Mitochondrial DNA integrity and metabolome profile are preserved in the human induced pluripotent stem cell reference line KOLF2.1J

This dataset corresponds to a manuscript submitted to Stem Cell Reports with the same title.
It includes the files necessary to reproduce the results described in the manuscript:
- GT19-38445_with_p_MT.bam (short-read whole genome sequencing data containing only reads mapped to the mitochondrial DNA)
- KOLF2.1J targeted ONT mtDNA.fastq (long-read targeted mitochondrial DNA sequencing of nine PCR amplicons spanning the entire mitochondrial genome)
- KOLF2.1J WGS ONT.bam (long-read whole genome sequencing data containing only reads mapped to the mitochondrial DNA)
- Jupyter Notebooks containing the code used to reproduce the results: Short-read WGS data processing.ipynb and Short-read WGS data visualization.ipynb; The latter is also used to visualize ONT data (file names need to be changed accordingly)
- The reference used for alignment and a shifted version to account for the artificial breakage point: rCRS.fasta and rCRS_shifted.fasta
- Jupyter Notebook containing code for targeted ONT mitochondrial DNA sequencing variant calling using Mutserve: Targeted ONT seq variant calling.ipynb
-- For analysis of WGS data, the BAM file KOLF2.1J WGS ONT.bam is used and variants are called according to the Targeted ONT seq variant calling.ipynb notebook with adjustment of the calling threshold to 0.01.
- Sanger sequencing results of m625 conspicuous position described in the manuscript: kolf_mt2_rev_mt2_internal_rev.fasta, kolf_mt2_rev_mt2_internal_rev.ab1, kolf_mt2_fwd_mt2_internal_fwd.fasta, kolf_mt2_fwd_mt2_internal_fwd.ab1

Additional information can be found below.
In case of any problems, please contact the authors.