ZENBU Config
ZENBU
Top page of the ZENBU instance for FANTOM5
Release Notes
In this page we are listing all the most common ZENBU configurations, by species. Our list is not comprehensive, for the use-cases being way too many, but it provides a good quick-start view. We will maintain those configurations and will update them when new libraries are loaded into the system.
- April 25 2012
Mouse and human configurations are updated. Timecourse samples for rinderpest experiments, stellate cells are added.
- March 15 2012
The main configuration view for pooled human + pooled freeze samples is updated to display RNA-Seq data.
- October 31st 2012
Creating a track with your favorite experiments pool coolated onto Phase2 clusters
Relevant configurations for the FANTOM5
Configuration Updates
Due to the nature of the ZENBU system, the url to the configurations are subject to changes and updates. Here are some ways to make your life -and ours- easier. Please,have a look at the following ways to bookmark your configurations:
Link to the base configuration
Just save the url of your interest. If you modify that configuration and want to save the changes, you must remember to save it and bookmark it to point to your just updated verson.
We are following some simple naming conventions in order to use the '#configbase' type of search. For this reason we kindly ask you to RENAME completely the configurations you modify for your own research before saving them, in a way that doesn't interfere with our conventional names.
Use the search box in zenbu
Type some key words in the search box from gLyphs, and if some configuration title or description matches your search term, zenbu will display a list of available configurations.
Content of ZENBU
The browser contains all the most common annotation data, such as gene models (RefSeq, Gencode,CCDS,etc), repeats, gaps, SNP, EST, miRNA and others for all the 5 species we use in FANTOM5. Please, browse the annotation from dex to have a complete view of the data annotation.
The expression data is at the CTSS level (CAGE Transcription Start Site), and both tag counts and TPM expression is available. Default views are based on TPM.
Configurations already present in the browser are solely for convenience purposes, so we encourage you to create your own configurations, if the basic ones we provide don't fit your needs. Anyway, we have prepared some standard views, where we group experiments for the same species, or, within one specie, for the same RNA type or category. Here follows a list of the most recent configurations created by us.
human
- F5 human + freeze pooled
- F5 human full 1+2
- F5 human tissues pooled
- F5 human cell lines pooled
- F5 human primary cells pooled
- F5 human fractionation pooled
- F5 human time course pooled
- Time course set configurations
- Adipocyte differentiation
- H9 Embryonic Stem cells to melanocyte
- K562 erythroblastic leukemia response to hemin
- Saos-2 osteosarcoma treated with ascorbic acid and BGP
- Monocyte-derived macrophages response to influenza
- Monocyte-derived macrophages response to LPS
- MCF7 breast cancer
- Lymphatic Endothelial cells response to VEGFC
- Aortic smooth muscle cell
- Mesenchymal stem cells adipose derived
- HES3-GFP Embryonic stem cells to cardiomyocyte
- iPS differentiation to neurons
- hIPS
- Myoblast differentiation to myotubes
- H1 embryonic Stem cells to CD34+
- Rinderpest series
- ARPE-19 series
mouse
- F5 mouse + freeze pooled
- F5 mouse full 1+2
- F5 mouse tissues pooled
- F5 mouse primary cells pooled
- F5 mouse cell lines
- F5 mouse time course pooled
- Time course set configurations
rat
dog
chicken
- F5 chicken galgal3 pooled
- F5 galGal4 chicken pooled
- Time course set configurations
macaque
others
NOTE : the human pooled+freeze configuration already displays all the ncRNA, (new)small RNA, RNA-Seq tracks as default. A warm recommendation is to refer to that one as the latest updated.
