GEO DataSets

Analysis of pineal glands from Sprague-Dawley rats at mid-day (ZT7) or midnight (ZT19). Similar samples from pineal gland-specific DNF2 transgenic rats also examined. The pineal plays a vital role in vertebrate chronobiology. Results provide insight into night/day changes in pineal gene expression.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, count, 2 genotype/variation, 2 time sets

Platform:

GPL341

Series:

GSE12342

12 Samples

Download data: CEL

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

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platforms:

GPL1355 GPL85 GPL341

50 Samples

Download data: CEL

(Submitter supplied) Biological processes are optimized by circadian and circannual biological timing systems. In vertebrates, the pineal gland plays an essential role in these systems by converting time into a hormonal signal, melatonin; in all vertebrates, circulating melatonin is elevated at night, independent of lifestyle. At night, sympathetic input to the pineal gland, originating from the circadian clock in the suprachiasmatic nucleus, releases norepinephrine. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Datasets:

GDS3701 GDS3702

Platform:

GPL1355

32 Samples

Download data: CEL

(Submitter supplied) Biological processes are optimized by circadian and circannual biological timing systems. In vertebrates, the pineal gland plays an essential role in these systems by converting time into a hormonal signal, melatonin; in all vertebrates, circulating melatonin is elevated at night, independent of lifestyle. We have analyzed the rat pineal transcriptome at mid-day and mid-night to identify genes that exhibit night/day changes in expression. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Dataset:

GDS3700

Platform:

GPL341

12 Samples

Download data: CEL

(Submitter supplied) Biological processes are optimized by circadian and circannual biological timing systems. In vertebrates, the pineal gland plays an essential role in these systems by converting time into a hormonal signal, melatonin; in all vertebrates, circulating melatonin is elevated at night, independent of lifestyle. We have analyzed the rat pineal transcriptome at mid-day and mid-night to identify genes that exhibit night/day changes in expression. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Dataset:

GDS3699

Platform:

GPL85

6 Samples

Download data: CEL

Analysis of pineal organ cultures treated with norepinephrine (NE) and cAMP. Effects of forskolin also examined. Previous studies of night/day differentially expressed genes suggest control by NE/cAMP signaling. Results of this study expand the scope of the NE/cAMP regulatory cascade.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, count, 4 agent sets

Platform:

GPL1355

Series:

GSE12343

12 Samples

Download data: CEL

Analysis of pineal glands and other tissues (retina, neocortex, cerebellum, hypothalamus, heart, and liver) obtained from Sprague-Dawley rats at mid-day (ZT7) or midnight (ZT19). Results provide insight into genes that characterize the pineal gland, independent of tonic or night/day influences.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, count, 2 time, 7 tissue sets

Platform:

GPL1355

Series:

GSE12343

20 Samples

Download data: CEL

Analysis of pineal glands from Sprague-Dawley rats at mid-day (Zeitgeber time ZT7) or midnight (ZT19). Rats were kept on a 14:10 light-dark (LD) cycle. The pineal gland plays a vital role in vertebrate chronobiology. Results provide insight into night/day changes in pineal gene expression.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, count, 2 time sets

Platform:

GPL85

Series:

GSE12341

6 Samples

Download data: CEL

(Submitter supplied) Homeobox genes generally encode transcription factors involved in regulating developmental processes. In the pineal gland, a brain structure devoted to nocturnal melatonin synthesis, a number of homeobox genes are also expressed postnatally; among these are the LIM homeobox 4 gene (Lhx4) and the brain‐specific homeobox gene (Bsx). As part of a larger study, we used of siRNA technology to knock down Lhx4 or Bsx expression in cultured adult rat pinealocytes. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18694

9 Samples

Download data: XLSX

(Submitter supplied) Pineal function follows a 24-hour schedule, dedicated to the conversion of night and day into a hormonal signal, melatonin. In mammals, 24-hour changes in pineal activity are controlled by a neural pathway that includes the central circadian oscillator in the suprachiasmatic nucleus and the superior cervical ganglia (SCG), which innervate the pineal gland. In this study, we have generated the first next-generation RNA sequencing evidence of neural control of the daily changes in the pineal transcriptome. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14844

36 Samples

Download data: TXT, XLSX

(Submitter supplied) In the article "Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers" by Bejjani et al., we mapped p300/CBP binding sites in MDA-MB-231 cells transfected with a control siRNA or a siRNA directed against Fra-1(FOSL1) to study whether Fra-1 can modulate p300/CBP recruitment on MDA-MB-231 genome

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

3 Samples

Download data: BED, BIGWIG

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. All the data are described in the article "Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers" by Bejjani et al.

