Similar protocols

Pipeline publication

[…] h sample was sequenced with between 2.3 million and 24.5 million read pairs. All read data are available using the project ID PRJEB16136. Code used for the analysis of these data are available at https://git.io/vPA09., The Rock Dove transcriptome assembly consists of 88,011 transcripts.This assembly, along with the annotations contained in gff3 format are available on dataDryad (doi:10.5061/dryad.1gk2p). The transcriptome contains 25,696 with at least 1 hit to the Pfam database, 46,854 hits to OrthoDB, 51,522 hits to Uniref90, 3,108 hits to the transporter database, and 452 hits to Rfam. These 88,011 assembled transcripts map to 15,102 unique genes in the Gallus genome. The evaluation using BUSCO and TransRate are presented in and respectively., Raw sequencing reads corresponding to individual samples of hypothalami, pituitary glands, and gonads were mapped to the Rock Dove reference HPG transcriptome using Salmon, which resulted in between 70% and 80% read mapping. These mapping data were imported into R and summarized into gene-level counts using tximport, after which, edgeR was used to generate normalized estimates of gene expression. Patterns of transcript-expression overlap are presented in . Of the 15,102 genes expressed in the HPG, 7,529 are expressed in all tissues (median CPM >10–). A total of 746 transcripts are expressed in the ovary, hypothalamus, and pituitary, 732 are expressed uniquely in the testes, 529 uniquely in ovary, 418 uniquely in the hypothalamus, and 230 uniquely in the pituitary. Dyads (genes expressed uniquely in pairs of tissues) follow an expected pattern, with the number of genes expressed uniquely in the gonads (testes and ovary) being more than the number of genes expressed uniquely in the pituitary and hypothalamus, follow […]

Pipeline specifications

Software tools BUSCO, TransRate, tximport, edgeR
Databases OrthoDB
Organisms Columba livia
Diseases Central Nervous System Neoplasms, Nervous System Neoplasms, Brain Diseases