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Items: 1 to 20 of 8942

1.

PIEZO2 mechanoreceptor-expressing fibroblasts in keloids cause short-term recurrence after surgical resection

(Submitter supplied) Keloids are characterized by persistent scar tissue growth that causes abnormal sensory perceptions due to mechanical stress. But the molecular dysfunction and disease-specific cells that fashion keloid pathophysiology are still not evident. Here, we found a distinct subpopulation of fibroblasts with enhanced expression of PIEZO2 in the dermal layer of keloid patients experiencing dysesthesia, including pain and pressure-tactile itch. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20301
30 Samples
Download data: TXT
Series
Accession:
GSE274709
ID:
200274709
2.

Identification of replicative aging and inflammatory aging signatures via whole-genome CRISPRi screens

(Submitter supplied) Aging is one of the greatest risk factors for chronic diseases. Research on aging at the cellular level, especially in adult stem cells, is conducive to a comprehensive understanding of the molecular processes of aging. We performed multiple systematic genome-wide CRISPR interference (CRISPRi) screenings in human primary mesenchymal stem cells (MSC) derived from adipose tissues. Notably, we identified potential novel regulators in the progress of MSC senescence in terms of both replicative senescence and inflammatory induced senescence. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL20301
6 Samples
Download data: XLSX
Series
Accession:
GSE268569
ID:
200268569
3.

Engineering biomimetic bone marrow niche with gene modified Mesenchymal Stromal Cells for ex vivo culture of human Hematopoietic Stem and Progenitor cells

(Submitter supplied) Hematopoietic Stem and Progenitor Cells (HSPCs) gene therapy has shown significant progress, with commercial approval for at least four distinct haematological disorders, and poised for a rapid expansion in the upcoming years. Despite these advancements, the ex vivo culture of HSPCs continues to present significant challenges. The stress induced by ex vivo culture can negatively impact transplantation outcomes, while the need for exogenous cytokine supplementation contributes to the high costs associated with gene therapy products. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20301
8 Samples
Download data: XLSX
Series
Accession:
GSE292072
ID:
200292072
4.

SLNCR-E2F1 oncogenic complexes promote melanoma formation

(Submitter supplied) The long non-coding RNA SLNCR and the transcription factor E2F1 both have oncogenic activities in melanoma. Here we show that melanoma metastasis depends upon the formation of an oncogenic SLNCR–E2F1 complex. Unbiased computational analyses of patient samples revealed worse overall survival only in melanoma patients overexpressing both SLNCR and E2F1. Blocking SLNCR–E2F1 complex formation without reducing the levels of either SLNCR or E2F1 reversed melanoma invasion ex vivo and melanoma extravasation in mice. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20301
6 Samples
Download data: TSV
Series
Accession:
GSE270372
ID:
200270372
5.

Dissecting Non-Coding GWAS Loci with High-Resolution 3D Chromatin Interactions Reveals Causal Genes with Relevance to Heart Failure [RNA-seq]

(Submitter supplied) Heart failure is caused in part by cardiac remodeling processes that include the death of cardiac myocytes and their replacement by cardiac fibroblasts. We hypothesized that these two cell types may harbor epigenetic contexts in which heart disease-associated non-coding SNPs perturb gene expression relevant to disease. Accordingly, we generated high-resolution Hi-C data layered with functional genomic information to annotate and link putative distal regulatory elements in heart disease-associated loci to gene promoters. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20301
3 Samples
Download data: TXT
Series
Accession:
GSE281465
ID:
200281465
6.

Dissecting Non-Coding GWAS Loci with High-Resolution 3D Chromatin Interactions Reveals Causal Genes with Relevance to Heart Failure [Hi-C]

(Submitter supplied) Heart failure is caused in part by cardiac remodeling processes that include the death of cardiac myocytes and their replacement by cardiac fibroblasts. We hypothesized that these two cell types may harbor epigenetic contexts in which heart disease-associated non-coding SNPs perturb gene expression relevant to disease. Accordingly, we generated high-resolution Hi-C data layered with functional genomic information to annotate and link putative distal regulatory elements in heart disease-associated loci to gene promoters. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL20301
4 Samples
Download data: HIC
Series
Accession:
GSE281463
ID:
200281463
7.

