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| Status |
Public on Jul 26, 2022 |
| Title |
RNA-Seq and ChIP-Seq gene profiling of retinal ganglion cells in Math5Cre-driven Knockout of Ezh2 and G9a in murine retinal ganglion cells at P0 |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Epigenetic mark deposition during embryonic development contribute to postnatal homeostasis and tissue stability. Previously, we found out that Ezh2 contributes critically to the function and postnatal cell survival in bipolar cells but not in retinal ganglion cells in the retina. (Yan et al. Postnatal onset of retinal degeneration by loss of embryonic Ezh2 repression of Six1. Sci Report. doi:10.1038/srep33887; (Cheng L, Wong LJ, Yan N, Han RC et al. Ezh2 does not mediate retinal ganglion cell homeostasis or their susceptibility to injury. PLoS One 2018;13(2):e0191853.). In this study, we used RNA-seq to define up- and down regulated genes in both Ezh2 and G9a deficient (Math5Cre; Ezh2f/fG9af/+; dKO) retinal ganglion cells (RGC) to evaluate the hypothesis of Ezh2 and G9a interaction that has been discussed in other tissues but in the retina. ChIP-Seq was applied to evaluate H3K27me3 histone marks in retinal ganglion cells in wild type (WT), Ezh2 (Math5Cre; Ezh2-/-, sKO) and combined G9a-Ezh2 (Math5Cre; G9a+/-Ezh2-/-, dKO) knockout mutant mice at P1.
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| Overall design |
mice pups (Math5Cre+;Ezh2f/fG9a+/- [dKO] or wild type [WT]) were sacrificed at P0 and the retina was harvested immediately. After enzymatic digestion, retinal ganglion cells (RGC) were purified from other retinal cells using magnetic labelling with anti-CD90-antibody which binds specifically to RGC. After elution, samples were immediately proceed to RNA extraction. We collected triplicates for each cell samples. Library was prepared with NEBNext Poly A, Sequencing was done with Mid-Output single read 75 cycles flow cell.
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| Contributor(s) |
Wong L |
| Citation missing |
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| Submission date |
Aug 26, 2019 |
| Last update date |
Jul 28, 2022 |
| Contact name |
Dong Feng Chen |
| Organization name |
Schepens Eye Research Institute
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| Street address |
20 Staniford St
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| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02114 |
| Country |
USA |
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| Platforms (2) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (30)
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| Relations |
| BioProject |
PRJNA562293 |
| SRA |
SRP219671 |
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