| description |
We collected (Illumina) RNA-seq data (polyadenylated RNA fraction) for a number of tissue samples from common marmoset and elephant. We developed a subtraction approach based on male/female RNA-seq data, Illumina genomic data and available genomes to identify and assemble Y transcripts.For marmoset samples, we added Y coding genes and noncoding sequences to the reference genomes in order to assess their expression levels. We then mapped all RNA-seq reads with TopHat 1.4.0 and used Cufflinks 2.0.0 (all mapped reads, embedded multi-read and fragment bias correction) to calculate the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for all genes in the genomes with our refined annotations.Overall design: Sequence and expression levels of reconstructed Y-linked genes |