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Functional
Annotation of
ANimal
Genomes (FAANG) Project
— A coordinated international action to accelerate Genome to Phenome
|
FAANG List Archived Post
From miguel.perez@uab.cat Tue Jan 12 11:14:15 2016
Subject: Re: Contribution to FAANG Sample collection
From: miguel <miguel.perez@uab.cat>
Date: Tue, 12 Jan 2016 17:42:54 +0100
To: Multiple Recipients of FAANG <faang@animalgenome.org>
Dear Laura and colleagues, A few years ago, we carried out a comprehensive tissue sampling study in pigs, sampling 16 tissues, and these samples have been preserved at -80 since then. They are freely available for research purposes, if you feel they can be useful for this or other projects, I can ship them and introduce the record metadata in the website. I am not planning to work on them. Best wishes Miguel REFS Transcriptome architecture across tissues in the pig. Ferraz AL, Ojeda A, L�pez-B�jar M, Fernandes LT, Castell� A, Folch JM, P�rez-Enciso M. BMC Genomics. 2008 Apr 16;9:173. doi: 10.1186/1471-2164-9-173. Impact of breed and sex on porcine endocrine transcriptome: a bayesian biometrical analysis. P�rez-Enciso M, Ferraz AL, Ojeda A, L�pez-B�jar M. BMC Genomics. 2009 Feb 24;10:89. doi: 10.1186/1471-2164-10-89. On 16-01-07 01:16 PM, Laura Clarke wrote: > > 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: hzhou |
ucdavis.edu>>
http://animalscience.ucdavis.edu/faculty/Zhou
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>
>
--
===============================================================
Miguel Perez-Enciso
ICREA professor
Centre for Research in Agricultural Genomics (CRAG)
and Facultat de Veterinaria UAB
Campus Universitat Autonoma Barcelona
Bellaterra
E-08193 Spain
Tel: +34 935636600 ext 3346
Fax: +34 935636601
miguel.perez