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| Status |
Public on Jul 29, 2014 |
| Title |
RNA Seq analysis of Mefs Isolated from STC1+/+ and STC1-/- mice |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Evaluation of X-linked gene expression in MEFs isolated from STC1 wild type and knock out mice
X chromosome inactivation (XCI) is initiated in cis by the Xist RNA, which coats the inactive X chromosome (Xi) from which it is produced. We performed a large-scale RNA interference screen to identify trans-acting XCI factors (XCIFs) that comprise regulators of cell signaling and transcription. We find that the XCIFs promote Xist expression and/or localization to the Xi. One of the XCIFs, STC1, is a glycoprotein found in both the cytoplasm and nucleus and whose function is poorly understood. A homozygous mouse knockout of STC1 has a defect in XCI but surprisingly is phenotypically normal. We performed transcriptome profiling (RNA-Seq) experiments to determine whether the expression levels of X-encoded genes were elevated in Stc1-/- female MEFs. In these experiments, RNA was prepared from three independent cultures of Stc1+/+ or Stc1-/- female MEFs. RNA samples were processed and amplified followed by deep sequencing. The similarity of X-linked gene expression between Stc1+/+ and Stc1-/- MEFs was statistically significant. The vast majority of autosomal genes were also expressed at comparable levels in Stc1+/+ and Stc1-/- MEFs.
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| Overall design |
Sequenced mRNA isolated from the STC1+/+ or STC1-/- MEFs.
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| Contributor(s) |
Bhatnagar S, Green MR, Lin L |
| Citation(s) |
25136103 |
| |
| Submission date |
May 27, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Sanchita Bhatnagar |
| Organization name |
University of California Davis
|
| Department |
Medical Microbiology and Immunology
|
| Lab |
Sanchita Bhatnagar Lab
|
| Street address |
1275 Health Sciences, Tupper Hall 3134
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA205462 |
| SRA |
SRP023177 |
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