FANTOM5 overview
FANTOM5 – five dimensions of cellular identity
Welcome to the FANTOM5 collaborator website. For those new to the FANTOM collaboration, please take some time to read the introductory material below. FANTOM is an international consortium coordinated from RIKEN Omics Science Center, Yokohama Japan.
Overview
The FANTOM5 project is built on our previous experiences in FANTOM3 and 4. In FANTOM3 Cap Analysis of Gene Expression of RNA from various mouse tissues was used to build up a picture of mammalian promoters in terms of tissue restriction, conservation and structure (http://fantom3.gsc.riken.jp/f3papers.html). In FANTOM4 we focused our study on a single cellular model and followed the differentiation of THP-1 cells from a monoblastic suspension culture phenotype to an attached monocytic phenotype (http://fantom.gsc.riken.jp/4/publications/). With this we built a transcriptional network model that identified putative key factors responsible for maintaining the two end states and for regulating state transition.
In FANTOM5 we are expanding the efforts made in FANTOM3 and 4 and aim to generate both a map of the majority of human promoters and comparative models of transcriptional regulatory network models of each cellular state. To achieve this we are carrying out deepCAGE sequencing on the Heliscope true single molecule sequencer on RNA isolated from every major human organ, over 200 cancer cell lines, 30 time courses of cellular differentiation, mouse developmental time courses and over 200 primary cell types File:WP1 overview.pdf.
The project has been broken into two phases. Broadly the first phase targets steady states while the second is focused on time course analyses.
Phase I: (Meeting in February 2011)
Phase I will generate two main papers on steady states. The first aims to define the global mammalian promoterome File:Paper1 overview.pdf, the second focuses on conservation of transcriptional regulatory networks between individuals, tissue locations and across species File:Paper4 overview.pdf. We aim to have the data for both papers collected by the end of December 2010, although preliminary data will be available from October. The first FANTOM5 meeting is scheduled for the last week of February and will aim to complete a draft of both manuscripts. It will also allow collaborators an opportunity to discuss satellite paper analyses and publication strategy.
Human primary cells:
The bulk of the primary cell material has been purchased from commercial sources while the remaining cell samples have been obtained through FANTOM5 material provider collaborators with ethical clearance. For each cell type 3 separate donors (where possible) are used so to capture the shared network rather than an individual specific picture. RNAs for every major human organ (and subsections) will be profiled to recover promoters missed in primary cell samples (either due to specific cell lineages missed in our collection, or due to intact tissue dependent expression that is absent in homogenous cell cultures). In addition cancer cell lines for up to 200 different cancer subtypes will be profiled to extend our collection of promoters and where possible 3 representatives of each cancer subtype will be used. The cell lines and tissues will only be sequenced once.
Role of mouse samples:
A set of 30 mouse primary cell types for which we have human counterparts have been purchased. These will be used to look at promoter conservation and also to estimate how much we can use mouse data to fill in gaps in the human promoterome. For some more rare cell types (eg. inner ear hair cells, paneth cells) we have been unable to obtain human samples so are using mouse cells instead and will aim to use this data to find the human counterpart network and promoterome.
Cross species set for network conservation:
For Human, Mouse, Rat, Dog and Chicken a set of three anatomically conserved cell types have been obtained for studying conservation of the regulatory network across species. Aortic smooth muscle cells, hepatocytes and bone marrow derived mesenchymal stem cells have been chosen for this analysis. In addition “Universal RNA” for each species has been sequenced to generate a broad overview of promoters in each species.
Phase II: (Meeting in October 2011)
The second phase is focused on time courses of differentiation. A few of the time courses will have been sequenced in time for the February meeting and can be used for method development and discussion, however the majority of time course data production will not be completed until the middle of 2011. Therefore the February meeting can be used for strategy discussions, while the October meeting should complete these analyses and draft the manuscripts. There are two classes of differentiations considered in FANTOM5. The first is stem (mainly ES) to differentiated cell. These experimental differentiations typically occur over several days or weeks and may involve multiple media changes, growth factors and selection. The second is progenitor to differentiated cell types with a focus on the immediate early gene response. The time points over the first 8 hours for the immediate early gene response series are kept constant, time points after 8 hours can vary from differentiation to differentiation.
Satellite strategy
Papers are broadly classified as Main or satellite. If a satellite is of high enough quality it can be promoted to a main paper. There are many options for satellite papers. Eg.
- Collaborator provides a particular cell type, writes small satellite on the transcriptome/promoterome relative to other cell types
- Combined satellite involving multiple collaborators – eg. all stem cell researchers combine their data for a stem cell focused paper. Or sample provider needs bioinformatics help.
- Gene family/pathway analyses
- Network analyses
- Conservation analyses
- Etc…
We would like to keep this as flexible as possible, to encourage multiple collaborators generating satellites. Mailing lists focused on subgroups such as (stem cells, cancer, adipogenesis, ncRNAs, alternative promoters etc. will be generated as requested to encourage online discussion). Please remember this is a collaborative effort and as much as possible we want to avoid duplicated work. When duplication becomes a problem we will ask both parties to discuss either combining manuscripts or agreeing on an approach where both parties can publish different aspects. We also ask all collaborators to list up their potential satellite papers on the website by adding them to the satellite paper category so that we can avoid duplicated efforts.
Of special mention regarding network predictions and transcription factor binding site predictions. Different approaches have different merits we would like all working in this area to generate a manuscript and for their efforts to appear in the final resource.
Work packages
Core tasks in the FANTOM5 are split into the following working packages
- WP1 (sample collection, led by Alistair Forrest) File:WP1 overview.pdf
- WP2 (data production, by Jun Kawai) WP2_overview
- WP3 (technology development, by Piero Carninci)
- WP4 (data control, by Hideya Kawaji) WP4_overview
- WP5 (data analysis and integration, by Carsten Daub) WP5_overview
- WP6+7 (cell biology and validation, by Harukazu Suzuki) File:WP6+7 overview.pdf
The WP leaders consisting of WP9, which decide strategy and take care management issue.
Archive of FANTOM5 Mailing List
By clicking on the link below you can download a zip folder containing all emails sent to the FANTOM5 Mailing list (fantom5@gsc.riken.jp) since the start. The link will be updated every Monday. If you have any difficulties, please contact fantom5-secretariat@gsc.riken.jp.
Mailing List Archive:
File:Archeve fantom5 ML 07Oct.zip
