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{{TimeCourse
{{TimeCourse
|TCOverview=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.
|TCQuality_control=<html><img src='/resource_browser/images/TC_qc/1000px-Human_ARPE-19.png' onclick='javascript:window.open("/resource_browser/images/TC_qc/1000px-Human_ARPE-19.png", "imgwindow", "width=1000,height=375");' style='width:700px;cursor:pointer'/></html><br>Figure 3: CAGE expression of marker genes in TPM.<br>
|TCSample_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.<br><html><img src='/resource_browser/images/TC_qc/800px-Human_ARPE-19_sample_protocols.png' width='700px'/></html><br>Figure 1: Sample protocol<br><br><html><img src='/resource_browser/images/TC_qc/600px-Human_ARPE-19_sample_photos.png'></html><br>Figure 2: Cell morphology<br><br>
|Time_Course=
|Time_Course=
|category_treatment=Differentiation
|collaborators=Soichi Ogishima
|collaborators=Soichi Ogishima
|description=human_ARPE-19
|description=human_ARPE-19
|germ_layer=mesoderm
|libraryids=CNhs14463,CNhs14464,CNhs14465,CNhs14466,CNhs14467,CNhs14468,CNhs14469,CNhs14470,CNhs14471,CNhs14472,CNhs14473,CNhs14474,CNhs14475,CNhs14476,CNhs14477,CNhs14478,CNhs14479,CNhs14480,CNhs14482,CNhs14483,CNhs14484,CNhs14485,CNhs14486,CNhs14487,CNhs14488,CNhs14489,CNhs14490,CNhs14491,CNhs14492,CNhs14493,CNhs14494,CNhs14495,CNhs14496,CNhs14497,CNhs14498,CNhs14499,CNhs14500,CNhs14501,CNhs14518,CNhs14519,CNhs14522,CNhs14523,CNhs14524,CNhs14525,CNhs14526,CNhs14527,CNhs14528,CNhs14530,CNhs14531,CNhs14532,CNhs14533,CNhs14534,CNhs14535,CNhs14537,CNhs14538,CNhs14539,CNhs14540,CNhs14541,CNhs14542,CNhs14543
|libraryids=CNhs14463,CNhs14464,CNhs14465,CNhs14466,CNhs14467,CNhs14468,CNhs14469,CNhs14470,CNhs14471,CNhs14472,CNhs14473,CNhs14474,CNhs14475,CNhs14476,CNhs14477,CNhs14478,CNhs14479,CNhs14480,CNhs14482,CNhs14483,CNhs14484,CNhs14485,CNhs14486,CNhs14487,CNhs14488,CNhs14489,CNhs14490,CNhs14491,CNhs14492,CNhs14493,CNhs14494,CNhs14495,CNhs14496,CNhs14497,CNhs14498,CNhs14499,CNhs14500,CNhs14501,CNhs14518,CNhs14519,CNhs14522,CNhs14523,CNhs14524,CNhs14525,CNhs14526,CNhs14527,CNhs14528,CNhs14530,CNhs14531,CNhs14532,CNhs14533,CNhs14534,CNhs14535,CNhs14537,CNhs14538,CNhs14539,CNhs14540,CNhs14541,CNhs14542,CNhs14543
|number_time_points=21
|page_name=human_ARPE_19
|page_name=human_ARPE_19
|primary_cells=cell line
|series=IN_VITRO DIFFERENTIATION SERIES
|series=IN_VITRO DIFFERENTIATION SERIES
|species=Human (Homo sapiens)
|species=Human (Homo sapiens)
|zenbu_config=http://fantom.gsc.riken.jp/zenbu/gLyphs/#config=6MLr303UKRFjRf00h2lL_D
|tet_config=https://fantom.gsc.riken.jp/5/suppl/tet/ARPE_19.tsv.gz
|TCOverview=Epithelial–mesenchymal 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 TNFα and TGFβ2. 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.
