GEO series

Hypoxia

GSE3537 Homo sapiens (human) Expression microarray 69 samples Submitted 2006/01/24 Platform GPL3017Platform GPL3020Platform GPL3018Platform GPL3019

At a glance

Expression microarray · human · 69 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 69 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

All mammalian cells need oxygen. Inadequate oxygen (hypoxia) triggers cellular responses for survival and the maintenance of homeostasis. A transcription factor, hypoxia-inducible factor (HIF), plays a central role in the hypoxia response; its activity is regulated by the oxygen-dependent degradation of the HIF-1a protein. Despite the ubiquity and importance of hypoxia responses, very little is known about the variation in the global transcriptional response to hypoxia among different cell types and its links to tissue and cell-specific diseases.

Read the full summary ↓

We analyzed the temporal changes in global transcript levels in response to hypoxia in primary renal proximal tubule epithelial cells (RPTECs), breast epithelial cells, smooth muscle (SMs), and endothelial cells (ECs) with DNA microarrays. The extent of the transcriptional response to hypoxia was greatest in the renal tubule cells. This exaggerated response was associated with a uniquely high level of HIF-1a RNA in renal cells and could be diminished by reducing HIF-1a expression via RNA interference (RNAi). A gene-expression signature of the hypoxia response, derived from our studies of cultured mammary and renal tubular epithelial cells, showed coordinated variation in several human cancers, and was a strong predictor of clinical outcomes in both breast and ovarian cancers. In an analysis of a large, published gene-expression dataset from breast cancers, we found that the prognostic information in the hypoxia signature was virtually independent of that provided by the previously reported wound signature and more predictive of outcomes than any of the clinical parameters in current use. A stimulus or stress experiment design type is where that tests response of an organism(s) to stress/stimulus. e.g. osmotic stress, behavioral treatment Keywords: stimulus_or_stress_design

This dataset

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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 (GSE3537_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 PRJNA93595. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 16417408) ↗

Samples in this study

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+ 69 more — browse all 69 samples with per-sample file links →

Datasets on a similar topic

GSE4185 Gene Expression Programs in Response to Hypoxia: Cell Type Specificity and Prognostic Significance in Human Cancers 57 samples shares hypoxia
GSE63563 YBX1-dependent LNA-tRF-mediated modulation of gene expression under hypoxia 8 samples shares hypoxia
GSE307666 eIF3d and eIF3e mediate selective translational control of hypoxia that can be inhibited by small molecules 120 samples shares hypoxia
GSE243418 Epigenetic coordination of transcriptional and translational programs in hypoxia. 115 samples shares hypoxia
GSE228336 Hypoxia and lactate influence VOC production in A549 lung cancer cells 108 samples shares hypoxia
GSE261324 NF-κB- and TET2-mediated macrophage reprogramming overrides the anti-inflammatory effects of hypoxia and improves responses in human cancer 88 samples shares hypoxia
GSE260795 Hypoxia-induced phase separation of ZHX2 drives 3D chromatin remodeling and cancer metastasis 88 samples shares hypoxia
GSE285077 Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles [RNA-seq] 76 samples shares hypoxia

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