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Naji, M. |
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Motta, Antonella |
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Aletan, Dirar |
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Mohamed, Tarek |
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Ertürk, Emre |
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Taccardi, Nicola |
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Kononenko, Denys |
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Petrov, R. H. | Madrid |
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Alshaaer, Mazen | Brussels |
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Bih, L. |
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Casati, R. |
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Muller, Hermance |
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Kočí, Jan | Prague |
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Šuljagić, Marija |
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Kalteremidou, Kalliopi-Artemi | Brussels |
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Azam, Siraj |
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Ospanova, Alyiya |
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Blanpain, Bart |
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Ali, M. A. |
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Popa, V. |
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Rančić, M. |
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Ollier, Nadège |
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Azevedo, Nuno Monteiro |
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Landes, Michael |
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Rignanese, Gian-Marco |
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González, Ignacio
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Publications (4/4 displayed)
- 2017Profiling the landscape of transcription, chromatin accessibility and chromosome conformation of cattle, pig, chicken and goat genomes [FAANG pilot project]
- 2017Profiling the landscape of transcription, chromatin accessibility and chromosome conformation of cattle, pig, chicken and goat genomes [FAANG pilot project]
- 2002Electrochemical deposition of silver and gold from cyanide leaching solutionscitations
- 2002Electrochemical recovery of silver from cyanide leaching solutionscitations
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document
Profiling the landscape of transcription, chromatin accessibility and chromosome conformation of cattle, pig, chicken and goat genomes [FAANG pilot project]
Abstract
Functional annotation of livestock genomes is a critical and obvious next step to derive maximum benefit for agriculture, animal science, animal welfare and human health. The aim of the Fr-AgENCODEprojectistogeneratemulti-speciesfunctionalgenomeannotationsbyapplyinghigh-throughputmolecularassaysonthree target tissues/cells relevant to the study of immune and metabolic traits. An extensive collection of stored samples from other tissues isavailableforfurtheruse(FAANGBiosamples‘FR-AGENCODE’).Fromeachoftwomalesandtwofemalesperspecies (pig, cattle, goat, chicken), strand-oriented RNA-seq and chromatinaccessibilityATAC-seqassayswereperformedonlivertissue and on two T-cell types (CD3+CD4+&CD3+CD8+)sorted from blood (mammals) or spleen (chicken). Chromosome Conformation Capture(insitu Hi-C)wasalsocarried out on liver. Sequencingreads from the 3 assays were processed using standard processing pipelines. While most (50–70%) RNA-seq reads mapped to annotated exons, thousands of novel transcripts and genes were found, includingextensionsofannotatedprotein-codinggenesandnewlncRNAs (see abstract #69857). Consistency of ATAC-seq results was confirmed by the significant proportion of called peaks in promoter regions (36–66%) and by the specific accumulation pattern ofpeaksaroundgenestarts(TSS)v. gene ends (TTS). Principal Component Analyses for RNA-seq (based on quantified gene expression) and ATAC-seq (based on quantified chromatin accessibility)highlightedclusterscharacterisedbycelltypeandsexinallspecies. From Hi-C data, we generated 40kb-resolution interactionmaps, profiled a genome-wide Directionality Index and identifiedfrom 4,100 (chicken) to 12,100 (pig) topologically-associating do- mains (TADs). Correlations were reported between RNA-seq andATAC-seq results (see abstract #71581). In summary, we presenthere an overview of the first multi-species and -tissue annotations of chromatin accessibility and genome architecture related to geneexpression for farm animals.