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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 24, 2015 |
| Title |
A survey of imprinted gene expression in mouse trophoblast stem cells |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Several hundred mammalian genes are expressed preferentially from one parental allele due to a process called genomic imprinting. Genomic imprinting is particularly prevalent in extra-embryonic tissue, where it plays an essential role during development. Here, we profiled imprinted gene expression via RNA-Seq in a panel of six mouse trophoblast stem (TSC) lines, which are ex vivo derivatives of a progenitor population that gives rise to the placental tissue of the mouse. We found evidence of imprinted expression for 48 genes, 31 of which had previously been described as imprinted and 17 of which we suggest as candidate imprinted genes. An equal number of maternally and paternally biased genes were detected. Several genes showed variability in imprinted expression between the six TSC lines. Sixteen of the 48 known and candidate imprinted genes were previously or newly annotated noncoding RNAs, and six encoded for a total of 60 annotated microRNAs. Pyrosequencing across a panel of six TSC lines returned levels of imprinted expression that were concordant with RNA-Seq measurements for eight genes examined in all six independently derived TSC lines. Our results solidify TSCs as a cell culture-based experimental model to study genomic imprinting, and provide a quantitative foundation upon which to delineate mechanisms by which the process is maintained in the mouse.
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| Overall design |
RNA-Seq from F1 hybrid TSC lines generated from crosses between Cast and B6 mice.
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| Contributor(s) |
Calabrese JM |
| Citation(s) |
25711832 |
| Submission date |
Dec 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
J Mauro Calabrese |
| E-mail(s) |
jmcalabr@med.unc.edu
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| Phone |
919-843-3257
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| Organization name |
UNC-Chapel Hill
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| Department |
Pharmacology
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| Street address |
120 Mason Farm Road
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27516 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA269732 |
| SRA |
SRP050982 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE63968_RAW.tar |
2.3 Gb |
(http)(custom) |
TAR (of BED, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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