|tet_file=https://fantom.gsc.riken.jp/5/tet#!/search/?filename=hg19.cage_peak_phase1and2combined_tpm_ann_decoded.osc.txt.gz&file=1&c=1&c=19&c=20&c=21&c=22&c=23&c=24&c=25&c=26&c=27&c=28&c=29&c=30&c=31&c=32&c=33&c=34&c=35&c=36&c=37&c=38&c=39&c=40&c=41&c=42&c=43&c=44&c=45&c=46&c=47&c=48&c=49&c=50&c=51&c=52&c=53&c=54&c=55&c=56&c=57&c=58&c=60&c=61&c=62&c=63&c=64&c=65&c=66&c=67&c=68&c=69&c=70&c=71&c=72&c=74&c=75&c=76&c=77&c=78&c=79&c=80
|TCSample_description=ARPE-19 cells were cultured in Dulbecco’s Modified Eagle’s Medium/Nutrient Mixture F-12 medium (Sigma-Aldrich) with 10% fetal bovine serum in a CO2 incubator at 37 °C. After 5 days of preculture, cells were treated with human recombinant TGF-β2 and human recombinant TNF-α and continuously incubated in serum free medium at 37 °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-β2 and TNF-α. Using miRNeasy Mini Kit (QIAGEN), total RNA was extracted from each cell lysate according to a manufacturer’s protocol.<br>
|time_points=0hr
<html><img src='https://fantom5-collaboration.gsc.riken.jp/resource_browser/images/TC_qc/800px-Human_ARPE-19_sample_protocols.png' width='700px'/></html><br>
|time_span=60 hours
Figure 1: Sample protocol<br>
|timepoint_design=Early focus
<br>
|tissue_cell_type=Epithelial>>mesenchymal cells
<html><img src='https://fantom5-collaboration.gsc.riken.jp/resource_browser/images/TC_qc/600px-Human_ARPE-19_sample_photos.png'></html><br>
|zenbu_config=https://fantom.gsc.riken.jp/zenbu/gLyphs/#config=ZkZynoPyAxHvl3-uzxZ27B
Figure 2: Cell morphology<br>
<br>
|TCQuality_control=<html><img src='https://fantom5-collaboration.gsc.riken.jp/resource_browser/images/TC_qc/1000px-Human_ARPE-19.png' onclick='javascript:window.open("https://fantom5-collaboration.gsc.riken.jp/resource_browser/images/TC_qc/1000px-Human_ARPE-19.png", "imgwindow", "width=1000,height=375");' style='width:700px;cursor:pointer'/></html><br>
Figure 3: CAGE expression of marker genes in TPM.
<br>
}}
}}

Latest revision as of 17:06, 14 March 2022

Series:IN_VITRO DIFFERENTIATION SERIES
Species:Human (Homo sapiens)
Genomic View:Zenbu
Expression table:FILE
Link to TET:TET
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


13625-146H7ARPE-19 EMT induced with TGF-beta and TNF-alpha00hr00minbiol_rep1
13626-146H8ARPE-19 EMT induced with TGF-beta and TNF-alpha00hr00minbiol_rep2
13627-146H9ARPE-19 EMT induced with TGF-beta and TNF-alpha00hr00minbiol_rep3
13628-146I1ARPE-19 EMT induced with TGF-beta and TNF-alpha00hr15minbiol_rep1
13629-146I2ARPE-19 EMT induced with TGF-beta and TNF-alpha00hr15minbiol_rep2
13630-146I3ARPE-19 EMT induced with TGF-beta and TNF-alpha00hr15minbiol_rep3
13631-146I4ARPE-19 EMT induced with TGF-beta and TNF-alpha00hr30minbiol_rep1
13632-146I5ARPE-19 EMT induced with TGF-beta and TNF-alpha00hr30minbiol_rep2
13633-146I6ARPE-19 EMT induced with TGF-beta and TNF-alpha00hr30minbiol_rep3
13634-146I7ARPE-19 EMT induced with TGF-beta and TNF-alpha00hr45minbiol_rep1
13635-146I8ARPE-19 EMT induced with TGF-beta and TNF-alpha00hr45minbiol_rep2
13636-146I9ARPE-19 EMT induced with TGF-beta and TNF-alpha00hr45minbiol_rep3
13637-147A1ARPE-19 EMT induced with TGF-beta and TNF-alpha01hr00minbiol_rep1
13638-147A2ARPE-19 EMT induced with TGF-beta and TNF-alpha01hr00minbiol_rep2
13639-147A3ARPE-19 EMT induced with TGF-beta and TNF-alpha01hr00minbiol_rep3
13640-147A4ARPE-19 EMT induced with TGF-beta and TNF-alpha01hr20minbiol_rep1
