GEO DataSets

(Submitter supplied) Hypoxia inducible transcription factor HIF is the master regulator of hypoxia response in metazoans. The stability and activity of HIF are tightly regulated. In the model organism C. elegans, the homolog of HIF is HIF-1. The stability and activity of HIF-1 are negatively regulated by vhl-1, egl-9, rhy-1 and swan-1 when HIF-1 is stabilized by vhl-1 mutation. Here, we are using Affymetrix microarray to measure the immediate gene expression changes under short-term hypoxia treatment (2 hours of 0.5% oxygen treatment). more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL200

24 Samples

Download data: CEL

(Submitter supplied) Hypoxia-inducible transcription factor HIF is the key regulator of hypoxia response. It is conserved from human to the model organism C. elegans. The homolog of HIF in C. elegans is HIF-1. In C. elegans, there are six alternative splicing isoforms for HIF-1. Isoform a (HIF1a) is the predominant one with important biological functions for stress response and longevity. Here, by performing chromatin immunoprecipitation DNA-sequencing (ChIP-seq), we identified the direct targets for HIF-1a at whole genome level.

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13657

4 Samples

Download data: NARROWPEAK, WIG

(Submitter supplied) The goal of the study was to identify hypoxia-induced gene expression changes in C. elegans and to determine which of these responses to hypoxia were regulated by hif-1. Towards these aims, we analyzed mRNA expression patterns in synchronized populations of wild-type worms that were cultured in standard lab conditions (normoxia) or in hypoxia. We also assayed mRNA from two mutant strains: (i) animals carrying the strong loss-of-function mutation in hif-1 and (ii) C. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Dataset:

GDS1379

Platform:

GPL2569

9 Samples

Download data

Analysis of wild type, hif-1-deficient, and vhl-1-deficient strains cultured for 4 hours in 21% oxygen (normoxia) or 0.1% oxygen (hypoxia). Results provide insight into pathways for adaptation to oxygen deprivation.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array, log2 ratio, 3 strain sets

Platform:

GPL2569

Series:

GSE2836

9 Samples

Download data

(Submitter supplied) The response to insufficient oxygen, termed hypoxia, is orchestrated by the conserved master regulator Hypoxia-Inducible Factor-1 (HIF-1), which is hyperactive in many cancers. Here, we describe a HIF-1 independent hypoxia response pathway controlled by Caenorhabditis elegans Nuclear Hormone Receptor NHR-49, an orthologue of mammalian lipid metabolism regulator Peroxisome Proliferator-Activated Receptor alpha (PPARα). more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18245

18 Samples

Download data: CSV, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13657 GPL18245 GPL22765

26 Samples

Download data: WIG

(Submitter supplied) RNA was isolated from L4 stage animals for the following genotypes: N2, hif-1(ia4), egl-9(sa307), hif-1(ia4);egl-9(sa307) grown at 20C. Total RNA was isolated and used to prepare libraries using the Illumina Truseq with polyA selection. Libraries were sequenced across two lanes on an Illumina HiSeq2000 (GeneWiz) or an Illumina HiSeq 2500 in Rapid Run Mode (RUCDR).

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18245 GPL13657

20 Samples

Download data: XLSX

(Submitter supplied) To identify genes directly regulated by HIF-1, we performed ChIP-seq on L4-stage egl-9(sa307); hif-1(ia4); odIs131[hif-1::gfp] animals, which have activated HIF-1 under aerobic conditions, using anti-GFP antibodies to precipitate DNA bound by HIF-1::GFP followed by high-throughput sequencing to identify peaks of reads corresponding to HIF-1 binding sites

Organism:

Caenorhabditis elegans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22765

6 Samples

Download data: WIG, XLSX

(Submitter supplied) The HIF (hypoxia-inducible factor) transcription factor is the master regulator of the metazoan response to chronic hypoxia. In addition to promoting adaptations to low oxygen, HIF drives cytoprotective mechanisms in response to stresses and modulates neural circuit function. How most HIF targets act in the control of the diverse aspects of HIF-regulated biology remains unknown. We discovered that a HIF target, the C. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13657

