FAANG List Archived Post

From hzhou@ucdavis.edu  Wed Jan  6 18:21:16 2016
From: Huaijun Zhou <hzhou@ucdavis.edu>
Subject: Contribution to FAANG Sample collection
Date: Thu, 7 Jan 2016 00:16:11 +0000
To: Multiple Recipients of FAANG <faang@animalgenome.org>

Hi, FAANG Contributors and supporters,

Thank you for your interest in contributing to international FAANG effort!

In order to foster further collaborations and reduce redundant efforts among
FAANG community by fully utilizing the resource and expertise of each group,
FAANG Animal, Sample and Assay (ASA) Committee have compiled a large data
sheet including institutes, species, genetic line, tissues, assays, funding
status for current potential FAANG associated projects. If you are interested
in contributing to the FAANG, please send the information using attached file
format by January 31, 2016 (Please feel free to forward this email to other
groups who may not be aware of this effort). We are going to upload the
updated information on the FAANG website.



Also, during our recent ASA committee meeting,  we proposed the following
important FAANG sampling and assay guide and are planning to finalize it during
our FAANG Workshop at the PAG (Golden West at 6:10-8:20 pm on Monday). Please
join us for a great discussion. Refreshment and finger foods will be provided.
See attached agenda for the detail.

* The focus of FAANG is to functionally annotate regulatory elements of animal
genomes using representative core samples (adult stage + certain developmental
stage, genetic line etc.) with core assays (see white paper).Thus planning
multiple assays from the same tissue and the same individual is required
(L-shaped sample/assay matrix).

* Maximize the number of tissues obtained from an animal. This minimizes the
number of animals being sacrificed.

* Sample processing: Snap frozen tissues are easily collected and stored and
proven to work well for both RNA-seq (or RNALater) and most ChIP-seq assays.
DNase-seq or ATAC-seq and Hi-C traditionally require fresh tissues/cells, but
emerging data from the group indicate that these assays can be applied to
snap-frozen tissues as well.

* Combining multiple assays is required for a dataset to be qualified as a FAANG
dataset, which is heavily limited by funding availability. Member suggested
combination of RNA-seq with at least one ChIP-seq (see white paper) and/or other
open chromatin assay such as DNAase-seq, or ATAC-seq would be valuable.

* Missing assays should be planned adequately in each study design. Limitations
can be largely overcome by sample sharing and by collaborations set with ASA
partners who are expert for missing assays.

* Guidelines on minimum number of QC reads per assay per sample is required (this
will be coordinated with B&DA Committee). B&DA committee will provide updates on
this point at the FAANG workshop (at PAG).


Hope to meet most of you next Monday evening at Sunny San Diego!


Huaijun

**************************
Huaijun Zhou, Ph.D.
Associate Professor
Chancellor's Fellow
Department of Animal Science
2247 Meyer Hall, One Shield Avenue
University of California, Davis, 95616 CA
Phone: 530-752-1034
Lab: 530-207-3381
Fax: 530-752-0175
Email: hzhouucdavis.eduhttp://animalscience.ucdavis.edu/faculty/Zhou