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SRX22428348: GSM7887091: ATAC Retinal ganglion cells, Ezh2-Y726D overexpression, replicate 1; Mus musculus; ATAC-seq
2 ILLUMINA (Illumina NovaSeq 6000) runs: 73.4M spots, 14.7G bases, 4.4Gb downloads

External Id: GSM7887091_r1
Submitted by: Xuewei Wang, Molecular Medicine, University of South Florida
Study: Histone methyltransferase Ezh2 coordinates mammalian axon regeneration via regulation of key regenerative pathways (ATAC-Seq)
show Abstracthide Abstract
Current treatments for neurodegenerative diseases and neural injuries fall short of success. One primary reason is that neurons in the mammalian central nervous system (CNS) lose their regeneration ability as they mature. Here, we investigated the role of Ezh2, a histone methyltransferase, in regulation of mammalian axon regeneration. We found that Ezh2 declined in the mouse nervous system during maturation but was upregulated in adult dorsal root ganglion neurons to support spontaneous axon regeneration following peripheral nerve injury. In addition, overexpression of Ezh2 in retinal ganglion cells in the CNS promoted optic nerve regeneration via both histone methylation-dependent and -independent mechanisms. Further investigation revealed that Ezh2 supported axon regeneration by systematically silencing the transcription of genes regulating synaptic function and inhibiting axon regeneration, while simultaneously activating various axon regeneration promoting factors. In particular, our study demonstrated that the GABA transporter 2 encoded by the gene Slc6a13 acted downstream of Ezh2 to control axon regeneration. Our study suggested that modulating chromatin accessibility was a promising strategy to promote CNS axon regeneration. Overall design: To study how Ezh2 and its mutant form Ezh2-Y726D support axon regeneration of retinal ganglion cells, we profiled the epigenetic changes in RGCs induced by Ezh2 or Ezh2-Y726D overexpression with RNA-seq. We intravitreally injected AAV2-GFP (control) or AAV2-Ezh2 and crushed the optic nerve after two weeks. Three days after the optic nerve crush, retinal ganglion cells were enriched from dissociated retinal cells.
Sample: ATAC Retinal ganglion cells, Ezh2-Y726D overexpression, replicate 1
SAMN38165547 • SRS19459893 • All experiments • All runs
Organism: Mus musculus
Library:
Name: GSM7887091
Instrument: Illumina NovaSeq 6000
Strategy: ATAC-seq
Source: GENOMIC
Selection: other
Layout: PAIRED
Construction protocol: 50,000 retinal ganglion cells were pelleted by centrifugation (500 g, 5 min, 4°C), washed with ice-cold PBS, pelleted again by centrifugation (500 g, 5 min, 4°C), and lysed in 50 μl ice-cold lysis buffer. Immediately after lysis, nuclei were pelleted by centrifugation (500 g, 10 min, 4°C), resuspended in 50 μl transposase reaction mix (Tagment DNA TDE1 Enzyme and Buffer Kits, Illumina 20034197) and incubated at 37°C for 30 min. After the transposition reaction, the product was purified with the DNA Clean & Concentrator-5 Kit (Zymo Research D4003). 20 μl tagmented DNA was PCR amplified with NEBNext High-Fidelity PCR Master mix (New England Biolabs M0541) and forward and reverse UDI primers. Amplification was first performed for 5 cycles, following which 5 μl of each partially amplified library was used to perform qPCR to determine the additional number of PCR cycles needed for each library. Final amplified libraries were purified using 1.1× Ampure XP bead purification (Beckman Coulter A63880).
Runs: 2 runs, 73.4M spots, 14.7G bases, 4.4Gb
Run# of Spots# of BasesSizePublished
SRR2672943827,765,0985.6G1.6Gb2023-12-22
SRR2672943945,683,6789.1G2.7Gb2023-12-22

ID:
30413780

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