|
| Status |
Public on Dec 22, 2023 |
| Title |
RRBS Retinal ganglion cells, GFP overexpression, uninjured, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Retinal ganglion cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Retinal ganglion cells
genotype: C57BL/6J
|
| Treatment protocol |
AAV2-GFP, AAV2-Ezh2, or AAV2-Ezh2-Y726D was injected into the vitreous body and the optic nerve was crushed after two weeks. Uninjured groups only received AAV2 injection but did not undergo optic nerve crush. Three days after the optic nerve crush (injured groups) or 17 days after AAV2 injection (uninjured groups), retinal ganglion cells were enriched from dissociated retinal cells.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from retinal ganglion cells using the Quick-DNA Microprep Plus Kit (Zymo Research D4074) following the manufacture’s manual.
RRBS library preparation and sequencing were done by Zymo Research. Briefly, 10 ng genomic DNA was digested with 30 units of MspI. Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine according to Illumina’s specified guidelines. Adaptor-ligated fragments ≥ 50 bp in size were recovered using the DNA Clean & Concentrator-5 Kit (Zymo Research D4003). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning Kit (Zymo Research D5030). Preparative-scale PCR was performed, and the product was purified with the DNA Clean & Concentrator-5 Kit (Zymo Research D4003).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing reads from bisulfite-treated classic RRBS libraries were identified using standard Illumina base calling software.
Raw FASTQ files were adapter, filled-in nucleotides, and quality trimmed using TrimGalore 0.6.4.
Alignment to the mouse reference genome (GRCm38) was performed using Bismark 0.19.0.
Methylated and unmethylated read totals for each CpG site were called using MethylDackel 0.5.0.
Assembly: GRCm38
Supplementary files format and content: Files containing DNA methylation tracks for each library
|
| |
|
| Submission date |
Nov 08, 2023 |
| Last update date |
Dec 22, 2023 |
| Contact name |
Xuewei Wang |
| E-mail(s) |
xueweiwang@usf.edu
|
| Phone |
8133960977
|
| Organization name |
University of South Florida
|
| Department |
Molecular Medicine
|
| Lab |
Xuewei Wang
|
| Street address |
4001 E Fletcher Ave, ALZ 339
|
| City |
Tampa |
| State/province |
FL |
| ZIP/Postal code |
33613 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE247319 |
Histone methyltransferase Ezh2 coordinates mammalian axon regeneration via regulation of key regenerative pathways (RRBS) |
| GSE247320 |
Histone methyltransferase Ezh2 coordinates mammalian axon regeneration via regulation of key regenerative pathways |
|
| Relations |
| BioSample |
SAMN38167484 |
| SRA |
SRX22443473 |
