Mouse genome browser track hub

 
tracks

Maps of PRC2 recruitment

A track data hub has been generated providing access to Veenstra lab chromatin state maps of mouse embryonic stem cells (wild type and mutant lines, treatment with EED inhibitor EED226). The data include ChIP-sequencing tracks of histone modifications (H3K4me3, H3K27me3) and Polycomb Repressive Complex (PRC1 and PRC2) subunits (EZH2, MTF2, JARID2, RNF2).


(Click for larger image)




Track hub instructions

The data can be browsed using a track data hub for the UCSC browser. Do the following to use this track hub:

  1. Visit the UCSC genome browser (mm10)
  2. Click the button "track hubs"
  3. Select the tab "My Hubs"
  4. Copy-paste the following URL in the text box:
    https://trackhub.science.ru.nl/hubs/veenstralab/trackhubs_public/mus.musculus/hub.txt
  5. Click "Add Hub"
  6. The newly added trackhub and its corresponding genome should be the default in the Genome Browser Gateway (home) page of the UCSC browser.
  7. If the track hub is not selected, or to select the trackhub again among previously loaded trackhubs: In the genome browser, click the top menu item "Genomes" to go to the Genome Browser Gateway page. To the left, under "Represented speces" the track hub "G.J.Veenstra mm10 trackhub" should be listed. Click it to select the trackhub.
  8. Click "Go" to move to a position in the genome.
  9. Browse the genome or modify track settings (right click on the track, or use track controls under main graphic)
The track hub contains data for the following genome assemblies:

Track data hub publications

Perino M., G. van Mierlo, I.D. Karemaker, S. van Genesen, M. Vermeulen, H. Marks, S.J. van Heeringen, G.J.C. Veenstra. 2018. MTF2 recruits Polycomb Repressive Complex 2 by helical shape-selective DNA binding. Nature Genetics, 2018/05/29 (doi: 10.1038/s41588-018-0134-8).
www Nature Genetics          download Springer Nature SharedIt Online access          data NCBI GSE GSE94300          tracks UCSC track hub
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Perino M., G. van Mierlo, C. Loh, S.M.T. Wardle, H. Marks, G.J.C. Veenstra. 2020. Two functional axes of feedback-enforced PRC2 recruitment in mouse embryonic stem cells. Stem Cell Reports, advance online. (doi: 10.1016/j.stemcr.2020.07.007).
www Stem Cell Reports          download PDF          data NCBI GSE133085          tracks UCSC track hub
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Radboud University Faculty of Science Radboud Institute for Molecular Life Sciences Dept. Molecular Developmental Biology