GEO DataSets

(Submitter supplied) Natural killer (NK) cells play an integral role in immunosurveillance against myeloid malignancies, with their mature phenotype and abundance linked to prolonged treatment-free remission in chronic myeloid leukemia (CML). However, NK cell function is suppressed during the disease, and the orchestrators of this impairment are not fully understood. Using a chimeric BCR::ABL1+ CML mouse model, we characterized the impact of the leukemic microenvironment on NK cell function and gene transcription. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

9 Samples

Download data: H5, XLSX

(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) DELLA proteins are members of the GRAS-domain family of transcriptional regulators and modulate transcriptional activity through protein-protein interactions with at least 15 different classes of transcription factor. The plant hormone gibberellin (GA) regulates a range of growth and development responses including promoting cell elongation, by triggering the degradation of DELLA proteins. More than 70% of modern wheat (Triticum aestivum L.) varieties carry alleles encoding DELLA proteins that are resistant to GA-mediated degradation. more...

Organism:

Triticum aestivum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23509

24 Samples

Download data: CSV

(Submitter supplied) Astrocyte maturation is crucial for brain function, yet the mechanisms regulating this process remain poorly understood. In this study, we identify the bHLH transcription factors Olig1 and Olig2 as essential coordinators of cortical astrocyte maturation. We demonstrate that Olig1 and Olig2 work synergistically to regulate cortical astrocyte maturation by modulating BMP7 expression. Genetic ablation of both Olig1 and Olig2 results in defective astrocyte morphology, including reduced process complexity, and an immature gene expression profile. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

1 Sample

Download data: MTX, TSV

(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) In Drosophila melanogaster, successful development relies on the precise coordination of both spatial and temporal regulatory axes. The temporal axis governs stage-specific identity and developmental transitions through a number of genes, collectively forming the Metamorphic Gene Network. Among these, Ecdysone inducible protein 93F (E93) serves as the critical determinant for adult specification, but its mechanism of action remains unclear. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30203

18 Samples

Download data: TXT

(Submitter supplied) The reproductive physiology of yaks differs significantly from that of other cattle breeds due to late sexual maturity, low fecundity and short oestrus time. How to improve the reproductive efficiency of yaks has become the main research content and goal of yak reproduction technology. In this study, we collected blood samples from adult female yaks (4-8 years old) during different reproductive periods, including the period of anestrus (Y-A), estrus (Y-E) and pregnancy (Y-P), and investigated the changes of RNA expression and steroid hormone levels in yaks during different reproductive periods by using RNA-seq and target metabolomics, and screened for the genes and regulatory pathways that were differentially expressed. more...

Organism:

Bos grunniens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30409

18 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) Vestimentiferan tubeworms are representative inhabitants of deep-sea chemosynthetic ecosystems. The plume serves as the primary organ in these invertebrates without mouths and guts, facilitating direct metabolic exchange with their surrounding environments. In this study, we present a single-cell transcriptome atlas of Paraescarpia echinospica plume and this study is the initial single-cell transcriptome sequencing for the plume of the deep-sea tubeworm. more...

Organism:

Paraescarpia echinospica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL35098

7 Samples

Download data: GTF, RDS, TXT

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

Organism:

Patiria miniata; Strongylocentrotus purpuratus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

4 related Platforms

16 Samples

Download data: BW, HIC, NARROWPEAK

(Submitter supplied) we generated new reference genome assemblies for two species belonging to two different echinoderm classes: the bat sea star Patiria miniata and the purple sea urchin Strongylocentrotus purpuratus

Organism:

Patiria miniata; Strongylocentrotus purpuratus

Type:

Other

Platforms:

GPL35097 GPL35096

2 Samples

Download data: HIC

(Submitter supplied) While mitochondrial dysfunction is implicated in metabolic dysfunction associated steatohepatitis (MASH), the precise underlying mechanisms remain obscure. Here, we identify the SIRT3-DsbA-L-TFAM axis as a crucial suppressor for mitochondrial stress-induced cGAS activation in the hepatocytes, thereby alleviating MASH in mice. SIRT3 facilitates the deacetylation of Disulfide-bond-A oxidoreductase-like protein (DsbA-L) at lysine residues (Lys165, Lys167, and Lys177), which promotes the interaction between DsbA-L and mitochondrial transcription factor A (TFAM), essential for the preservation of mitochondrial integrity and function. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: TXT

(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) We identified conserved cis-regultaory elements based on their dynamic chromatin accessibility over the gastrula-larva stages

Organism:

Strongylocentrotus purpuratus; Patiria miniata

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL28450 GPL33874

14 Samples

Download data: BW, NARROWPEAK

(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:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

12 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:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34328

2 Samples

Download data: CSV, MTX, TSV