|
| Status |
Public on Dec 10, 2023 |
| Title |
SASD_mouse_bulk_DNA_biorep_3 |
| Sample type |
SRA |
| |
|
| Source name |
hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: hippocampus
cell line: B6.129-Tg(APPSw)40Btla/Mmjax
cell type: neuron
genotype: 650kb YAC insert human APP(K670N/M671L), copy number ~3
treatment: AAVrh10 split SpRY-ABE8e APP ex17 SA and SD Targeting gRNAs
Sex: male
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For Illumina Miseq experiments, libraries were constructed with the nextera XT indexing primer kits and utilized manufacturer protocols
Targeted genomic and exon high throughput sequencing with nextera indexing primers
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
23M3_bulk_ DNA
Hipocampus extraction; DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and allele frequency
|
| Data processing |
Crispresso2 utilized for base calling and base editing frequency quantification for all DNA NGS files. Sequences were filtered for 90% homology with a phred33 read qualitty of >30. Sequencecs were aligned to an inputted PCR amplicon with the gRNA region of interest
RNAstar utilized for exon junction analysis, creating bam and SJ outputs to visualize and quantify RNA splicing. 2-pass mapping was used with a MAPQ quality score of 60
Assembly: chr38
Supplementary files format and content: Excel sheet containing editing data sorted by figure number; .txt file containing nucleotide frequencies
Supplementary files format and content: DNA base editing analysis outputted in .txt files containing nucleotide frequencies in gRNA windows
Supplementary files format and content: RNAstar files outputted as .txt files containing splice junctions and quantification of junction occurance
|
| |
|
| Submission date |
Oct 30, 2023 |
| Last update date |
Dec 10, 2023 |
| Contact name |
Pablo Pinera |
| E-mail(s) |
angelom3@illinois.edu
|
| Organization name |
University of Illinois at Urbana-Champaign
|
| Department |
Bioengineering
|
| Lab |
Perez
|
| Street address |
2332 West John Street, Apt. D
|
| City |
Champaign |
| State/province |
Illinois |
| ZIP/Postal code |
61821 |
| Country |
USA |
| |
|
| Platform ID |
GPL16417 |
| Series (2) |
| GSE246586 |
SPLICER: A Highly Efficient Base Editing Toolbox That Enables in vivo Exon Skipping For Targeting Alzheimer’s Disease [miSeq] |
| GSE246588 |
SPLICER: A Highly Efficient Base Editing Toolbox That Enables in vivo Exon Skipping For Targeting Alzheimer’s Disease |
|
| Relations |
| BioSample |
SAMN38042637 |
| SRA |
SRX22289366 |
