Epithelial to mesenchymal: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
No edit summary |
||
| (2 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
{{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. | |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=' | |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=' | |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 | |category_treatment=Differentiation | ||
| Line 14: | Line 14: | ||
|series=IN_VITRO DIFFERENTIATION SERIES | |series=IN_VITRO DIFFERENTIATION SERIES | ||
|species=Human (Homo sapiens) | |species=Human (Homo sapiens) | ||
|tet_config= | |tet_config=https://fantom.gsc.riken.jp/5/suppl/tet/ARPE_19.tsv.gz | ||
|tet_file= | |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 | ||
|time_points=0hr | |time_points=0hr | ||
|time_span=60 hours | |time_span=60 hours | ||
|timepoint_design=Early focus | |timepoint_design=Early focus | ||
|tissue_cell_type=Epithelial>>mesenchymal cells | |tissue_cell_type=Epithelial>>mesenchymal cells | ||
|zenbu_config= | |zenbu_config=https://fantom.gsc.riken.jp/zenbu/gLyphs/#config=ZkZynoPyAxHvl3-uzxZ27B | ||
}} | }} | ||
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. |
| Quality control |
|---|
|
|
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
| 13625-146H7 | 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 |