Dissecting Non-Coding GWAS Loci with High-Resolution 3D Chromatin Interactions Reveals Causal Genes with Relevance to Heart Failure [ATAC-seq]

(Submitter supplied) Heart failure is caused in part by cardiac remodeling processes that include the death of cardiac myocytes and their replacement by cardiac fibroblasts. We hypothesized that these two cell types may harbor epigenetic contexts in which heart disease-associated non-coding SNPs perturb gene expression relevant to disease. Accordingly, we generated high-resolution Hi-C data layered with functional genomic information to annotate and link putative distal regulatory elements in heart disease-associated loci to gene promoters. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL20301 GPL18573
4 Samples
Download data: NARROWPEAK
Series
Accession:
GSE281462
ID:
200281462
8.

Cuttag sequencing revealed the regulatory targets of transcription factor c-MYC in human chondrocytes

(Submitter supplied) The transcription factor MYC can promote chondrocyte differentiation in previous studies, but its target remains unclear. We used cutt sequencing to explore its regulatory targets.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20301
2 Samples
Download data: BW
Series
Accession:
GSE270645
ID:
200270645
9.

Changes in chromatin accessibilityof chondrocytes identified by ATAC-seq in vitro

(Submitter supplied) Chromatin accessibility change of chondrocytes in vitro remains unclear. We performed ATAC-seq of P1,P3, and P6 cells in vitro to explore chromatin accessibility change.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20301
3 Samples
Download data: BW
Series
Accession:
GSE270644
ID:
200270644
10.

Genome-wide flow sorting CRISPRi screen identify PTGES3 as a novel therapeutic target of AR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL24676 GPL20301
14 Samples
Download data: BED
Series
Accession:
GSE180036
ID:
200180036
11.

Genome-wide flow sorting CRISPRi screen identify PTGES3 as a novel therapeutic target of AR [mRNA-seq]

(Submitter supplied) Comprehensively understanding the gene regulatory network that modulates the biology of the Androgen Receptor (AR) oncogene is a central goal of prostate cancer research. To study regulators of AR, we knock-in a split neon green fluorescent protein onto the AR in prostate cancer cells creating an endogenous AR reporter cell line. Using our endogenous AR reporter, we performed a genome-scale fluorescence-activated cell sorting based CRISPRi screen to comprehensively identify genes that modulate AR protein levels. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20301
4 Samples
Download data: TXT
Series
Accession:
GSE180035
ID:
200180035
12.

Genome-wide flow sorting CRISPRi screen identify PTGES3 as a novel therapeutic target of AR [ATAC-seq]

(Submitter supplied) Comprehensively understanding the gene regulatory network that modulates the biology of the Androgen Receptor (AR) oncogene is a central goal of prostate cancer research. To study regulators of AR, we knock-in a split neon green fluorescent protein onto the AR in prostate cancer cells creating an endogenous AR reporter cell line. Using our endogenous AR reporter, we performed a genome-scale fluorescence-activated cell sorting based CRISPRi screen to comprehensively identify genes that modulate AR protein levels. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20301
6 Samples
Download data: BED
Series
Accession:
GSE180034
ID:
200180034
13.

PIK3CA and KRAS codon-specific mutations differentially toggle pathway activity and alter sensitivity to inavolisib (GDC-0077)

(Submitter supplied) To explore the single and combinatorial effect of MEK and PI3KCA inhibitors in CRC lines with PIK3CA/KRAS mutations, we used the MULTI-seq CMOs to perform a highly multiplexed single-cell RNA-seq.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL20301 GPL18573 GPL24676
26 Samples
Download data: CSV, MTX, TXT
Series
Accession:
GSE248412
ID:
200248412
14.

