|
| Status |
Public on Oct 23, 2017 |
| Title |
WT Heart [CM29] |
| Sample type |
SRA |
| |
|
| Source name |
WT Heart
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: wild-type
tissue/cell type: Heart
tissue/cell subtype: Primary tissue
molecule subtype: Total DNA from homogenized tissue
|
| Treatment protocol |
Cells and tissues were homogenized and in the case of heart DNA extracted immediately, for other samples mitochondria were prepared by differential centrifugation, and in most cases with additional purification on a single step sucrose gradient
|
| Growth protocol |
cultured cells were grown on 90% dulbecco's modified growth medium containing 25 mM glucose and 100 mM pyruvate supplemented with 10% fetal bovine serum
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted by the phenol chloroform extraction after proteinase K digestion of cells or tissue in 0.25% SDS
EmRibo-seq libraries were prepared according to Ding et al 2015 - doi: 10.1038/nprot.2015.099
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
Differential centrifugation and single step sucrose gradient for mitochondrial DNA enirchment
|
| Data processing |
Trimming of residual adaptor sequences. Code for all data processing steps is available at https://github.com/taylorLab/mito
Alignment to reference genome (masked for nuclear inserted mitochondrial sequences).
Alignment to reference genome masked for nuclear inserted mitochondrial sequences and containing additional circularisation junction for the mitochondrial genome.
Resolution of coordinates for circularisation junction mapping
Calculation of embeded ribonucleotide position – one nucleotide upstream and on the opposite strand to the read 5’ end.
Genome_build: mm9 with additional sequence corresponding to the circularisation junction of the mitochondrial genome
Supplementary_files_format_and_content: Bed format files showing the coordinates and strand of inferred ribonucleotide incorporation sites, counts per nucleotide of the reference genome at all sites with signal indicated by the 5’ end of at least one read.
|
| |
|
| Submission date |
Sep 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin Taylor |
| E-mail(s) |
martin.taylor@igmm.ed.ac.uk
|
| Organization name |
University of Edinburgh
|
| Department |
MRC Institute of Genetics and Molecular Medicine
|
| Street address |
Crewe Road
|
| City |
Edinburgh |
| State/province |
Midlothian |
| ZIP/Postal code |
EH4 2XU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE103429 |
Aberrant ribonucleotide incorporation and multiple deletions in mitochondrial DNA of the murine MPV17 disease model [EmRibo-seq] |
|
| Relations |
| BioSample |
SAMN07602862 |
| SRA |
SRX3157208 |
