GEO series

Gene expression response to mitochondrial DNA depletion

GSE55311 Homo sapiens (human) Expression microarray 24 samples Submitted 2016/02/01 Platform GPL570

At a glance

Expression microarray · human · 24 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 24 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Mitochondrial defects are associated with a spectrum of human disorders, ranging from rare, inborn errors of metabolism to common, age-associated diseases such as diabetes and neurodegeneration. In lower organisms, genetic “retrograde” signaling programs have been identified that promote cellular and organism survival in the face of mitochondrial dysfunction.

Read the full summary ↓

Here, we characterized the transcriptional component of the human mitochondrial retrograde response in an inducible model of mitochondrial dysfunction. We used an HEK293-derived cell line that expresses a dominant negative DNA polymerase gamma (PolGdn) under tet repressor control. Upon induction with doxycycline, PolGdn inhibits replication of mitochondrial DNA (mtDNA), so that existing copies of mtDNA are progressively diluted as cells continue to divide. Upon removal of doxycycline, repression of PolGdn is re-established, and mtDNA copy number, as well as mitochondrial protein expression and oxidative phosphorylation complex abundance, recovers. We used microarrays to study transcriptional changes arising from mtDNA depletion. We found a robust transcriptional response that is partially mediated by ATF4, which appears to effect an adaptive rewiring of serine and one-carbon metabolism.

This dataset

Open GSE55311 in finder → Find more human microarray datasets →

Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE55311_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

What the files usually look like: For arrays the series matrix is normally the normalised expression table you want; the raw array files (CEL and similar) are in the RAW.tar.

Also filed as BioProject PRJNA239305. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 27307216) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 24 more — browse all 24 samples with per-sample file links →

Datasets on a similar topic

GSE299462 REP-1 depletion causes altered mitochondrial energy metabolism in CHM disease, shifting from glycolysis to lipid oxidation 12 samples shares mitochondrial, depletion
GSE224689 Regulatory principles of human mitochondrial gene expression revealed by kinetic analysis of the RNA life cycle. 113 samples shares mitochondrial
GSE224662 Regulatory principles of human mitochondrial gene expression revealed by kinetic analysis of the RNA life cycle 98 samples shares mitochondrial
GSE263641 CTCF depletion uncouples the role of enhancer-promoter interactions and higher-order chromatin hubs in gene regulation during cellular differentiation. 137 samples shares depletion
GSE261505 Effect of depletion of ZFC3H1, PABPN1 and CNOT4 on gene expression in human cells. 12 samples shares depletion
GSE217642 Effect of SNHG6 depletion on gene expression in radioresistant RTR61 cells 12 samples shares depletion
GSE233722 Effect of RNF4 depletion on GSK3685032-induced gene expression changes in MV4-11 cells [RNA-seq] 12 samples shares depletion
GSE268804 Effect of depletion of hypoxia-inducible factor (HIFs) on gene expression in MDA231-BrM2 breast cancer brain-selective metastatic cells with RNA-Seq. 12 samples shares depletion

Search all human microarray 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.