GEO DataSets

(Submitter supplied) Background The safety of CRISPR-based gene editing methods is of the utmost priority in clinical applications. Previous studies have reported that Cas9 cleavage induced frequent aneuploidy in primary human T cells, but whether cleavage-mediated editing of base editors would generate off-target structure variations remains unknown. Here, we investigated the potential off-target structural variations associated with CRISPR/Cas9, ABE and CBE editing in mouse embryos and primary human T cells by whole-genome sequencing and single-cell RNA-seq analyses. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: MTX, TSV

(Submitter supplied) Despite antiretroviral therapy, HIV mainly persists in memory CD4+ T cells in people living with HIV. Most long-lived viral reservoir cells are infected near the time of therapy initiation. A better understanding of the early events in reservoir seeding presents opportunities for preventing latent reservoir formation. Here, we demonstrated that CD4+ T cells expressing CCR5, permissive to HIV-1 infection, are effector or terminally differentiated cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT

(Submitter supplied) Since its first identification in prostate cancers and prostate tissues, transient receptor potential melastatin-subfamily member 8 (TRPM8) is subsequently found to be overexpressed in a wide range of cancers and is shown to be implicated in tumorigenesis and tumor progression. Here, we used N-(3-aminopropyl)-2-[(3-methylphenyl) methoxy] -N-(2-thienylmethyl) benzamide hydrochloride (AMTB), a specific TRPM8 antagonist, to explore its antitumoral effect on osteosarcoma. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: TXT

(Submitter supplied) In this study, we explored the role of FXR in the response to ionizing radiation (IR) in A549 human lung cancer cells. FXR was stably knocked down in A549 cells using shRNA, and four experimental groups were established: control A549 cells (non-irradiated), control A549 cells (irradiated), FXR knockdown A549 cells (non-irradiated), and FXR knockdown A549 cells (irradiated). RNA sequencing (RNA-seq) was performed to identify gene expression changes associated with FXR knockdown and irradiation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: XLS

(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; Other

6 related Platforms

99 Samples

Download data: BED, BEDGRAPH, BW

(Submitter supplied) RNA modifications regulate how RNAs metabolize and function to impact development and diseases. N6,2’-O-dimethyladenosine (m6Am) is one such modification and despite being abundant, m6Am function remains unclear. Here, we identified cleavage and polyadenylation factor, PCF11 as a m6Am-specific binding protein. Direct quantification of mature versus nascent RNAs revealed that m6Am does not regulate mRNA stability but promotes transcription of nascent RNAs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL20795 GPL11154

8 Samples

Download data: BEDGRAPH, XLSX

(Submitter supplied) Releated to the single nucleus RNA sequencing data displayed in Extended Data Figure 1

Organism:

Macaca mulatta; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL14954

28 Samples

Download data: MTX, TSV

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare the transcriptome differences between knockdown LINC00205 and negative control gastric cancer cells. Methods: Total RNA from the BGC823 cells with LINC00205 knockdown and negative control were isolated using RNeasy mini kit (Qiagen, Germany). Paired-end libraries were synthesized by using the TruSeq RNA Sample Preparation Kit (Illumina, USA) following TruSeq RNA Sample Preparation Guide. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT

(Submitter supplied) UHRF1 maintains DNA methylation by recruiting DNA methyltransferases (DNMT’s) to chromatin. These dynamics are well defined for mouse STELLA (mSTELLA) but poorly characterized for human STELLA (hSTELLA). Herein, we demonstrate that hSTELLA is defective, while mSTELLA is fully proficient in associating with UHRF1 and inhibiting the abnormal DNA methylation and oncogenic functions of UHRF1 in human cancer cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

51 Samples

Download data: TXT

(Submitter supplied) Adenosine deaminases acting on RNA (ADARs) impact diverse cellular processes and pathological conditions. While we possess important insights into their roles in adult tissues, their functions in early cell fate specification remain less understood. To address this, we devised a comprehensive framework to investigate ADARs in human development. We began by charting time-course RNA editing profiles in human organs from fetal to adult stages, enabling broad insights into RNA editing trends across diverse tissues. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL13112 GPL11154

