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Links from GEO DataSets

Items: 20

1.
Full record GDS3699

Night and day effects on pineal gland (Expt. A)

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
2.

Daily Rhythm in Expression of over 600 Genes in the Rodent Pineal Gland: Dominant Role of Adrenergic/cAMP Signaling

(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
Series
Accession:
GSE12344
ID:
200012344
3.

Expt. C; Daily Rhythm in Expression of >600 Genes in the Rodent Pineal Gland: Dominant Role of Adrenergic/cAMP Signaling

(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
Series
Accession:
GSE12343
ID:
200012343
4.

Expt. B; Daily Rhythm in Expression of >600 Genes in the Rodent Pineal Gland: Dominant Role of Adrenergic/cAMP Signaling

(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
Series
Accession:
GSE12342
ID:
200012342
5.

Expt. A; Daily Rhythm in Expression of >600 Genes in the Rodent Pineal Gland: Dominant Role of Adrenergic/cAMP Signaling

(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
Series
Accession:
GSE12341
ID:
200012341
6.
Full record GDS3702

In vitro pineal gland organ culture response to adrenergic/cAMP stimulation (Expt. C)

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
7.
Full record GDS3701

Night and day effects on pineal gland and various other tissues (Expt. C)

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
8.
Full record GDS3700

Night and day effects on pineal gland (Expt. B)

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
9.

The role of Lhx4 and Bsx homeobox genes in the rat adult pineal gland

(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
Series
Accession:
GSE142476
ID:
200142476
10.

Single-cell RNA sequencing of the mammalian pineal gland identifies two pinealocyte subtypes and cell type-specific daily patterns of gene expression

(Submitter supplied) The vertebrate pineal gland is dedicated to the production of the hormone melatonin, which increases at night to influence circadian and seasonal rhythms. This increase is associated with dramatic changes in the pineal transcriptome. Here, single-cell analysis of the rat pineal transcriptome was approached by sequencing mRNA from ~17,000 individual pineal cells, with the goals of profiling the cells that comprise the pineal gland and examining the proposal that there are two distinct populations of pinealocytes differentiated by the expression of Asmt, which encodes the enzyme that converts N-acetylserotonin to melatonin. more...
Organism:
Rattus norvegicus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18694
10 Samples
Download data: GTF, MTX, TSV, TXT
Series
Accession:
GSE115723
ID:
200115723
11.

Mapping of p300/CBP binding sites in MDA-MB-231 cells transfected with a control siRNA or a siRNA directed against Fra-1(FOSL1)

(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
Series
Accession:
GSE163304
ID:
200163304
12.

Transcriptional regulation by Fra-1 in triple negative breast cancers

(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
Series
Accession:
GSE146825
ID:
200146825
13.

NG-Capture C analysis of 35 gene loci regulated by Fra-1 in MDA-MB-231 cells

(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
14.

Identification of Fra-1 and/or Fra-2 regulated genes in MDA-MB231 cells

(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
Series
Accession:
GSE146823
ID:
200146823
15.

Mapping of epigenetic marks (H3K4me1, H3K4me3, H3K27ac), p300/CBP, PolII and CTCF on MDA-MB-231 genome

(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
Series
Accession:
GSE146822
ID:
200146822
16.

genome-wide mapping of Fra-1 and Fra-2 binding sites in MDA-MB-231 cell line

(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
Series
Accession:
GSE132098
ID:
200132098
17.

RNA-Seq of the rat pineal transcriptome, with in-vivo and in-vitro samples, under various treatment and surgical conditions

(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
Series
Accession:
GSE63309
ID:
200063309
18.

Circadian Transcriptome of the Chicken Pineal In Vitro

(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
Series
Accession:
GSE5292
ID:
200005292
19.

Transcriptome analysis of the zebrafish pineal gland

(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
Series
Accession:
GSE13371
ID:
200013371
20.
Full record GDS3824

Pineal gland development

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
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