Computational protocol: Evidence for independent evolution of functional progesterone withdrawal in primates and guinea pigs

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Protocol publication

[…] RNA library preparation and high-throughput sequencing were performed on an Illumina HiSeq 2000 sequencing system following the protocol recommended by Illumina for sequencing total RNA samples. Sequencing was done for each biological replicates at 1 × 75 bp strand specific by the Yale Center for Genome Analysis. Sequence reads were aligned to the Cavia porcellus reference genome (cavPor3.69) using the splice junction mapper for RNA-seq reads TopHat2 []. Sequencing depth for RNA-seq samples averaged 45 million reads per biological sample with >80% overall alignment rate. After alignment, read counts were determined with HTSeq-count v0.5.4p1 as described by the authors. All RNA-seq data are deposited in GEO under accession number GSE47986. […]

Pipeline specifications

Software tools TopHat, HTSeq
Application RNA-seq analysis
Organisms Cavia porcellus, Homo sapiens
Diseases Abnormalities, Drug-Induced
Chemicals Estrogens, Progesterone