Journal: Scientific Reports

Article Title: An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues

doi: 10.1038/s41598-020-77586-x

Figure Lengend Snippet: Extended gene catalogue features. ( a ) Expressions of the newly modelled genes compared to expression of the Ensembl genes and background noise, here given in the liver. The red line corresponds to the 0.1 TPM threshold. ( b ) Heatmap of the overlap between databases expressed in % of LNC (in line) shared among databases (in column), using 1 bp-or-more overlap. The number of LNC per database is mentioned in line. ( c ) The extended catalogue gathers 6.5 × more lncRNA genes and 1.1 × more PCG compared to Ensembl alone. ( d ) Correlation of LNC gene density to protein-coding gene density across the chicken macro-, medium- and micro-chromosomes. TPM: Transcript Per Million, chr: chromosome, Mb: Megabase.

Article Snippet: Since this work proposes a GTF build on the Ensembl v94 annotation in Gallus_gallus-5.0 genome coordinates, we also generated an extended version of the Ensembl v100 annotation of the new Gallus gallus genome reference ( GRCg6a ), comprising genes present in our present catalogue that did not overlap genes from the Ensembl v100 annotation.

Techniques: Expressing

Journal: BMC Genomics

Article Title: RNA-sequencing analysis of shell gland shows differences in gene expression profile at two time-points of eggshell formation in laying chickens

doi: 10.1186/s12864-019-5460-4

Figure Lengend Snippet: Putative functions of mRNA sequences that did not annotate to any known gene IDs during Ensembl annotations of RNA-Seq transcripts

Article Snippet: The Ensembl annotations (Gallus_gallus.Gallus_gallus-5.0.86.gtf) for genome were used as a guide.

Techniques: Sequencing, Binding Assay, Activity Assay, Ubiquitin Proteomics, Protein Binding