8 Samples

Download data: TXT

(Submitter supplied) The von Hippel-Lindau (VHL) tumor suppressor functions as a ubiquitin ligase that mediates proteolytic inactivation of hydroxylated a subunits of hypoxia-inducible factor (HIF). Although studies of VHL defective renal carcinoma cells suggest the existence of other VHL tumor suppressor pathways, dysregulation of the HIF transcriptional cascade has extensive effects that make it difficult to distinguish whether, and to what extent, observed abnormalities in these cells represent effects on pathways that are distinct from HIF. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platforms:

GPL2647 GPL2646

4 Samples

Download data

(Submitter supplied) We report the transcritional targets of transcription factor downstream of insulin signalling. We knocked down transcription factors under reduced insulin signalling in Caenorhabditis elegans and did transcriptom analysis. This study identified target genes interaction complexity in analogous genetic and experimental conditions. It aid in gaining insight into the new molecular mechanisms downstream of rIIS

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18245 GPL13776

14 Samples

Download data: XLSX

(Submitter supplied) Hydrogen sulfide (H2S) has dramatic physiological effects on animals that are associated with improved survival in changing conditions. C. elegans grown in H2S are long-lived and thermotolerant (1). To begin to identify mechanisms by which adaptation to H2S effects fundamental physiological functions, we have defined transcriptional changes associated with the response to H2S. Using microarray analysis we observe rapid changes in the abundance of specific mRNAs. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL11171

3 Samples

Download data: PAIR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL20301 GPL16791

34 Samples

Download data: BED, BW

(Submitter supplied) Hypoxia inducible factor (HIF) directs an extensive transcriptional cascade that transduces numerous adaptive responses to hypoxia. Pan-genomic analyses, using chromatin immunoprecipitation and transcript profiling, have revealed large numbers of HIF-binding sites that are generally associated with hypoxia-inducible transcripts, even over long chromosomal distances. However, these studies do not define the specific targets of HIF-binding sites and do not reveal how induction of HIF affects chromatin conformation over distantly connected functional elements. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

26 Samples

Download data: BED

(Submitter supplied) Hypoxia inducible factor (HIF) directs an extensive transcriptional cascade that transduces numerous adaptive responses to hypoxia. Pan-genomic analyses, using chromatin immunoprecipitation and transcript profiling, have revealed large numbers of HIF-binding sites that are generally associated with hypoxia-inducible transcripts, even over long chromosomal distances. However, these studies do not define the specific targets of HIF-binding sites and do not reveal how induction of HIF affects chromatin conformation over distantly connected functional elements. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL20301 GPL16791

8 Samples

Download data: BW, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL10816 GPL14875

10 Samples

Download data: BW, TXT

(Submitter supplied) Analysis of gene expression changes in the von Hippel Lindau when mutant compared to wild-type at 4dpf using a whole genome microarray expression profiling. The von Hippel Lindau mutant displays a systemic hypoxic response under normoxic conditions. We performed single-colour microarrays to identify the gene expression changes which underpin the hypoxic phenotype. We used 3 biological replicates from both mutant and control, followed by analysis using Limma to identify significant gene expression changes. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL10816

6 Samples

Download data: TXT

(Submitter supplied) Analysis of the binding sites of Hif-1α in both wild-type and von Hippel Lindau mutant zebrafish lines at 4dpf by ChIP linked next generation sequencing. The von Hippel Lindau mutant displays a systemic hypoxic response under normoxic conditions. Results show the extent of Hif-1α binding to the genome, and provide a basis for analysis of the transcriptional response to genetically induced hypoxia in zebrafish.

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL14875

4 Samples

Download data: BW, TXT

(Submitter supplied) Purpose: We aimed to investigate in depth the regulation of microRNA expression by hypoxia in the breast cancer cell line MCF-7, establish the relationship between microRNA expression and HIF binding sites, pri-miRNA transcription and microRNA processing gene expression. Methods: microRNA sequencing data and gene expression microarray data were generated from MCF-7 cells submitted to an hypoxia timecourse (16h, 32h and 48h at 1% Oxygen). more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array; Expression profiling by array; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL11154 GPL6884 GPL8227

31 Samples

Download data: TXT