FR-AgENCODE · data & results

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Data

Samples

Biological samples of 40+ tissues are available from the 4 animals per species at the INRAE biobank CRB-Anim and registered at the EMBL-EBI BioSamples repository under the keyword « FR-AgENCODE ».

If you wish to perform some experimental assay on these tissue samples you can order them at the INRAE biobank. Just go to the CRB-Anim web portal and enter the keyword "FRAGENCODE" in the search box to browse the collection. A registration is required to request samples. Shipping fees are not covered.

Raw reads

Sequencing data for RNA-seq, ATAC-seq and Hi-C can be retrieved from the EMBL-EBI’s ENA using the keyword « FR-AgENCODE » or using the following identifiers:

RNA-seq: PRJEB27455
ATAC-seq: PRJEB27111
Hi-C: PRJEB27364

Metadata

Information about animals, samples, protocols and sequencing data is available at the FAANG Data Coordination Center (DCC) using the following identifiers:

RNA-seq: PRJEB27455
ATAC-seq: PRJEB27111
Hi-C: PRJEB27364

Results

To visualize the FR-AgENCODE data in the UCSC Genome Browser
Go to the UCSC browser, tab My Data // Track Hubs. Under the "My Hubs" tab, copy the URL "http://www.fragencode.org/mixhub/2018/hub.txt" and click on "Add Hub". You can now select the genome of your choice from the main page and browse normally.

RNA-seq ATAC-seq Hi-C

RNA-seq gene annotation and differential expression.
The FR-AgENCODE annotation is an extension of the ENSEMBL/NCBI gene model annotation. It describes the exon-intron structure of transcripts that have been identified from RNA-seq data with a minimum expression value of 0.1 TPM in at least 2 samples (file format= GFF2).
Genes with a significantly different expression between liver and T cells (model 2 from the manuscript) are also provided along with their TMM-normalized read counts (file format= BED, with field description in the corresponding index file).

Cattle (version UMD3.1): annotation file and differentially expressed genes (field index)
Goat (version CHIR_ARS1): annotation file and differentially expressed genes (field index)
Chicken (version GalGal5): annotation file and differentially expressed genes (field index)
Pig (version Sscrofa11.1): annotation file and differentially expressed genes (field index)

ATAC-seq peaks of chromatin accessibility.
ATAC-seq peaks of chromatin accessibility are provided for the 4 species in BED format along with the corresponding read counts from the different samples (description of each field in the index file). Peaks that are significantly more accessible in liver or T cells are provided along with their LOESS-normalized read counts (same index), fold-change and q-value (model 2 from the manuscript).

Cattle (version UMD3.1): all peaks with raw read counts (index)
Goat (version CHIR_ARS1): all peaks with raw read counts (index) and differentially accessible peaks (index)
Chicken (version GalGal5): all peaks with raw read counts (index) and differentially accessible peaks (index)
Pig (version Sscrofa11.1): all peaks with raw read counts (index) and differentially accessible peaks (index)

Hi-C interaction maps, TADs and A/B compartments.
Hi-C interaction map (contact matrix or heatmap) for each available species are provided at the 40Kb resolution (HiTC/HiC-Pro format: [bin1] [bin2] [raw_read_count]) along with the corresponding index file for the genomic bins (format: [chr] [beg] [end] [bin]). Armatus TADs and A/B compartments are provided in BED format.

Goat (version CHIR_ARS1): Hi-C matrix (index), TADs and A/B compartments (same index)
Chicken (version GalGal5): Hi-C matrix (index), TADs and A/B compartments (same index)
Pig (version Sscrofa11.1): Hi-C matrix (index), TADs and A/B compartments (same index)

Juicer ".hic" matrix files and arrowhead TADs are also available on request.

Publications

FR-AgENCODE main paper FAANG white paper GO-FAANG meeting report All publications and presentations

Multi-species annotation of transcriptome and chromatin structure in domesticated animals.
Foissac S, Djebali S, Munyard K, Vialaneix N, Rau A, Muret K, Esquerré D, Zytnicki M, Derrien T, Bardou P, Blanc F, Cabau C, Crisci E, Dhorne-Pollet S, Drouet F, Faraut T, Gonzalez I, Goubil A, Lacroix-Lamandé S, Laurent F, Marthey S, Marti-Marimon M, Momal-Leisenring R, Mompart F, Quéré P, Robelin D, Cristobal MS, Tosser-Klopp G, Vincent-Naulleau S, Fabre S, der Laan MP, Klopp C, Tixier-Boichard M, Acloque H, Lagarrigue S, Giuffra E.
BMC Biology volume 17(1), 108 (2019).
PMID: 31884969; PMCID: PMC6936065; DOI: 10.1186/s12915-019-0726-5

Published in Genome Biology, doi: 10.1186/s13059-015-0622-4.
Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project.
The FAANG Consortium, Leif Andersson, Alan L. Archibald, Cynthia D. Bottema, Rudiger Brauning, Shane C. Burgess, Dave W. Burt, Eduardo Casas, Hans H. Cheng, Laura Clarke, Christine Couldrey, Brian P. Dalrymple, Christine G. Elsik, Sylvain Foissac, Elisabetta Giuffra, Martien A. Groenen, Ben J. Hayes, LuSheng S. Huang, Hassan Khatib, James W. Kijas, Heebal Kim, Joan K. Lunney, Fiona M. McCarthy, John C. McEwan, Stephen Moore, Bindu Nanduri, Cedric Notredame, Yniv Palti, Graham S. Plastow, James M. Reecy, Gary A. Rohrer, Elena Sarropoulou, Carl J. Schmidt, Jeffrey Silverstein, Ross L. Tellam, Michele Tixier-Boichard, Gwenola Tosser-Klopp, Christopher K. Tuggle, Johanna Vilkki, Stephen N. White, Shuhong Zhao and Huaijun Zhou (2015).

Published in Animal Genetics, doi: 10.1111/age.12466.
GO‐FAANG meeting: a Gathering On Functional Annotation of Animal Genomes.
Christopher K. Tuggle, Elisabetta Giuffra, Stephen N. White, Laura Clarke, Huaijun Zhou, Pablo J. Ross, Hervé Acloque, James M. Reecy, Alan Archibald, Rebecca R. Bellone, Michèle Boichard, Amanda Chamberlain, Hans Cheng, Richard P.M.A. Crooijmans, Mary E. Delany, Carrie J. Finno, Martien A. M. Groenen, Ben Hayes, Joan K. Lunney, Jessica L. Petersen, Graham S. Plastow, Carl J. Schmidt, Jiuzhou Song, Mick Watson (2016).

FAANG publications.

Papers
Presentations
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