Retinal pigment mesenchyme transition

Editing Retinal pigment mesenchyme transition

Time course ID: human_ARPE-19
Sample provider: Soichi Ogishima, Hiroshi Tanaka, Ken Miyaguchi, Afsaneh Eslami

Samples

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.

Quality control

https://fantom5-collaboration.gsc.riken.jp/webdav/home/arner/timecourse/time_course_main_paper_freeze_feb2013/qc_release_130226/human_ARPE-19/

References

[1] Tumor necrosis factor-alpha regulates transforming growth factor-beta-dependent epithelial-mesenchymal transition by promoting hyaluronan-CD44-moesin interaction. Takahachi E et al, J Biol Chem, 2010, 285(6):4060-73. PMID:19965872

[2] Epithelial-mesenchymal transitions in development and disease, Thiery JP et al, Cell, 2009, 139(5):871–890. PMID:19945376

Data

Expression profiles

• Gene and CAGE cluster expression for the retinal epithelium series
• https://fantom5-collaboration.gsc.riken.jp/webdav/home/arner/timecourse/time_course_main_paper_freeze_feb2013/qc_release_130226/human_ARPE-19/expression_tables/

Zenbu configuration and status

• • ARPE-19
  • ARPE-19 timecourse - update Oct 26th

MARA based network results

MARA

• https://fantom5-collaboration.gsc.riken.jp/webdav/home/arner/timecourse/time_course_main_paper_freeze_feb2013/qc_release_130226/human_ARPE-19/mara/

ISMARA analysis results

All samples: http://ismara.unibas.ch/timecourses/retinal_pigment_EMT/ismara_report/index.html

Replicate averaged: http://ismara.unibas.ch/timecourses/ARPE19-avgd/averaged_report/index.html

For more information, see ISMARA.