Transcriptomics

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Origins and functional evolution of Y chromosome gene repertoires across the class Mammalia


ABSTRACT: 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.

ORGANISM(S): Callithrix jacchus Rattus norvegicus Notamacropus eugenii Loxodonta africana

PROVIDER: GSE50747 | GEO | 2014/04/15

SECONDARY ACCESSION(S): PRJNA218629

REPOSITORIES: GEO

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