|
| Status |
Public on Oct 16, 2024 |
| Title |
Non-targeting gRNA 25, 7 Day Treatment; Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Neurons
|
| Organism |
Mus musculus |
| Characteristics |
experiment type: in vitro
developmental stage: E15.5 (gestational day 15.5)
cell type: Neurons
strain: C57BL/6J
agent: None
viral day: 7
|
| Treatment protocol |
Neurons were transduced with NmCas9-AAV-gRNA or with SaCas9-AAV-gRNA virus on day-in-vitro (DIV) 3 and collected on DIV 10. For in vivo experiments, C57BL/6J mice were bilaterally i.c.v. (intracerebroventricularly) injected on P1 with SaCas9-AAV and collected on P30.
|
| Growth protocol |
Neurons used in AMP-seq experiments were derived from E15.5 (gestational day 15.5) C57BL/6J embryos.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
All genomic DNA extractions were performed using DNeasy Blood & Tissue Kit (Qiagen #69504).
KAPA HyperPlus Kit (Roche #KK8514). Prep method was based off of AMP-seq (https://www.nature.com/articles/nm.3729). Sequenced on the Illumina MiniSeq using MiniSeq Mid Output Kit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiniSeq |
| |
|
| Data processing |
Briefly, reads were binned into editing event categories where + 20 bp from the expected Cas9 cleavage site was analyzed for an editing event. This included unedited (Wt) reads, or reads containing insertions/deletions (indels), AAV-integration, unresolved double-stranded breaks, translocations, or foreign DNA integration.
Assembly: mm10
Supplementary files format and content: The read counds Excel sheet contains sample metadata as well as counts for different read types, such as: unedited reads, AAV integration reads, indel readss, translocation reads, DSB reads at the gRNA site, and foreign DNA integration reads.
Library strategy: AMP-seq
|
| |
|
| Submission date |
Jun 28, 2024 |
| Last update date |
Oct 16, 2024 |
| Contact name |
Austin J Hepperla |
| E-mail(s) |
hepperla@unc.edu
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Genetics
|
| Street address |
7018B Mary Ellen Jones Building
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL23969 |
| Series (1) |
| GSE271068 |
AAV vector-derived elements integrate into Cas9-generated double strand breaks and disrupt gene transcription |
|
| Relations |
| BioSample |
SAMN42159900 |
| SRA |
SRX25146925 |