Organism:

Homo sapiens

Type:

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

Platforms:

GPL16791 GPL16686

40 Samples

Download data: CEL

(Submitter supplied) In the article "Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers" by Bejjani et al., we used NG Capture-C approach to identify regulatory elements interacting with the promoters of 35 Fra-1 regulated genes in the triple negative breast cancer cell line MDA-MB-231

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

6 Samples

Download data: XLSX

(Submitter supplied) In the paper "Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers" by Bejjani et al., we identified Fra-1 and/or Fra-2 target genes in MDA-MB-231 cells. si RNA against Fra-1 and against Fra-2 were transfected in MDA-MB-231 cells either independenlty or simultaneously to identify genes regulated specifically by Fra-1 or Fra-2 and genes regulated redundantly or complementarily by Fra-1 and Fra-2 total RNA were purified and biotinylated sense-strand cDNA were produced. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

21 Samples

Download data: CEL, TXT

(Submitter supplied) In the article "Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers" by Bejjani et al., we mapped epigenetic marks (H3K4me1, H3K4me3, H3K27ac), p300/CBP, PolII and CTCF to characterize the binding sites of Fra-1 and Fra-2 on MDA-MB-231 genome. Data for Fra-1 and Fra-2 ChIP-seq are available on GEO database, accession number GSE132098 (Tolza et al., 2019, MCR 17, 1999-2014)

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

13 Samples

Download data: BED, WIG

(Submitter supplied) we report the mapping of Fra-1 and Fra-2 binding site on MDA-MB-231 cell line genome

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

3 Samples

Download data: BED, WIG

(Submitter supplied) Chick pinealocytes exhibit all the characteristics of a complete circadian system, comprising photoreceptive inputs, molecular clockworks and an easily measured rhythmic output, melatonin biosynthesis. We used microarray analysis to investigate the expression of approximately 8000 genes within cultured pinealocytes subjected to both LD and DD cycles. We report that a reduced subset of genes were rhythmically expressed in vitro compared to those previously published in vivo, and that gene expression rhythms were lower in amplitude, although the functional distribution of the rhythmic transcriptome was largely similar. more...

Organism:

Gallus gallus

Type:

Expression profiling by array

Platform:

GPL3731

196 Samples

Download data

(Submitter supplied) Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death. HCC incidence is on the rise, while treatment options remain limited. Thus, a better understanding of the molecular pathways involved in HCC development has become a priority to guide future therapies. While previous studies implicated the AP-1 (Fos/Jun) transcription factor family members c-Fos and c-Jun in HCC formation, the contribution of Fos-related antigens 1 and 2 (Fra-1/2) is unknown. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

19 Samples

Download data: TSV

(Submitter supplied) The zebrafish pineal gland (epiphysis) is an autonomous clock organ. In addition to being a site of melatonin production, it contains photoreceptor cells and functions as a circadian clock pace maker, making zebrafish a useful model system to study the developmental control of expression of genes associated with melatonin synthesis and photodetection, and the circadian clock. Here we have used DNA microarray technology to study the zebrafish pineal transcriptome. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Dataset:

GDS3824

Platform:

GPL1319

69 Samples

Download data: CEL

Analysis of pineal gland across 5 developmental stages (3 larval, 2 adult) during the day and night. Pineal gland is a site of melatonin production, contains photoreceptor cells, and acts as a circadian clock pace maker. Results provide insight into the molecular basis of pineal gland development.

Organism:

Danio rerio

Type:

Expression profiling by array, count, 5 age, 2 development stage, 2 time, 2 tissue sets

Platform:

GPL1319

Series:

GSE13371

69 Samples

Download data: CEL