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| Status |
Public on Mar 20, 2019 |
| Title |
AAV3 |
| Sample type |
SRA |
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| Source name |
Retina
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| Organism |
Mus musculus |
| Characteristics |
sample type: P21 retinae
treatment: intravitreally injected with AAV-Cas9-VQR and AAV-U6sgRNAmMUT-RHOp-GFP-t2a-rtTA PHP.B serotype
background strain: Heterozygous P23H knock-in mice (The Jackson Laboratory, Bar Harbor, ME)
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| Treatment protocol |
Electoporated retinae were dissected under a fluorescence dissecting microscope. GFP+ retinae were selected for further analysis based on fluorescence intensity and diffusion but also retinal integrity.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
In case of indel analysis, retinae were dissociated (papain 10 U/ml, Worthington, 10 min, 37°C) (68) and FACS-sorted (MoFlo, Beckman Coulter, Inc.).
Genomic PCR products were subjected to library preparation using the NEBNext Ultra II DNA library Kit (NEB). Briefly, common primers are added by ligation, following by limited number of PCR cycles (eight cycles) where specific barcode for each sample was added. Amplicones were purificated with AMPure beads (Beckman Coulter) and run onto Bioanalyzer 2100 (Agilent). Equimolar amounts of library were mixed, diluited and sequenced with an Illumina MiSeq system. CASAVA software (Illumina) was used for demultiplexing.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Data processing |
Fastq reads were aligned to the mm10 reference genome with Bowtie.
NHEJ as well as frameshift/in-frame mutations were quantified with CRISPResso.
Genome_build: mm10
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| Submission date |
Mar 20, 2019 |
| Last update date |
Mar 21, 2019 |
| Contact name |
Luca Massimino |
| E-mail(s) |
admin@lucamassimino.com
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| Phone |
+393389039500
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| Organization name |
Ospedale San Raffaele
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| Department |
Gastroenterology
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| Street address |
Via Olgettina, 58
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| City |
Milano |
| State/province |
MI |
| ZIP/Postal code |
20100 |
| Country |
Italy |
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| Platform ID |
GPL16417 |
| Series (1) |
| GSE128579 |
Cas9/sgRNA selective targeting of the P23H Rhodopsin mutant allele for treating retinitis pigmentosa by intravitreal AAV9.PHP.B-based delivery |
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| Relations |
| BioSample |
SAMN11176070 |
| SRA |
SRX5546880 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3680567_AAV3_S4_mm10.bedGraph.gz |
1.3 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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