GEO DataSets

(Submitter supplied) Macrophages engulf apoptotic bodies and cellular debris as part of homeostasis, but they can also phagocytosis live cells such as aged red blood cells. Pharmacologic reprogramming with the SMAC mimetic LCL-161 in combination with T cell-derived cytokines can induce macrophages to phagocytosis live cancer cells in mouse models. Here we extend these findings to encompass a wide range of monovalent and bivalent SMAC mimetic compounds, demonstrating that live cell phagocytosis is a class effect of these agents. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

32 Samples

Download data: CSV

(Submitter supplied) Background: Effective treatment for Alzheimer’s disease (AD) remains an unmet need. Thus, identifying patients with mild cognitive impairment (MCI) who are at high-risk of progressing to AD is crucial for early intervention. Methods: Blood-based transcriptomics analyses were performed using a longitudinal study cohort to compare progressive MCI (P-MCI, n=28), stable MCI (S-MCI, n=39), and AD patients (n=49). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

116 Samples

Download data: TXT

(Submitter supplied) Regulatory T cells (Tregs) are promising cellular therapies to induce immune tolerance in organ transplantation and autoimmune disease. The success of chimeric antigen receptor (CAR) T-cell therapy for cancer has sparked interest in using CARs to generate antigen-specific Tregs. Here, we compared CAR with endogenous T cell receptor (TCR)/CD28 activation in human Tregs. Strikingly, CAR Tregs displayed increased cytotoxicity and diminished suppression of antigen-presenting cells and effector T (Teff) cells compared with TCR/CD28 activated Tregs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

22 Samples

Download data: TXT

(Submitter supplied) Secondary mutation of KIT/PDGFRA is the main reason that contributes to the multi-drug resistance phenotype of advanced GIST in the clinical setting. SHP2 is a specific signal transducer of KIT. Therefore, the combination of approved KIT/PDGFRA kinase inhibitors and SHP2 inhibitors is a promising treatment strategy for advanced GIST patients. Here, we treated GIST cells with the SHP2 inhibitor SHP099 and sequenced the total mRNA to analyze the effect of SHP2 inhibition on GIST cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

18 Samples

Download data: TXT, XLSX

(Submitter supplied) In stem cell-derived β (SC-β) cells, metabolic abnormalities persist as obstacles to glucose responsiveness and functional maturation, with the primary metabolic bottlenecks yet to be identified. This study demonstrated that restoring pyruvate kinase 1 (PKM1) re-established pyruvate kinase activity, effectively reversing the SC-β-cell identity loss and functional impairment associated with phosphoenolpyruvate (PEP) accumulation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: MTX, TSV

(Submitter supplied) To investigate how the major HIV-1 structural protein Gag packages viral genomes efficiently, we replaced the NC domain of Gag with RNA binding domains from heterologous cellular RNA binding proteins to generate Gag chimeras. We hypothesize that the Gag chimeras that preferentially bind to purine-rich RNA sequences will package viral genomes efficiently. We performed CLIP-seq to identify the RNA sequences bound by WT Gag and Gag chimeras in cells, at the plasma membrane, and in virions.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

20 Samples

Download data: TXT

(Submitter supplied) To investigate how the major HIV-1 structural protein Gag packages viral genomes efficiently, we replaced the NC domain of Gag with RNA binding domains from heterologous cellular RNA binding proteins to generate Gag chimeras. We hypothesize that the Gag chimeras that preferentially bind to purine-rich RNA sequences will package viral genomes efficiently. We performed CLIP-seq to identify the RNA sequences bound by WT Gag and Gag chimeras in cells, at the plasma membrane, and in virions.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

37 Samples

Download data: TXT

(Submitter supplied) To investigate how the major HIV-1 structural protein Gag packages viral genomes efficiently, we replaced the NC domain of Gag with RNA binding domains from heterologous cellular RNA binding proteins to generate Gag chimeras. We hypothesize that the Gag chimeras that preferentially bind to purine-rich RNA sequences will package viral genomes efficiently. We performed CLIP-seq to identify the RNA sequences bound by WT Gag and Gag chimeras in cells, at the plasma membrane, and in virions.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

49 Samples

Download data: TXT

(Submitter supplied) During mouse gastrulation, the formation of germ layers proceeds concurrently with the transition pluripotency state and the allocation of the multipotent epiblast cells to the germ layer derivatives. Lineage analysis and fate-mapping studies have revealed that groups of cells in different regions of the epiblast and the primitive streak of the gastrulating embryo are allocated to separate progenitors of the ectoderm, mesoderm and endoderm lineages three germ layers with descendants of each progenitor contributing to specific types of germ layer derivatives. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34281

