GEO DataSets

(Submitter supplied) In the post COVID-19 pandemic era, long COVID has emerged as a serious health concern. We generated single-cell RNA sequencing (scRNA-seq) data of peripheral whole blood cells from 18 patients involved in clinical trial studying the effectiveness of comercially available herbal medications in long COVID.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

13 Samples

Download data: CSV

(Submitter supplied) Metastasis is the leading cause of the cancer-related death. To systemically study the dependent factors impacting cancer metastasis, we conducted serial transplantation to obtain ES-2-MC2-Liver cells, a cell line with high metastatic efficiency. We then performed in vivo CRISPR screen using phosphatase and metabolism-focused sgRNA library and ranked differential targeting genes. For further validating the identified gene essentialities in previous results, we generated a mini-library targeting the top-depleted and -enriched genes in metastatic organs and performed in vivo CRISPR screen on ES-2-MC2-Liver cells and SKHEP1 cells. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20795

68 Samples

Download data: TXT

(Submitter supplied) To gain a deeper understanding of the mechanism by lncRNAs involved in glucose metabolism during the progression of HCC, we conducted transcriptome sequencing on HCC cells treated with low (5 mM) and high (25 mM) glucose and carried out analyses for the lncRNAs with a significant change of expression combined with TCGA-LIHC data. Huh7 and PLC cells were treated with low glucose (5mM) or high glucose (25mM) for 48 h, whole-transcriptome sequencing (RNA-Seq) was performed to identify the significant changed lncRNAs with glucose.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

4 Samples

Download data: CSV, XLS

(Submitter supplied) Studies have demonstrated the correlation between kallikrein-related peptidase 5 (KLK5) and cervical cancer prognosis, but studies on the correlation between KLK5 and radiation resistance are rare. Therefore, we aimed to investigate the role of high KLK5 expression in improving radiation resistance in cervical cancer and the underlying mechanisms. Samples from 29 patients with cervical cancer who received definitive radiotherapy without surgical treatment and other antineoplastic treatments (2014–2016) were analyzed. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

10 Samples

Download data: TXT

(Submitter supplied) As a new type of cell death mediated by Gasdermin (GSDM) family, pyroptosis has increasingly become a research hotspot in the fields of biology and medicine. Studies have found that a variety of drugs (such as etoposide and traditional Chinese medicine extracts) can effectively inhibit the occurrence and development of tumors by activating caspase family and GSDM protein family to induce pyroptosis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

6 Samples

Download data: GTF

(Submitter supplied) This study aims to investigate genes regulated by NKX2-3

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20795

2 Samples

Download data: BW, XLS

(Submitter supplied) The precise function of NR4A1 as a transcriptional regulator in cancer remains under investigation. To investive the biological functions and molecular mechanims by which NR4A1 suppresses breast cancer growth, we perform RNA sequence analysis in NR4A1-knockout and control MCF7 cell lines to identify the alterated signaling pathway and celluar possesses in breast cancer. Besides, we also performed ChIP sequences by c-Fos ChIP in in NR4A1-knockout and control MCF7 cell lines to investigate the competitive function of NR4A1 on c-Fos binding to genome.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

6 Samples

Download data: TXT

(Submitter supplied) Purpose: While viruses play critival roles in many human malignancies, the influence of virus infection on the tumor microenviroment(TME) and how this impacts disease progression are poorly characterized. Methods: we applied both Smart-seq2 and 10X Genomics chemistry to ~104000 cells from 19 EBV+ NPC patients and 7 nonmalignant nasopharyngeal biopsies. Results: 1. We have defined the complex interplay between tumor cells, virus infection, and the TME at single-cell resolution. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL20795

56 Samples

Download data: MATRIX, MTX, TSV, TXT

(Submitter supplied) Redondoviridae is a recently identified family of DNA viruses associated with periodontitis. Circular RNAs (circRNAs) emerged as a novel endogenous, conserved noncoding RNAs, which contributed to the virus related immune‐inflammatory response. However, the characteristics and function of circRNAs in Redondoviridae related periodontal inflammation are not yet understood. The present study aimed to analyze the expression profiles of circRNAs in gingival tissues in periodontitis patients with and without Redondoviridae-infection and healthy controls using high-throughput RNA sequencing combined with experimental validation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20795

