|
Status |
Public on Jan 19, 2022 |
Title |
Vehicle, mouse_23 |
Sample type |
SRA |
|
|
Source name |
heart
|
Organism |
Mus musculus |
Characteristics |
tissue: heart ddcbe halves: Vehicle time: 3 week(s) after intervention injected as: Neonate
|
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 DNA resequencing
|
|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina MiSeq |
|
|
Description |
mouse_23 23_S23
|
Data processing |
Quality and 3' end adapter trimming with Trim_Galore! Reads longer than 20nt were aligned to ChrM (GRCm38) 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; counts_ddCBE = xls file with Adaptor counts generated by Cutadapt
|
|
|
Submission date |
Sep 13, 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 |
SAMN21419046 |
SRA |
SRX12172983 |