Raphaelle Momal-Leisenring
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View article: MOESM9 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM9 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 9 ATAC-seq peaks (coordinates, quantification, positional classification): the archive contains four folders, one for each species (bos_taurus, capra_hircus, gallus_gallus, sus_scrofa). Each folder contains the following si…
View article: MOESM4 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM4 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 4 Reference DE genes (all combinations): the archive contains four folders, one for each species (bos_taurus, capra_hircus, gallus_gallus, sus_scrofa). Each folder contains itself two subfolders, one for each model: diffcou…
View article: MOESM5 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM5 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 5 FR-AgENCODE genes and transcripts (structure, expression, positional and coding classes).• bos_taurus_cuff_tpm0.1_2sample_complete.gff• bos_taurus_cuff_tpm0.1_2sample_trid_4posclasses_3codingclasses_booleans.tsv• bos_taur…
View article: MOESM8 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM8 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 8 lncRNAs (information from FEELnc, orthology, structure, etc). Archive content:• bos_taurus.lncrna.TPM0.1in2samples.classif.tsv• capra_hircus.lncrna.TPM0.1in2samples.classif.tsv• ConservedLncRNABySynteny_73_19_6.xlsx• gall…
View article: MOESM11 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM11 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 11 Four livestock species ATAC-seq peak orthology.
View article: MOESM3 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM3 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 3 Orthologs between the 4 livestock species. We used Biomart to retrieve the 1 to 1 orthology relationships between chicken, pig and cattle and added goat via gene name. The human gene id is given for reference.
View article: MOESM2 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM2 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 2 Reference genes and transcripts (structure, expression) of the 4 species. Archive content:• bos_taurus.gtf• bos_taurus.refgn.tpm.tsv• capra_hircus.gtf• capra_hircus.refgn.tpm.tsv• gallus_gallus.gtf• gallus_gallus.refgn.tp…
View article: MOESM12 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM12 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 12 Hi-C TADs and A/B compartments: the archive contains three folders, one for each species (capra_hircus, gallus_gallus, sus_scrofa). Each folder contains the following two files:• compartments.bed• mat.40000.longest25chr.…
View article: MOESM6 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM6 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 6 Four livestock species FR-AgENCODE gene orthology.
View article: MOESM8 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM8 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 8 lncRNAs (information from FEELnc, orthology, structure, etc). Archive content:• bos_taurus.lncrna.TPM0.1in2samples.classif.tsv• capra_hircus.lncrna.TPM0.1in2samples.classif.tsv• ConservedLncRNABySynteny_73_19_6.xlsx• gall…
View article: MOESM7 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM7 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 7 FR-AgENCODE DE genes (all combinations). The archive has the same structure than de.refgn.tar.gz with names starting with cuffgenes instead of refgenes.
View article: MOESM10 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM10 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 10 DA ATAC-seq peaks (all combinations). The archive has the same structure as de.refgn.tar.gz with names starting with mergedpeaks.peaknb.allexp.readnb instead of refgenes.counts.min2tpm0.1.
View article: MOESM13 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM13 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 13 Three livestock species TAD boundary orthology.
View article: MOESM4 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM4 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 4 Reference DE genes (all combinations): the archive contains four folders, one for each species (bos_taurus, capra_hircus, gallus_gallus, sus_scrofa). Each folder contains itself two subfolders, one for each model: diffcou…
View article: MOESM9 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM9 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 9 ATAC-seq peaks (coordinates, quantification, positional classification): the archive contains four folders, one for each species (bos_taurus, capra_hircus, gallus_gallus, sus_scrofa). Each folder contains the following si…
View article: MOESM10 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM10 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 10 DA ATAC-seq peaks (all combinations). The archive has the same structure as de.refgn.tar.gz with names starting with mergedpeaks.peaknb.allexp.readnb instead of refgenes.counts.min2tpm0.1.
View article: MOESM13 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM13 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 13 Three livestock species TAD boundary orthology.
View article: MOESM2 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM2 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 2 Reference genes and transcripts (structure, expression) of the 4 species. Archive content: • bos_taurus.gtf • bos_taurus.refgn.tpm.tsv • capra_hircus.gtf • capra_hircus.refgn.tpm.tsv • gallus_gallus.gtf • gallus_gallus.re…
View article: MOESM12 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM12 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 12 Hi-C TADs and A/B compartments: the archive contains three folders, one for each species (capra_hircus, gallus_gallus, sus_scrofa). Each folder contains the following two files: • compartments.bed • mat.40000.longest25ch…
View article: MOESM3 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM3 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 3 Orthologs between the 4 livestock species. We used Biomart to retrieve the 1 to 1 orthology relationships between chicken, pig and cattle and added goat via gene name. The human gene id is given for reference.
View article: MOESM5 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM5 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 5 FR-AgENCODE genes and transcripts (structure, expression, positional and coding classes). • bos_taurus_cuff_tpm0.1_2sample_complete.gff • bos_taurus_cuff_tpm0.1_2sample_trid_4posclasses_3codingclasses_booleans.tsv • bos_t…
View article: MOESM7 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM7 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 7 FR-AgENCODE DE genes (all combinations). The archive has the same structure than de.refgn.tar.gz with names starting with cuffgenes instead of refgenes.
View article: MOESM11 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM11 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 11 Four livestock species ATAC-seq peak orthology.
View article: MOESM8 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM8 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 8 lncRNAs (information from FEELnc, orthology, structure, etc). Archive content: • bos_taurus.lncrna.TPM0.1in2samples.classif.tsv • capra_hircus.lncrna.TPM0.1in2samples.classif.tsv • ConservedLncRNABySynteny_73_19_6.xlsx • …
View article: MOESM6 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals
MOESM6 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals Open
Additional file 6 Four livestock species FR-AgENCODE gene orthology.
View article: Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig
Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig Open
Functional annotation of livestock genomes is a critical step to decipher the genotype-to-phenotype relationship underlying complex traits. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aims…
View article: Transcriptome and chromatin structure annotation of liver, CD4+ and CD8+ T cells from four livestock species
Transcriptome and chromatin structure annotation of liver, CD4+ and CD8+ T cells from four livestock species Open
Background Functional annotation of livestock genomes is a critical step to decipher the genotype-to-phenotype relationship underlying complex traits. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE p…