18 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) Gene expression profile of different prostate cancer PDX tumor, and cell models to study tumorigenic programs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

20 Samples

Download data: TXT

(Submitter supplied) Genome-wide measurements of histone modifications and transcripton factors binding in Luca145.2 PDX tumor and 42D cell models to studyBRD4 and H3K27ac regulate the tumorigenic programs

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

16 Samples

Download data: BED, BROADPEAK, BW

(Submitter supplied) Genome-wide measurements of chromatin accessibility in prostate cancer cells to study the tumorigenic programs.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

3 Samples

Download data: BED, BW

(Submitter supplied) Atherosclerosis, characterized by the buildup of plaque in arteries, is a major cause of cardiovascular mortality worldwide, as there is no efficient strategy for targeted therapy. However, we have developed a new drug delivery platform called MoNP, which is loaded with VP, a potent inhibitor of YAP/TAZ signaling. To investigate the MoNP-VP treatment effect, EC were pretreated with MoNP or MoNP-VP then induced the inflammation by TNFalpha. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: TXT

(Submitter supplied) Proteasomes hydrolyze most intracellular proteins. Immunoproteasome is a specific form of proteasome implicated in inflammation, cancer and autoimmune diseases. Modulation of immunoproteasome activity and content is a promising direction for the management of socially important pathologies. Using previously obtained reporter colorectal cancer cell lines, we tested how various commonly used compounds including ibuprofen, acetylsalicylic acid, vitamin C, caffeine and others, affect immunoproteasome expression. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: COUNTS

(Submitter supplied) The 5’ cap, catalyzed by capping enzyme, RNGTT, is a vital mRNA modification for the functionality of mRNAs and dysregulated in cancer cells. The m6A writer METTL3 is a regulator of mRNA stability and protein translation, and its expression is altered in various cancers, including lung cancer cells. We identified a METTL3 motif in the mRNA of RNGTT and investigated whether METTL3 could regulate the expression of RNGTT. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT

(Submitter supplied) This dataset features transcriptomic profiles of feeder-free extended pluripotent stem cells (ffEPSCs) and their parentalderived from human embryonic stem cells (ESCs). ffEPSCs were generated using a Matrigel-based feeder-free system combined with a chemical cocktail to convert conventional ESCs into ffEPSCs. Generated using Smart-seq2 and sequenced on Illumina HiSeq 2000, the dataset explores transcriptional profiles and heterogeneity of ESCs and ffEPSCs, providing insights into early human development and stem cell biology.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: TXT

(Submitter supplied) Genome-wide association studies (GWAS) have identified over 300 loci associated with the inflammatory bowel diseases (IBD), but putative causal genes for most are unknown. We conducted the largest disease-focused expression quantitative trait loci (eQTL) analysis using colon tissue from 252 IBD patients to determine genetic effects on gene expression and potential contribution to IBD. Combined with two non-IBD colon eQTL studies, we identified 194 potential target genes for 108 GWAS loci. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

4 related Platforms

191 Samples

Download data: TXT

(Submitter supplied) Appropriate responses to environmental challenges are imperative for the survival of all living organisms. Exposure to low-dose stresses is recognized to yield increased cellular fitness, a phenomenon termed hormesis. However, our molecular understanding of how cells respond to low-dose stress remains profoundly limited. Here we report that histone variant H3.3-specific chaperone, HIRA, is required for acquired tolerance, where low-dose heat stress exposure confers resistance to subsequent lethal heat stress. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: XLSX

(Submitter supplied) Appropriate responses to environmental challenges are imperative for the survival of all living organisms. Exposure to low-dose stresses is recognized to yield increased cellular fitness, a phenomenon termed hormesis. However, our molecular understanding of how cells respond to low-dose stress remains profoundly limited. Here we report that histone variant H3.3-specific chaperone, HIRA, is required for acquired tolerance, where low-dose heat stress exposure confers resistance to subsequent lethal heat stress. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: BW