FAANG List Archived Post

From hzhou@ucdavis.edu  Wed Jan  6 23:30:40 2016
From: Huaijun Zhou <hzhou@ucdavis.edu>
Date: Wednesday, January 6, 2016 at 4:16 PM
Subject: Contribution to FAANG Sample collection
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 this Excel
file format (http://www.faang.org/docs/db/0046.xlsx) 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).

Agenda for FAANG Workshop at PAG: http://www.faang.org/docs/db/0046.pdf

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