RNA-seq analysis of Parkin (Prkn) expression in wild-type and TKO mouse hearts under normal chow and high-fat diet [RNA-Seq]
RNA-seq (gene expression) · mouse · 12 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 12 samples: 3 × heart, WT, normal chow, vs 3 × heart, TIGAR KO, normal chow, vs 3 × heart, WT, high fat diet, vs 3 × heart, TIGAR KO, high fat diet,Groups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- TIGAR deficiency enhances cardiac resilience through epigenetic programming of Parkin expressionJCI insight · 2026
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE317050_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1405709 and SRA study SRP664843. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM9464254 heart, WT, normal chow, rep1 heart, WT, normal chow,
- GSM9464255 heart, WT, normal chow, rep2 heart, WT, normal chow,
- GSM9464256 heart, WT, normal chow, rep3 heart, WT, normal chow,
- GSM9464257 heart, TIGAR KO, normal chow, rep1 heart, TIGAR KO, normal…
- GSM9464258 heart, TIGAR KO, normal chow, rep2 heart, TIGAR KO, normal…
- GSM9464259 heart, TIGAR KO, normal chow, rep3 heart, TIGAR KO, normal…
- GSM9464260 heart, WT, high fat diet, rep1 heart, WT, high fat die…
- GSM9464261 heart, WT, high fat diet, rep2 heart, WT, high fat die…
- GSM9464262 heart, WT, high fat diet, rep3 heart, WT, high fat die…
- GSM9464263 heart, TIGAR KO, high fat diet, rep1 heart, TIGAR KO, high f…
- GSM9464264 heart, TIGAR KO, high fat diet, rep2 heart, TIGAR KO, high f…
- GSM9464265 heart, TIGAR KO, high fat diet, rep3 heart, TIGAR KO, high f…
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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.