT induced with TGF-beta and TNF-alpha 16hr00min biol_rep2
13678-147E6 ARPE-19 EMT induced with TGF-beta and TNF-alpha 16hr00min biol_rep3
13679-147E7 ARPE-19 EMT induced with TGF-beta and TNF-alpha 24hr00min biol_rep1
13681-147E9 ARPE-19 EMT induced with TGF-beta and TNF-alpha 24hr00min biol_rep3
13682-147F1 ARPE-19 EMT induced with TGF-beta and TNF-alpha 42hr00min biol_rep1
13683-147F2 ARPE-19 EMT induced with TGF-beta and TNF-alpha 42hr00min biol_rep2
13684-147F3 ARPE-19 EMT induced with TGF-beta and TNF-alpha 42hr00min biol_rep3
13685-147F4 ARPE-19 EMT induced with TGF-beta and TNF-alpha 60hr00min biol_rep1
13686-147F5 ARPE-19 EMT induced with TGF-beta and TNF-alpha 60hr00min biol_rep2
13687-147F6 ARPE-19 EMT induced with TGF-beta and TNF-alpha 60hr00min biol_rep3