GEO series

TRPML3 regulates expression of development-related neuronal genes, and augments starvation-induced autophagy mediated transcriptional regulation in HEK cells

GSE300275 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/06/20 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 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: Homo sapiens (human)
Samples: 12 samples: 3 × Vector control, Fed vs 3 × Vector control, Starved vs 3 × TRPML3, Fed vs 3 × TRPML3, StarvedGroups 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)

Autophagy (self-eating) involves sorting of cargo like aggregated or misfolded proteins and damaged organelles, and their degradation via the endo-lysosomal system. It is a conserved process that is crucial in survival, cell stress response, and differentiation. Transient Receptor Potential Mucolipin-3 (TRPML3) is an endolysosomal calcium channel largely implicated in the mechanisms of endocytosis and autophagy.

Read the full summary ↓

Overexpression and channel activation of TRPML3 has been reported to induce autophagy in cell-line models. However, its effect on the gene expression patterns, both before and during autophagy induction, is not clearly understood. Here, we have explored the changes in the transcriptomic profile of an in vitro serum starvation model of autophagy by RNA sequencing experiments in an over-expression background of TRPML3. We report that serum-starvation induced autophagy leads to downregulation of development-related neuronal genes and gene sets. TRPML3 overexpression during autophagy induction further amplifies the effect of starvation in downregulating neuronal gene sets. But, when nutrition is not a limiting condition, TRPML3 overexpression upregulates neuronal genes that promote development. In summary, overexpression of TRPML3 promotes neuronal development under ‘fed’ conditions, while significantly arresting development by augmenting the effects of starvation-induced autophagy in HEK293T cells.

This dataset

Open GSE300275 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 GSE300275_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 PRJNA1280010 and SRA study SRP593543. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × Vector control, Fed vs 3 × Vector control, Starved vs 3 × TRPML3, Fed vs 3 × TRPML3, Starved

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.

Samples in this study

GSM9056864 Vector control, Fed 1 Vector control, Fed
GSM9056865 Vector control, Fed 2 Vector control, Fed
GSM9056866 Vector control, Fed 3 Vector control, Fed
GSM9056867 Vector control, Starved 1 Vector control, Starved
GSM9056868 Vector control, Starved 2 Vector control, Starved
GSM9056869 Vector control, Starved 3 Vector control, Starved
GSM9056870 TRPML3, Fed 1 TRPML3, Fed
GSM9056871 TRPML3, Fed 2 TRPML3, Fed
GSM9056872 TRPML3, Fed 3 TRPML3, Fed
GSM9056873 TRPML3, Starved 1 TRPML3, Starved
GSM9056874 TRPML3, Starved 2 TRPML3, Starved
GSM9056875 TRPML3, Starved 3 TRPML3, Starved

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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.