|
| Status |
Public on Jul 17, 2022 |
| Title |
Liver mitochondria, 65 week, bio rep 4 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
cell line: Isolated Mitochondria
strain: C57BL/6N
genotype: WT
time point: 65 week
|
| Treatment protocol |
Mitochondria were further purified using sucrose gradient centifugation
|
| Growth protocol |
Livers were excised from 12 and 65 week mice and mitochondria were isolated by homogenizaion using dounce homogenizers and differential centrifugations
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The isolated and purified mitochondria were lysed in 1 ml TRIzol using the vendor’s protocol. The samples were then treated with DNase I (Thermo Scientific) following the manufacturer´s instructions. For purification of the sample, the RNA Clean and Concentrator Kit (R1013, Zymo Research) was used
Library was constructed using vendors protocol of PCR-cDNA Barcoding (SQK-PCB109)
PCR steps adds barcodes to each reverse transcribed RNA (cDNA) sample. The 8 barcodes provided in the kit were used to multiplex individual samples on a single flow cell
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Data processing |
EPI2ME Labs Differential gene expression Workflow
python was ued for statistical analysis and reporting,
minimap2 was used to align sequence reads in a splice-aware manner against a reference transcriptome,
samtools was used to process the aligned reads and prepares BAM files,
salmon was used for defining the expressed genes and quantifying aligned reads,
edgeR and StageR were used for differential expression analysis,
DEXSeq was used to quantify differential transcript usage.
Assembly: Mus_musculus GRCm38(mm10)
Supplementary files format and content: tab-delimited merged tsv file for differential counts from all samples
|
| |
|
| Submission date |
Jul 14, 2022 |
| Last update date |
Jul 17, 2022 |
| Contact name |
Abhishek Aich |
| E-mail(s) |
[email protected]
|
| Organization name |
Universitätsmedizin Göttingen
|
| Street address |
Humboldtallee 23,
|
| City |
Göttingen |
| State/province |
Please Select… |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24973 |
| Series (1) |
| GSE208177 |
Effect of aging on mitochondrial gene expression using C57BL/6N liver mitochondria |
|
| Relations |
| BioSample |
SAMN29723143 |
| SRA |
SRX16221940 |
