GEO series
The retinoid X receptor has a critical role in synthetic rexinoid-induced increase in cellular all-trans-retinoic acid
GSE244387
Homo sapiens (human)
RNA-seq (gene expression)
24 samples
Submitted 2024/04/02
Platform GPL21697
At a glance
RNA-seq (gene expression) · human · 24 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Samples
- 24 samples: 6 conditions, mostly with about 4 replicates eachGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- The retinoid X receptor has a critical role in synthetic rexinoid-induced increase in cellular all-trans-retinoic acidPloS one · 2024
Summary (written by the submitters)
Rexinoids are agonists of nuclear rexinoid X receptors (RXR) that heterodimerize with other nuclear receptors to regulate gene transcription. A number of selective RXR agonists have been developed for clinical use but their application has been hampered by the unwanted side effects associated with the use of rexinoids and a limited understanding of their mechanisms of action across different cell types.
Read the full summary ↓
Our previous studies showed that treatment of organotypic human epidermis with the low toxicity UAB30 and UAB110 rexinoids resulted in increased steady-state levels of all-trans-retinoic acid (ATRA), the obligatory ligand of the RXR-RAR heterodimers. Here, we investigated the molecular mechanism underlying the increase in ATRA levels using a dominant negative RXRα that lacks the activation function 2 (AF-2) domain. The results demonstrated that overexpression of dnRXRα in human organotypic epidermis markedly reduced signaling by resident ATRA, suggesting the existence of endogenous RXR ligand, diminished the biological effects of UAB30 and UAB110 on epidermis morphology and gene expression, and nearly abolished the rexinoid-induced increase in ATRA levels. Global transcriptome analysis of dnRXRα-rafts in comparison to empty vector-transduced rafts showed that over 95% of the differentially expressed genes in rexinoid-treated rafts constitute direct or indirect ATRA-regulated genes. Thus, the biological effects of UAB30 and UAB110 are mediated through the AF-2 domain of RXRα with minimal side effects in human epidermis. As ATRA levels are known to be reduced in certain epithelial pathologies, treatment with UAB30 and UAB110 may represent a promising therapy for normalizing the endogenous ATRA concentration and signaling in epithelial tissues.
Published in
Belyaeva OV, Klyuyeva AV, Vyas A et al.
· PloS one 2024
· PMID 38557762
· doi:10.1371/journal.pone.0301447
This dataset
Download · which file do I need?
Direct links to NCBI and ENA, 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.
2 · Re-analyse it
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE244387_RAW.tar (it can run to tens of gigabytes).
3 · Start from the raw reads
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1022499 and SRA study SRP463954. Searching any of these in the dataset finder brings you back here.
Study design
6 conditions, mostly with about 4 replicates each
Primary keratinocytes, Control untreated ×4
Primary keratinocytes, Control UAB110 treated ×4
Primary keratinocytes, Control UAB30 treated ×4
Primary keratinocytes, Dominant negative RXRa… ×4
Primary keratinocytes, Dominant negative RXRa… ×4
Primary keratinocytes, Dominant negative RXRa… ×4
Supports a between-group comparison across 24 samples.
How we read this: 6 replicated groups read from 24 sample titles; they account for 24 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
Samples in this study
- GSM7814571 Primary keratinocytes, Control untreated replicate 1 Primary keratinocytes, …
- GSM7814572 Primary keratinocytes, Control untreated replicate 2 Primary keratinocytes, …
- GSM7814573 Primary keratinocytes, Control untreated replicate 3 Primary keratinocytes, …
- GSM7814574 Primary keratinocytes, Control untreated replicate 4 Primary keratinocytes, …
- GSM7814575 Primary keratinocytes, Control UAB110 treated replicate 1 Primary keratinocytes, …
- GSM7814576 Primary keratinocytes, Control UAB110 treated replicate 2 Primary keratinocytes, …
- GSM7814577 Primary keratinocytes, Control UAB110 treated replicate 3 Primary keratinocytes, …
- GSM7814578 Primary keratinocytes, Control UAB110 treated replicate 4 Primary keratinocytes, …
- GSM7814579 Primary keratinocytes, Control UAB30 treated replicate 1 Primary keratinocytes, …
- GSM7814580 Primary keratinocytes, Control UAB30 treated replicate 2 Primary keratinocytes, …
- GSM7814581 Primary keratinocytes, Control UAB30 treated replicate 3 Primary keratinocytes, …
- GSM7814582 Primary keratinocytes, Control UAB30 treated replicate 4 Primary keratinocytes, …
- GSM7814583 Primary keratinocytes, Dominant negative RXRa untreated replicate 1 Primary keratinocytes, …
- GSM7814584 Primary keratinocytes, Dominant negative RXRa untreated replicate 2 Primary keratinocytes, …
- GSM7814585 Primary keratinocytes, Dominant negative RXRa untreated replicate 3 Primary keratinocytes, …
- GSM7814586 Primary keratinocytes, Dominant negative RXRa untreated replicate 4 Primary keratinocytes, …
- GSM7814587 Primary keratinocytes, Dominant negative RXRa UAB110 treated replicate 1 Primary keratinocytes, …
- GSM7814588 Primary keratinocytes, Dominant negative RXRa UAB110 treated replicate 2 Primary keratinocytes, …
- GSM7814589 Primary keratinocytes, Dominant negative RXRa UAB110 treated replicate 3 Primary keratinocytes, …
- GSM7814590 Primary keratinocytes, Dominant negative RXRa UAB110 treated replicate 4 Primary keratinocytes, …
- GSM7814591 Primary keratinocytes, Dominant negative RXRa UAB30 treated replicate 1 Primary keratinocytes, …
- GSM7814592 Primary keratinocytes, Dominant negative RXRa UAB30 treated replicate 2 Primary keratinocytes, …
- GSM7814593 Primary keratinocytes, Dominant negative RXRa UAB30 treated replicate 3 Primary keratinocytes, …
- GSM7814594 Primary keratinocytes, Dominant negative RXRa UAB30 treated replicate 4 Primary keratinocytes, …
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Share this dataset
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.