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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 22, 2023 |
| Title |
ATAC Retinal ganglion cells, Ezh2 overexpression, replicate 2 |
| Sample type |
SRA |
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| Source name |
Retinal ganglion cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: Retinal ganglion cells
genotype: C57BL/6J
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| Treatment protocol |
AAV2-GFP, AAV-Ezh2, or AAV2-Ezh2-Y726D was injected into the vitreous body and the optic nerve was crushed after two weeks. Three days after the optic nerve crush, retinal ganglion cells were enriched from dissociated retinal cells by fluorescence-activated cell sorting.
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| Extracted molecule |
genomic DNA |
| Extraction 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).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Adapters of Illumina reads were removed with Cutadapt.
Pair-end ATAC-seq reads were mapped to the mouse reference genome (GRCm38) using Bowtie2 with default parameters.
Qualified properly paired reads (MAPQ score > 10) were assessed by SAMTools.
Duplicate reads were removed with MarkDuplicates function in Picard.
MACS2 was used to call peak regions of each sample
multiBamSummary function in deepTools was used to calculate read counts for all samples.
Assembly: GRCm38
Supplementary files format and content: narrow.Peak
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| Submission date |
Nov 08, 2023 |
| Last update date |
Dec 22, 2023 |
| Contact name |
Xuewei Wang |
| E-mail(s) |
xueweiwang@usf.edu
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| Phone |
8133960977
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| Organization name |
University of South Florida
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| Department |
Molecular Medicine
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| Lab |
Xuewei Wang
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| Street address |
4001 E Fletcher Ave, ALZ 339
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| City |
Tampa |
| State/province |
FL |
| ZIP/Postal code |
33613 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE247315 |
Histone methyltransferase Ezh2 coordinates mammalian axon regeneration via regulation of key regenerative pathways (ATAC-Seq) |
| GSE247320 |
Histone methyltransferase Ezh2 coordinates mammalian axon regeneration via regulation of key regenerative pathways |
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| Relations |
| BioSample |
SAMN38165549 |
| SRA |
SRX22428346 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7887089_Ezh2-2_peaks.narrowPeak.gz |
3.0 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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