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Links from GEO DataSets

Items: 20

1.

Transcript levels in CCE WT and RARgamma knockout murine embryonic stem cells treated with either all-trans retinoic acid (8 and 24 hr) or with vehicle control

(Submitter supplied) Retinoic acid receptors (RARs) α, β, and γ heterodimerize with Retinoid X receptors (RXR) α, β, and γ and bind the cis-acting response elements known as RAREs to execute the biological functions of retinoic acid during mammalian development. RARγ mediates the anti-proliferative and apoptotic effects of retinoids in certain tissues and cancer cells, such as melanoma and neuroblastoma cells. Furthermore, ablation of RARγ enhanced the tumor incidence of Ras transformed keratinocytes and was associated with resistance to retinoid mediated growth arrest and apoptosis. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6885
24 Samples
Download data: TXT
Series
Accession:
GSE43221
ID:
200043221
2.

Microarray screening of RARgamma responsive genes in F9 teratocarcinoma cells

(Submitter supplied) We compared the differentially expressed genes between the F9 Wt cells and F9 RAR gamma knock out cells before and after RA treatment. 3 replicates for each conditions. We also identified the RA responsive genes in the F9 Wt cells. Keywords: mutant type
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
12 Samples
Download data: CEL, CHP, EXP
Series
Accession:
GSE8431
ID:
200008431
3.

Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL6246 GPL9250
38 Samples
Download data: BED, CEL
Series
Accession:
GSE30539
ID:
200030539
4.

Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics [ChIP-seq]

(Submitter supplied) Retinoic acid (RA) triggers physiological processes by activating heterodimeric transcription factors comprising retinoic acid (RARa,b,g) and retinoid X (RXRa,b,g) receptors. How a single signal induces highly complex temporally controlled networks that ultimately orchestrate physiological processes is unclear. Using an RA-inducible differentiation model we defined the temporal changes in the genome-wide binding patterns of RARg and RXRa and correlated them with transcription regulation. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9250
20 Samples
Download data: BED
Series
Accession:
GSE30538
ID:
200030538
5.

Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics [mRNA profiling]

(Submitter supplied) Retinoic acid (RA) triggers physiological processes by activating heterodimeric transcription factors comprising retinoic acid (RARa,b,g) and retinoid X (RXRa,b,g) receptors. How a single signal induces highly complex temporally controlled networks that ultimately orchestrate physiological processes is unclear. Using an RA-inducible differentiation model we defined the temporal changes in the genome-wide binding patterns of RARg and RXRa and correlated them with transcription regulation. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6246
18 Samples
Download data: CEL
Series
Accession:
GSE30537
ID:
200030537
6.

Gene expression of Wt vs CYP26A1-/- murine ES cells treated with control or 100 nM RA for 8 or 72 hr.

(Submitter supplied) The goal of this study was to identify genes that are differentially expressed after genetic deletion of both alleles of the Cyp26a1 gene in murine embryonic stem cells. Cyp26a1 codes for the CYP26A1 enzyme which metabolizes RA to polar RA metabolites, such as 4-oxo-RA and 4-OH-RA. CYP26A1-/- ES cells do not metabolize RA within 48 hours of RA treatment while in Wt ES cells, polar RA metabolites are already detectable by 8 hr. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
18 Samples
Download data: CEL, CHP
Series
Accession:
GSE7528
ID:
200007528
7.

Combinatorial knockout of RARα, RARβ, and RARγ completely abrogates transcriptional responses to retinoic acid in murine embryonic stem cells

(Submitter supplied) All-trans retinoic acid (ATRA) alters gene expression in CCE WT embryonic stem cells, but has no effect on gene expression in RAR-deficient TKO cells (devoid of Retinoic Acid Receptors α, β, and γ)
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21103
12 Samples
Download data: XLS
Series
Accession:
GSE112412
ID:
200112412
8.