13641-147A5ARPE-19 EMT induced with TGF-beta and TNF-alpha01hr20minbiol_rep2
13642-147A6ARPE-19 EMT induced with TGF-beta and TNF-alpha01hr20minbiol_rep3
13643-147A7ARPE-19 EMT induced with TGF-beta and TNF-alpha01hr40minbiol_rep1
13644-147A8ARPE-19 EMT induced with TGF-beta and TNF-alpha01hr40minbiol_rep2
13645-147A9ARPE-19 EMT induced with TGF-beta and TNF-alpha01hr40minbiol_rep3
13646-147B1ARPE-19 EMT induced with TGF-beta and TNF-alpha02hr00minbiol_rep1
13647-147B2ARPE-19 EMT induced with TGF-beta and TNF-alpha02hr00minbiol_rep2
13648-147B3ARPE-19 EMT induced with TGF-beta and TNF-alpha02hr00minbiol_rep3
13649-147B4ARPE-19 EMT induced with TGF-beta and TNF-alpha02hr30minbiol_rep1
13650-147B5ARPE-19 EMT induced with TGF-beta and TNF-alpha02hr30minbiol_rep2
13651-147B6ARPE-19 EMT induced with TGF-beta and TNF-alpha02hr30minbiol_rep3
13652-147B7ARPE-19 EMT induced with TGF-beta and TNF-alpha03hr00minbiol_rep1
13653-147B8ARPE-19 EMT induced with TGF-beta and TNF-alpha03hr00minbiol_rep2
13654-147B9ARPE-19 EMT induced with TGF-beta and TNF-alpha03hr00minbiol_rep3
13655-147C1ARPE-19 EMT induced with TGF-beta and TNF-alpha03hr30minbiol_rep1
13656-147C2ARPE-19 EMT induced with TGF-beta and TNF-alpha03hr30minbiol_rep2
13657-147C3ARPE-19 EMT induced with TGF-beta and TNF-alpha03hr30minbiol_rep3
13658-147C4ARPE-19 EMT induced with TGF-beta and TNF-alpha04hr00minbiol_rep1
13659-147C5ARPE-19 EMT induced with TGF-beta and TNF-alpha04hr00minbiol_rep2
13660-147C6ARPE-19 EMT induced with TGF-beta and TNF-alpha04hr00minbiol_rep3
13661-147C7ARPE-19 EMT induced with TGF-beta and TNF-alpha05hr00minbiol_rep1
13662-147C8ARPE-19 EMT induced with TGF-beta and TNF-alpha05hr00minbiol_rep2
13663-147C9ARPE-19 EMT induced with TGF-beta and TNF-alpha05hr00minbiol_rep3
13664-147D1ARPE-19 EMT induced with TGF-beta and TNF-alpha06hr00minbiol_rep1
13666-147D3ARPE-19 EMT induced with TGF-beta and TNF-alpha06hr00minbiol_rep3
13667-147D4ARPE-19 EMT induced with TGF-beta and TNF-alpha07hr00minbiol_rep1
13668-147D5ARPE-19 EMT induced with TGF-beta and TNF-alpha07hr00minbiol_rep2
13669-147D6ARPE-19 EMT induced with TGF-beta and TNF-alpha07hr00minbiol_rep3
13670-147D7ARPE-19 EMT induced with TGF-beta and TNF-alpha08hr00minbiol_rep1
13671-147D8ARPE-19 EMT induced with TGF-beta and TNF-alpha08hr00minbiol_rep2
13672-147D9ARPE-19 EMT induced with TGF-beta and TNF-alpha08hr00minbiol_rep3
13674-147E2ARPE-19 EMT induced with TGF-beta and TNF-alpha12hr00minbiol_rep2
13675-147E3ARPE-19 EMT induced with TGF-beta and TNF-alpha12hr00minbiol_rep3
13676-147E4ARPE-19 EMT induced with TGF-beta and TNF-alpha16hr00minbiol_rep1
13677-147E5ARPE-19 EMT induced with TGF-beta and TNF-alpha16hr00minbiol_rep2
13678-147E6ARPE-19 EMT induced with TGF-beta and TNF-alpha16hr00minbiol_rep3
13679-147E7ARPE-19 EMT induced with TGF-beta and TNF-alpha24hr00minbiol_rep1
13681-147E9ARPE-19 EMT induced with TGF-beta and TNF-alpha24hr00minbiol_rep3
13682-147F1ARPE-19 EMT induced with TGF-beta and TNF-alpha42hr00minbiol_rep1
13683-147F2ARPE-19 EMT induced with TGF-beta and TNF-alpha42hr00minbiol_rep2
13684-147F3ARPE-19 EMT induced with TGF-beta and TNF-alpha42hr00minbiol_rep3
13685-147F4ARPE-19 EMT induced with TGF-beta and TNF-alpha60hr00minbiol_rep1
13686-147F5ARPE-19 EMT induced with TGF-beta and TNF-alpha60hr00minbiol_rep2
13687-147F6ARPE-19 EMT induced with TGF-beta and TNF-alpha60hr00minbiol_rep3
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