GEO DataSets

(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:

GPL24676 GPL18573 GPL20301

26 Samples

Download data: CSV, MTX, TXT

(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

(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

(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

(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

(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

(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

(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:

GPL20301 GPL24676

93 Samples

Download data: BW, NARROWPEAK

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL20301 GPL18573

17 Samples

Download data: BROADPEAK, BW, CSV, GAPPEDPEAK

(Submitter supplied) Using a hCD34+ humanized mouse tumor model, the single-cell sequencing analysis revealed that in vivo knockdown of EPIC1 enhanced the T cells and macrophage infiltration by activating type I IFNs signaling.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

2 Samples

Download data: CSV

(Submitter supplied) To investigate and determine the role of EPIC1 overexpression in cancer cells, we established EPIC1 overexpressing MCF7 stable cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

2 Samples

Download data: CSV

(Submitter supplied) RNA-Sequencing to determine transcriptome changes in MCF7 cells after treatment with NONO ligands and controls. NONO knockout (sgNONO) or control (sgControl) cells were treated.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

30 Samples

Download data: TXT

(Submitter supplied) Colorectal cancer (CRC) remains a leading cause of cancer death, primarily due to metastatic spread. LIN28B, an RNA-binding protein overexpressed in 30% of CRCs, acts as an oncogene and promotes CRC metastasis. However, the mechanisms through which LIN28B drives these effects remain unclear. In this study, we genetically modified CRC cell lines to overexpress LIN28B, leading to enhanced activation of the PI3K/AKT pathway and increased metastatic potential in mice. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

18 Samples

Download data: CSV, XLSX

(Submitter supplied) A previous study has successfully identified the binding sites of Transcription Factor MIZ1 in murine B cells. In order to shed light on the potential relevance between mouse and human, this experiment aimed to identify MIZ1's binding sites in human B cell lines. By uncovering these binding sites, we can gain insights into the conservation and potential functional significance of MIZ1 in B cell biology across species.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: BW, TXT

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

Organism:

Homo sapiens

Type:

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

5 related Platforms

206 Samples

Download data: BIGWIG, BW, H5, MCOOL, NARROWPEAK, TSV, TXT

(Submitter supplied) Emerging evidence suggests that the epigenetic state, including the DNA methylation, chromatin accessibility and histone modification, is substantially remodeled, leading to transcriptional reprogramming during the transformation of castration resistant adenocarcinoma (CRPC-Adeno) to neuroendocrine (CRPC-NE) lineage and LUAD to LUAD-SCLC lineage . However, the underlying mechanism is largely unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL20301

52 Samples

Download data: TXT

(Submitter supplied) Emerging evidence suggests that the epigenetic state, including the DNA methylation, chromatin accessibility and histone modification, is substantially remodeled, leading to transcriptional reprogramming during the transformation of castration resistant adenocarcinoma (CRPC-Adeno) to neuroendocrine (CRPC-NE) lineage and LUAD to LUAD-SCLC lineage . However, the underlying mechanism is largely unknown. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24676 GPL34284 GPL20301

104 Samples

Download data: BW

(Submitter supplied) Emerging evidence suggests that the epigenetic state, including the DNA methylation, chromatin accessibility and histone modification, is substantially remodeled, leading to transcriptional reprogramming during the transformation of castration resistant adenocarcinoma (CRPC-Adeno) to neuroendocrine (CRPC-NE) lineage and LUAD to LUAD-SCLC lineage . However, the underlying mechanism is largely unknown. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

12 Samples

Download data: NARROWPEAK

(Submitter supplied) The brain avidly consumes glucose to fuel neurophysiology. Cancers of the brain, such as glioblastoma (GBM), relinquish physiological integrity and gain the ability to proliferate and invade healthy tissue. How brain cancers rewire glucose utilization to drive aggressive growth remains elusive. Here, we infused 13C-labeled glucose into patients and mice with brain cancer, coupled with quantitative metabolic flux analysis, to map the fates of glucose-derived carbon in tumor vs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

3 Samples

Download data: TXT

(Submitter supplied) Monkeypox virus (MPXV) infection-associated intestinal manifestations including diarrhea and proctitis have been frequently reported during mpox outbreaks. The clade IIb MPXV strain has caused the 2022-2023 global outbreak, whereas the Ia and Ib strains are causing the concurrent outbreaks in Africa. Here, we found clinical evidence that MPXV can directly infect human intestine to induce lesions. Intriguingly, primary organoids cultured from human ileum and rectum support productive infections of MPXV clade IIb, Ia and Ib strains. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

18 Samples

Download data: TXT