← BioTransfer GEO Dataset Finder
GEO series

in vivo proximity-based mapping of subcellular proteomes, transcriptomes, and RNA structuromes

GSE295471 Homo sapiens (human) RNA-seq (gene expression) 8 samples Submitted 2026/07/31 Platform GPL29480
At a glance

RNA-seq (gene expression) · human · 8 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
Homo sapiens (human)
Samples
8 samples: 2 × MITO (Mitochondrial Matrix) in vitro unlabel biol vs 2 × MITO (Mitochondrial Matrix) in vitro label biol vs 2 × MITO (Mitochondrial Matrix) in vivo unlabel biol vs 2 × MITO (Mitochondrial Matrix) in vivo label biolGroups 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.
Summary (written by the submitters)
Understanding the spatial organization of biomolecules in living organisms is a central but challenging goal in biology. Here we introduce Peroxidase Reactions Activated by D-amino Acids (PRADA), which uses an engineered oxidase to convert non-proteinogenic D-amino acid into H2O2 for in situ activation of a genetically fused peroxidase.
Read the full summary ↓
PRADA enables versatile proximity-based chemistries, including protein labeling, RNA labeling, and functional polymer assembly, with minimal toxicity and background. We demonstrate that PRADA is broadly applicable inside living organisms, including flies, worms, fish, and mice. By further leveraging a unique RNA reactivity of PRADA, we develop a mutational profiling sequencing strategy for spatiotemporally-resolved mapping of RNA secondary structure. Application of this multifaceted PRADA platform in a mouse tumor model offered insights into its mitochondrial proteome, transcriptome, and RNA structurome, revealing distinct RNA folding pattern as a critical layer of mitochondrial gene expression regulation. Collectively, the application of PRADA in diverse systems holds promise to uncover the intricate organization of biomolecules in vivo.
This dataset
Open GSE295471 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE295471_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1254737 and SRA study SRP580828. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
2 × MITO (Mitochondrial Matrix) in vitro unlabel biol vs 2 × MITO (Mitochondrial Matrix) in vitro label biol vs 2 × MITO (Mitochondrial Matrix) in vivo unlabel biol vs 2 × MITO (Mitochondrial Matrix) in vivo label biol

Supports a between-group comparison across 8 samples.

How we read this: 4 replicated groups read from 8 sample titles; they account for 8 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.

Samples in this study
Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

Share this dataset

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.