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| Status |
Public on Jun 15, 2011 |
| Title |
Profiling of differential allelic expression in mouse placenta from reciprocal crosses |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Many questions about the regulation, functional specialization, computational prediction, and evolution of genomic imprinting would be better addressed by having an exhaustive genome-wide catalog of genes that display parent-of-origin differential expression. As a first-pass scan for novel imprinted genes, we performed mRNA-seq experiments on E17.5 mouse placenta cDNA samples from reciprocal cross F1 progeny of AKR and PWD mouse strains, and quantified the allele-specific expression and the degree of parent-of-origin effect transcriptome-wide. We confirmed the imprinting status of 23 known imprinted genes in the placenta, and found that 12 genes reported previously to be imprinted in other tissues are also imprinted in mouse placenta. Through a well-replicated design using an orthogonal technology, we verified five novel imprinted genes that are not known to be imprinted in mouse. It appears that most of the strongly imprinted genes have already been identified, at least in the placenta, and that evidence supports perhaps 100 additional weakly imprinted genes. Despite previous appearance that the placenta tends to display an excess of maternally-expressed imprinted genes, when the full set of genes is uniformly scored as in this study, this maternal bias disappeared.
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| Overall design |
Examine allelic expression in E17.5 placenta tissues from two individual samples, one from each of the two reciprocal crosses.
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| Contributor(s) |
Wang X, Clark A |
| Citation(s) |
21705755 |
| Submission date |
Jun 02, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew Clark |
| E-mail(s) |
ac347@cornell.edu
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| Organization name |
Cornell University
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| Street address |
227 Biotech Building
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| City |
Ithaca |
| ZIP/Postal code |
14853 |
| Country |
USA |
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| Platforms (1) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
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| Samples (2) |
| GSM736474 |
Mouse placenta RNAseq AKR/J mother x PWD/PhJ father PA |
| GSM736475 |
Mouse placenta RNAseq PWD/PhJ mother x AKR/J father AP |
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| Relations |
| SRA |
SRP006971 |
| BioProject |
PRJNA141109 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE29690_RAW.tar |
5.4 Gb |
(http)(custom) |
TAR (of SAM) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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