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| Status |
Public on Apr 15, 2014 |
| Title |
Origins and functional evolution of Y chromosome gene repertoires across the class Mammalia |
| Organisms |
Notamacropus eugenii; Callithrix jacchus; Loxodonta africana; Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
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.
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| |
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| Overall design |
Sequence and expression levels of reconstructed Y-linked genes
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| |
|
| Contributor(s) |
Cortez D, Marin R, Froidevaux L, Liechti A, Waters PD, Grützner F, Kaessmann H |
| Citation(s) |
24759410 |
| Submission date |
Sep 10, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Diego Cortez |
| E-mail(s) |
diegoclaudio.cortezquezada@unil.ch
|
| Organization name |
Univerity of Lausanne - CIG
|
| Street address |
Rue de Lausanne
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| Platforms (6)
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| GPL14844 |
Illumina HiSeq 2000 (Rattus norvegicus) |
| GPL17712 |
Illumina HiSeq 2000 (Callithrix jacchus) |
| GPL17713 |
Illumina Genome Analyzer IIx (Callithrix jacchus) |
| GPL17714 |
Illumina Genome Analyzer IIx (Loxodonta africana) |
| GPL18016 |
Illumina HiSeq 2000 (Loxodonta africana) |
| GPL18017 |
Illumina HiSeq 2000 (Macropus eugenii) |
|
| Samples (31)
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| Relations |
| BioProject |
PRJNA218629 |
| SRA |
SRP029760 |
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