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| Status |
Public on Jul 03, 2018 |
| Title |
Gene expression profiling in Dis3l2-null and wild-type nephron progenitor cells |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: Loss of DIS3L2 in humans is associated with congenital overgrowth in Perlman syndrome, as well as with the development of Wilms tumors. DIS3L2 is an exoribonuclease with a demonstrated preference for 3’-uridylated RNA substrates. However, its targets relevant to human disease are poorly understood. Our goal was to address transcriptomic changes in DIS3L2 deficient mouse nephron progenitor cells, a cell type of the developing kidney with demonstrated relevance to Wilms tumorigenesis.
Methods: RNA-seq libraries were prepared using the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina) and sequenced using 50 base pair single-end reads on an Illumia HiSeq2500 at the McDermott Center Next Generation Sequencing core at UT Southwestern. Samples were 2 biological replicates of wild-type and 3 of Dis3l2-null from embryos of the same litter.
Results: Upregulated genes included replication-dependent histone mRNA and small non-coding Polymerase III transcripts, as expected from previous reports, as well as Igf2, a gene that has not previously been established to be regulated by DIS3L2 and whose upregulation is associated with overgrowth and Wilms tumor development.
Conclusions: These data implicate Igf2 as a promising candidate for the overgrowth and Wilms tumorigenesis observed in DIS3L2-deficient disease states.
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| Overall design |
Gene expression profiles of Dis3l2 null or wild-type primary nephron progenitor cells were determined by RNA-seq.
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| Contributor(s) |
Hunter RW, Liu Y, Manjunath H, Acharya A, Jones BT, Zhang H, Chen B, Ramalingam H, Hammer RE, Xie Y, Richardson JA, Rakheja D, Carroll TJ, Mendell JT |
| Citation(s) |
29950491 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R35 CA197311 |
The intersection of RNA biology and tumor biology |
UT SOUTHWESTERN MEDICAL CENTER |
Joshua T Mendell |
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| |
| Submission date |
May 19, 2018 |
| Last update date |
Mar 21, 2019 |
| Contact name |
Joshua Mendell |
| Organization name |
UT Southwestern Medical Center Dallas
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| Department |
Molecular Biology
|
| Street address |
5323 Harry Hines Boulevard
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-9148 |
| Country |
USA |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (5)
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| Relations |
| BioProject |
PRJNA472143 |
| SRA |
SRP148489 |
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