FAANG List Archived Post

From laura@ebi.ac.uk  Thu Jan  7 08:34:58 2016
Subject: Re: Contribution to FAANG Sample collection
From: Laura Clarke <laura@ebi.ac.uk>
Date: Thu, 7 Jan 2016 12:16:36 +0000
To: Multiple Recipients of FAANG <faang@animalgenome.org>

Hello

Seeing more samples available for FAANG experiments will be great.

I just wanted to add that the FAANG metadata and data sharing group is
establishing standards about the metadata which needs to be collected
for sample records.

You can see our standards here

https://github.com/FAANG/faang-metadata/blob/master/docs/faang_sample_metadata.md


We welcome feedback.

All FAANG samples will need to have the required fields in this standard
associated with them. We have not finalised the standard yet so if there
is anything you feel is missing or too difficult to record please let us
know.

Looking forward to catching up with everyone at PAG

thanks

Laura

On 1/6/16 4:16 PM, Huaijun Zhou wrote:

>
> 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/46.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/46.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.edu>
http://animalscience.ucdavis.edu/faculty/Zhou