3 Samples

Download data: MTX, TSV

(Submitter supplied) Breastfeeding is vital for reducing morbidity and mortality, yet exclusive breastfeeding rates are low, with insufficient milk supply being a major weaning factor whose molecular causes remain largely unknown. In this study, we collected fresh milk samples from 30 lactating individuals, classified as low, normal, or high milk producers at multiple postpartum stages, and conducted extensive genomic and microbiome analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

11 Samples

Download data: CSV, ZIP

(Submitter supplied) Breastfeeding is vital for reducing morbidity and mortality, yet exclusive breastfeeding rates are low, with insufficient milk supply being a major weaning factor whose molecular causes remain largely unknown. In this study, we collected fresh milk samples from 30 lactating individuals, classified as low, normal, or high milk producers at multiple postpartum stages, and conducted extensive genomic and microbiome analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

22 Samples

Download data: CSV

(Submitter supplied) The cells were treated with a combination of media containing 10 or 5 mM glucose and 0 or 25 μM cariporide for 48 hours. A total of four groups were established: NG (normal glucose), CAR (cariporide), LG (low glucose), and LGCAR (low glucose and cariporide).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: TXT

(Submitter supplied) The fetal brain is thought to be dependent upon the placenta for factors that play a specific role in its early development. The tight linkage between the two organs has given rise to the term, the placenta-brain axis. The mouse placenta produces a unique signature pattern of miRNAs target transcripts associated with early fetal brain development, including ones regulating neurogenesis. We hypothesize that placenta-derived extracellular vesicles (EV) transport their molecular cargo, including small RNA, from the placenta to the brain, whereupon their contents can induce pleiotropic effects. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: CSV, TXT

(Submitter supplied) As an essential regulator of higher-order chromatin structures, CTCF is a highly conserved DNA binding protein with a central DNA-binding domain of 11 tandem zinc fingers, which are flanked by N- and C-terminal domains of intrinsically disordered regions. The N-terminal domain interacts with cohesin complex and the central ZF domains recognize a large range of diverse genomic sites. However, the function of C-terminal unstructured domain remains less understood. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: BW

(Submitter supplied) As an essential regulator of higher-order chromatin structures, CTCF is a highly conserved DNA binding protein with a central DNA-binding domain of 11 tandem zinc fingers, which are flanked by N- and C-terminal domains of intrinsically disordered regions. The N-terminal domain interacts with cohesin complex and the central ZF domains recognize a large range of diverse genomic sites. However, the function of C-terminal unstructured domain remains less understood. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: BW

(Submitter supplied) As an essential regulator of higher-order chromatin structures, CTCF is a highly conserved DNA binding protein with a central DNA-binding domain of 11 tandem zinc fingers, which are flanked by N- and C-terminal domains of intrinsically disordered regions. The N-terminal domain interacts with cohesin complex and the central ZF domains recognize a large range of diverse genomic sites. However, the function of C-terminal unstructured domain remains less understood. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

32 Samples

Download data: BW

(Submitter supplied) As an essential regulator of higher-order chromatin structures, CTCF is a highly conserved DNA binding protein with a central DNA-binding domain of 11 tandem zinc fingers, which are flanked by N- and C-terminal domains of intrinsically disordered regions. The N-terminal domain interacts with cohesin complex and the central ZF domains recognize a large range of diverse genomic sites. However, the function of C-terminal unstructured domain remains less understood. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

12 Samples

Download data: BEDGRAPH

(Submitter supplied) RNA modification play vital roles in renal fibrosis. However, whether ac4C modification functions in renal fibrogenesis remains unknown. Here, we found that NAT10-ac4C axis plays pro—fibrotic role in kidney. ac4C RIP sequencing demonstrated NAT10-ac4C axis functions via regulating multiple master genes of exosome secretion in tubular epithelial cells. In summary, targeting NAT10-ac4C axis is a promising strategy for renal fibrosis.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

12 Samples

Download data: XLSX

(Submitter supplied) To investigate the differentially expressed genes and the pathways they might alter upon loss of MUC16 and subsequent perturbation of its downstream signaling We performed gene expression profiling analysis using data obtained from RNA-seq of the two different conditions (WT versus MUC16-knockout) (three replicates each).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: TXT

(Submitter supplied) Gene expression in glioma cell lines

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

18 Samples

Download data: TSV