12 Samples

Download data: TXT

(Submitter supplied) Lysine-specific demethylase 1 (LSD1/KDM1A) is a pivotal epigenetic enzyme that contributes to several malignancies including malignant glioma. LSD1 is a flavin adenine dinucleotide dependent histone demethylase that specifically targets histone H3 lysine (K) 4 mono- (me1) and di-methylation (me2) and H3K9me1/2 for demethylation. Herein we report the development of an LSD inhibitor, S2172, which efficiently penetrates the blood-brain barrier. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

8 Samples

Download data: CSV

(Submitter supplied) Lysine-specific demethylase 1 (LSD1/KDM1A) is a pivotal epigenetic enzyme that contributes to several malignancies including malignant glioma. LSD1 is a flavin adenine dinucleotide dependent histone demethylase that specifically targets histone H3 lysine (K) 4 mono- (me1) and di-methylation (me2) and H3K9me1/2 for demethylation. Herein we report the development of an LSD inhibitor, S2172, which efficiently penetrates the blood-brain barrier. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20795

10 Samples

Download data: BW

(Submitter supplied) TFIIB-related factor 2 (BRF2) crucially recruits RNA polymerase III (Pol III) to type III promoters containing a TATA box. These promoters encompass crucial components such as U6 spliceosomal RNA, tRNA processing enzyme RNase P, and selenocysteine tRNA. The results on cancer occurrence due to overexpression of BRF2 are known, but genetic disorders caused by mutations in BRF2 are still not well understood. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

6 Samples

Download data: RESULTS

(Submitter supplied) To investigate the molecular mechanism that triggers endoplasmic reticulum (ER) stress-induced cellular senescence in breast cancer cells, we established MCF7 cell lines exposed to ATF6α ectopic expression. We then performed gene expression profiling analysis using data obtained from RNA-seq of 9 different cells at three time points.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20795 GPL24676

9 Samples

Download data: TXT

(Submitter supplied) Limited oxygen in solid tumors poses a challenge to successful immunotherapy with NK cells. NK cells have impaired cytotoxicity when cultured in hypoxia (1% oxygen), but not physiologic or atmospheric oxygen (>5%). We sought to analyze the impact of oxygen concentrations on human NK cell biology to determine what factors were driving loss of cytotoxicity and where there were opportunities to overcome hypoxia-induced dysfunction in NK cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

63 Samples

Download data: CSV

(Submitter supplied) Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare undamage chondrocyte and damage chondrocyte whole transcriptomes

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

6 Samples

Download data: TXT

(Submitter supplied) Although HIV-1 integration sites are considered to favor active transcription units in the human genome, high-resolution analysis of individual HIV-1 integration sites have shown that the virus can integrate in a variety of host genomic locations, including non-genic regions, challenging the traditional understanding of HIV-1 integration site selection. Here, we showed that HIV-1 targets R-loops, a genomic structure made up of DNA–RNA hybrids, for integration. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20795

12 Samples

Download data: BED, CSV

(Submitter supplied) Although HIV-1 integration sites are considered to favor active transcription units in the human genome, high-resolution analysis of individual HIV-1 integration sites have shown that the virus can integrate in a variety of host genomic locations, including non-genic regions, challenging the traditional understanding of HIV-1 integration site selection. Here, we showed that HIV-1 targets R-loops, a genomic structure made up of DNA–RNA hybrids, for integration. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20795

72 Samples

Download data: BED

(Submitter supplied) RNA sequencing was performed to analyze the genes whose expression was suppressed by K-975 treatment.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

36 Samples

Download data: CSV

(Submitter supplied) Circular RNA (circRNA) is a type of endogenous single-stranded and covalently closed non-coding RNA that plays emerging roles in tumorigenesis and aggressiveness. However, the functions and underlying mechanisms of circRNAs in regulating gastric cancer progression still remain elusive. We identify circ-hnRNPU, a circRNA derived from exons 5, 6, 7 and 8 of heterogeneous nuclear ribonucleoprotein U (hnRNPU), as a tumor suppressor of gastric cancer progression. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

4 Samples

Download data: TXT

(Submitter supplied) As a core subunit of the m6A methyltransferase complex, the downregulation of METTL3 expression in response to Ang II suggests the potential regulation of m6A modification. Our data suggests METTL3 may mediate the dynamic change in m6A landscapes between Ang II with and without overexpression of METTL3.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL30209 GPL20795

14 Samples

Download data: TXT