Spatial transcriptome profiling for nasopharyngeal carcinoma [GeoMx-DSP]

(Submitter supplied) As the first human DNA tumour virus Epstein-Barr virus (EBV) is detectable in over 90% of nasopharyngeal carcinoma (NPC) patients in the endemic regions. Genome-wide analysis of 3D chromosome conformation revealed the virus-host chromatin interactions induce spatial reorganisation of loops and compartments, exhibiting “enhancer infestation” and “H3K27 bivalency” at EBV interaction regions (EBVIRs). Through this mechanism, EBV hijacks KDM5B, a genome stability gatekeeper, and its binding targets leading to aberrant activation of the EBVIRs-enhancer-KDM5B signature. The cancer cells with this signature had increased MYC activation, DNA damage responses, and epigenetic plasticity for epithelial-immune cell dual features with metastatic potential. Our multi-centre multi-omics study further confirmed that this signature was highly relevant to chromosome instability and could be utilised as a risk factor for distant metastasis. This study highlights a novel paradigm where latent viral episomes could alter host high-order epigenotype, promoting transcriptional rewiring and risk of metastasis in NPC.
Organism:
Homo sapiens
Type:
Other
Platform:
GPL20301
28 Samples
Download data: DCC, PKC, TXT
Series
Accession:
GSE299775
ID:
200299775
15.

Rapid generation of functional vascular organoids via simultaneous transcription factor activation of endothelial and mural lineages

(Submitter supplied) Vascular organoids (VOs) are valuable tools for studying vascular development, disease, and regenerative medicine. However, controlling endothelial and mural compartments independently remains challenging. Here, we present a streamlined method to generate VOs from induced pluripotent stem cells (iPSCs) via orthogonal activation of the transcription factors ETV2 and NKX3.1 using Dox-inducible or modRNA systems. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20301
15 Samples
Download data: MTX, TSV, TXT
Series
Accession:
GSE281002
ID:
200281002
16.

Blood transcriptome of ICU pateints with blood stream infections on admission

(Submitter supplied) Knowledge of the contribution of the pathogen to the heterogeneity of the host response to severe infection is limited. We aimed to compare the host response in critically ill patients with a blood stream infection (BSI).
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20301
132 Samples
Download data: TXT
Series
Accession:
GSE276095
ID:
200276095
17.

Phenotypic and transcriptomic characterisation of the human B cell response to a novel Ebola vaccine regimen (Ad26.ZEBOV, MVA-BN-Filo)

(Submitter supplied) Ebola virus disease (EVD) outbreaks are increasing in frequency — threatening health and wellbeing of affected communities. Early and effective public health measures to manage outbreaks rely on health care and frontline workers; consequently, protecting these at high-risk groups is a key pillar of EVD vaccination strategies. IgG specific to the viral glycoprotein is used as the correlate of protection in recent vaccine licensure. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20301
126 Samples
Download data: CSV
Series
Accession:
GSE273114
ID:
200273114
18.

Systematic characterization of human placenta-derived miRNAs and identification of autophagy-related miRNAs in gestational diabetes mellitus [miRNA-seq]

(Submitter supplied) The objective of this study was to identify and investigate the roles of miRNAs in GDM. In the current study, placental miRNA expression profiles of normal controls and GDM patients were analyzed using high-throughput sequencing. Bioinformatics analysis identified that 4 were upregulated and 6 were downregulated in 10 most differential miRNA in GDM placentas compared with NC placentas. GO and KEGG enrichment analyses demonstrated that metabolic process-associated terms and metabolic pathways that may be related to GDM were significantly enriched. more...
Organism:
Homo sapiens
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL20301
6 Samples
Download data: XLS
Series
Accession:
GSE206042
ID:
200206042
19.

TRIM33 loss reduces Androgen Receptor transcriptional output and H2BK120 ubiquitination

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL20301 GPL24676
129 Samples
Download data: BW, NARROWPEAK
Series
Accession:
GSE284522
ID:
200284522
20.

TRIM33 loss reduces Androgen Receptor transcriptional output and H2BK120 ubiquitination [ChIP-seq]

(Submitter supplied) The Androgen Receptor (AR) is a ligand-dependent transcription factor that drives prostate cancer development and progression. Although, a detailed effect on AR biology has been described for a number of interacting proteins, many AR coregulators remain to be characterized in relation to their distinct impact on AR function. Here, we describe TRIM33 as a conserved AR-interactor across multiple prostate cancer cell lines. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL24676 GPL20301
93 Samples
Download data: BW, NARROWPEAK
Series
Accession:
GSE284519
ID:
200284519
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