Transcript level in F9 teratocarcinoma WT and RARalpha knockout in presence and absence of all-trans retinoic acid

(Submitter supplied) Retinoic acid receptors (RARs) α, β and γ are key regulators of embryonic development. Hematopoietic differentiation is regulated by RARα, and several types of leukemia show aberrant RARα activity. We demonstrate that RARα plays an important role in cellular memory and imprinting by regulating the CpG methylation status of specific promoter regions. We used microarrays to identify genes, which display differential expression in F9 RARalpha knockout (RARaKO) cells relative to F9 wt cells.
Organism:
Mus musculus
Type:
Expression profiling by array
Dataset:
GDS4294
Platform:
GPL1261
12 Samples
Download data: CEL
Series
Accession:
GSE31280
ID:
200031280
9.
Full record GDS4294

All-trans retinoic acid effect on retinoic acid receptor α-deficient F9 teratocarcinoma cells

Analysis of F9 teratocarcinoma cells depleted of retinoic acid receptor (RAR)α and treated with all trans retinoic acid (atRA) in the presence of cycloheximide. RARα translocation events are associated with acute promyelocytic leukemia (APL). Results provide insight into the role of RARα in APL.
Organism:
Mus musculus
Type:
Expression profiling by array, transformed count, 2 agent, 2 genotype/variation sets
Platform:
GPL1261
Series:
GSE31280
12 Samples
Download data: CEL
10.

CARM1 (PRMT4) acts as a transcriptional coactivator during retinoic acid-induced embryonic stem cell differentiation

(Submitter supplied) Our data demonstrate that CARM1 is required for transcriptional activation of a subset of retinoic acid (RA) target genes in J1 murine embryonic stem cells
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
6 Samples
Download data: XLSX
Series
Accession:
GSE115818
ID:
200115818
11.

Vitamin A nutritional status and retinoic acid as regulators of gene expression in rat liver

(Submitter supplied) Vitamin A (retinol) is an essential precursor for the production of retinoic acid (RA), which in turn is a major regulator of gene expression, affecting cell differentiation throughout the body. Understanding how vitamin A nutritional status, as well as therapeutic retinoid treatment, regulates the expression of retinoid homeostatic genes is important for improving dietary recommendations and therapeutic strategies using retinoids. more...
Organism:
Rattus norvegicus
Type:
Expression profiling by array
Platform:
GPL1355
47 Samples
Download data: CEL
Series
Accession:
GSE24104
ID:
200024104
12.

Gene expression before or 3 hours after t-RA treatment in HeLa cells expressing an shRNA control or shRNA against PARG

(Submitter supplied) The goal of this experiment was to compare gene expression after t-RA treatment in cells with or without the presence of the PolyADP ribose Glycohydrolase protein (PARG)
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL6244
8 Samples
Download data: CEL
Series
Accession:
GSE40883
ID:
200040883
13.

Cellular retinoic acid binding protein 2 (CRABP2) inhibits tumor growth by two distinct mechanisms

(Submitter supplied) CRABP2 potently suppresses carcinoma cell growth, yet the mechanism(s) that underlie this activity remain incompletely understood. Two distinct functions are known for CRABP2: 1) the classical function of this protein is to directly deliver retinoic acid (RA) to the nuclear retinoic-acid receptorthereby activate gene expression, and 2) in the absence of RA, CRABP2 directly binds to the RNA-binding and stabilizing protein, HuR, and markedly strengthens its interactions with target mRNAs. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL16686
12 Samples
Download data: CEL, CHP
Series
Accession:
GSE62291
ID:
200062291
14.

SIRT1 deficiency enhances RA induced mESC differentiation

(Submitter supplied) Retinoid homeostasis is critical for normal embryonic development, and both the deficiency and excess of these compounds are associated with congenital malformations. Here we found that SIRT1, the most conserved mammalian NAD+-dependent deacetylase, contributes to the maintenance of homeostatic retinoic acid (RA) signaling and modulates mouse embryonic stem cell (mESC) differentiation. Our data show that SIRT1 deficiency enhances RA signaling, thereby accelerating mES cell differentiation in response to RA. more...
Organism:
Homo sapiens; Mus musculus
Type:
Expression profiling by array
Platform:
GPL4133
16 Samples
Download data: TXT
Series
Accession:
GSE59140
ID:
200059140
15.

