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Sample GSM5736856 Query DataSets for GSM5736856
Status Public on Jan 19, 2022
Title AAV-Nd3-9577-(1)-NUMT-Ch14 [mouse_14_D1]
Sample type SRA
 
Source name AAV-Nd3-9577-(1)-NUMT-Ch14
Organism Mus musculus
Characteristics tissue: heart
ddcbe halves: L-strand: 1333C ; H-strand: 1333N
weeks after intervention: 3
injected as: Neonate
target: NUMT-Ch14
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 SAMN24102852
SRA SRX13439707

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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