|
| Status |
Public on Jan 19, 2022 |
| Title |
AAV-Nd3-9577-(1)-mtDNA [mouse_14_F1] |
| Sample type |
SRA |
| |
|
| Source name |
AAV-Nd3-9577-(1)-mtDNA
|
| Organism |
Mus musculus |
| Characteristics |
tissue: heart
ddcbe halves: L-strand: 1333C ; H-strand: 1333N
weeks after intervention: 3
injected as: Neonate
target: mtDNA
|
| Treatment protocol |
In adult experiments, 8-week-old mice were administered systemically by tail vein injection with 1 x 10*12 AAV particles of each monomer [AAV- DdCBE (L) - Nd3-9577 - G1333-C and AAV- DdCBE (H) - Nd3-9577- G1333-N]. An equal dose was applied in newborn pups (Postnatal day 1) via the temporal vein
|
| Growth protocol |
The animals were maintained in a temperature- and humidity-controlled animal care facility with a 12-h light/12-h dark cycle and free access to water and food, and they were sacrificed by cervical dislocation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
NIH/3T3 mouse cells were collected by trypsinization, washed once in PBS and re-suspended in lysis buffer (1mM EDTA, 1 % Tween20, 50 mM Tris (pH = 8)) with 200 µg/ml of proteinase K. Lysates were incubated at 56 ºC with agitation (300 RPM) for 1 h, and then incubated 95 ºC for 10 min before use in downstream applications. Genomic DNA from mouse heart samples (~50 mg) was extracted with a Maxwell® 16 Tissue DNA Purification Kit in a Maxwell® 16 Instrument (Promega), according to manufacturer´s instructions.
Illumina NexteraXT
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Quality and 3' end adapter trimming with Trim_Galore!
Reads longer than 20nt were aligned to ChrM (GRCm38) or the NUMT sequence on Chr 1 or Chr14 with Bowtie2
Samtools mpileup and Cutadapt to count nucleotides surrounding the editing site
Genome_build: GRChm38
Supplementary_files_format_and_content: Supp Dataset 1 = excel file showing the % of base editing at individual Cs within the editing window for each sample; Supp Dataset 2=excel file showing the % of off targets on ChrM and a NUMT region of Chr1 and Chr14 for each sample
|
| |
|
| Submission date |
Dec 15, 2021 |
| Last update date |
Jan 19, 2022 |
| Contact name |
Lindsey Van Haute |
| Organization name |
University of Cambridge
|
| Department |
MRC Mitochondrial Biology Unit
|
| Street address |
Hills Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0XY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE184064 |
Mitochondrial DNA base editing in vivo via viral DdCBE delivery to somatic cells |
|
| Relations |
| BioSample |
SAMN24102838 |
| SRA |
SRX13439659 |