An essential role for UTX in resolution and activation of bivalent promoters

(Submitter supplied) In the present study, we show that UTX plays an essential role in resolving and activating many retinoic acid (RA)-inducible bivalent genes during the RA-driven differentiation of mouse ESCs treated with a physiologically relevant RA concentration (0.2 μM). We showed that UTX loss and UTX knockdown interfered with the RA-induced differentiation of mouse ESCs. Therefore, our findings indicate that the UTX-mediated resolution and activation of many RA-inducible bivalent genes, including numerous Hoxa-d cluster genes, are required for RA-driven differentiation of mouse ESCs.
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
36 Samples
Download data: WIG
Series
Accession:
GSE76692
ID:
200076692
16.

Global identification of retinoic acid regulated enhancers and silencers

(Submitter supplied) Retinoic acid (RA) is known to regulate many genes during development by acting as a ligand for nuclear RA receptors that bind RA response elements (RAREs). However, identification of RAREs required to activate or repress specific genes during development has been quite difficult. Here, we focused on identification of RAREs in the developing trunk of vertebrate embryos during the early stages of body axis extension when RA controls neuromesodermal progenitor differentiation, spinal cord neurogenesis, somitogenesis, and forelimb bud initiation. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
10 Samples
Download data: BW
Series
Accession:
GSE131624
ID:
200131624
17.

Global identification of retinoic acid regulated genes

(Submitter supplied) Retinoic acid (RA) signaling plays a major role in controlling several developmental processes in vertebrate embryos. RA repression of caudal Fgf8 has emerged as a crucial mechanism through which RA controls body axis extension, somitogenesis, and spinal cord neurogenesis. The role of RA in Fgf8 repression is supported by mechanistic studies demonstrating direct RA repression through a nearby RA response element that recruits NCOR in an RA-dependent manner. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
2 Samples
Download data: XLSX
Series
Accession:
GSE131584
ID:
200131584
18.

Retinoic acid specifically enhances embryonic stem cell metastate marked by Zscan4

(Submitter supplied) Pluripotency confers Embryonic Stem Cells (ESCs) the ability to differentiate in ectoderm, endoderm, and mesoderm derivatives, producing the majority of cell types. Although the majority of ESCs divide without losing pluripotency, it has become evident that ESCs culture consists of multiple cell populations with different degrees of potency that are spontaneously induced in regular ESC culture conditions. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL4358
8 Samples
Download data: TXT
Series
Accession:
GSE75977
ID:
200075977
19.

A distal enhancer maintaining Hoxa1 expression orchestrates retinoic acid-induced early ESCs differentiation

(Submitter supplied) Retinoic acid (RA) induces rapid differentiation of ESCs, partly by activating expression of the transcription factor Hoxa1, which regulates downstream target genes that promote ESCs differentiation. However, mechanisms of RA-induced Hoxa1 expression and ESCs early differentiation remain largely unknown. Here, we identify a distal enhancer interacting with the Hoxa1 locus through a long-range chromatin loop. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL21273 GPL17021
9 Samples
Download data: TXT, WIG
20.

Reconstructing divergent retinoid-induced cell fate-regulatory programs in stem cells [ChIP-Seq]

(Submitter supplied) We have integrated dynamic RXRa binding, chromatin accessibility and promoter epigenetic status with the transcriptional activity inferred from RNA polymerase II mapping and transcription profiling. This demonstrated a temporal organization structure, in which early events are preferentially enriched for common GRNs, while cell fate specification is reflected by the activation of late programs in a cell-type specific manner. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
52 Samples
Download data: BED, PDF, TXT
Series
Accession:
GSE68540
ID:
200068540
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