GEO DataSets

(Submitter supplied) In this study we provide evidence that cancer associated fibroblasts in mouse and human PDAC models are proficient in the synthesis of monounsaturated fatty acids and may feed these MUFAs to cancer cells, enabling their evasion of SFA-associated lipotoxicity in the tumor microenvironment. The desaturation of SFAs to MUFAs by SCD is an oxygen-dependent process and cancer cells experience hypoxia in the PDAC TME. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL33762

8 Samples

Download data: H5AD

(Submitter supplied) We isolated E11.5 TrkC neurons and profiled chromatin accessibility (ATAC), Runx3, Brn3a, Islet1 binding and Histone H3 acetylated on lysine 27 (H3K27Ac) during early development of DRG TrkC neurons by Cut&Run

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21626

26 Samples

Download data

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

Organism:

Mus musculus

Type:

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

Platform:

GPL21626

21 Samples

Download data: BW, TXT

(Submitter supplied) CD4+ T helper 17 (Th17) cells encompass a spectrum of cell states including homeostatic cells that maintain physiological functions such as barrier integrity and pathogenic cells that drive autoimmune tissue inflammation. Identifying the regulators that determine these cell states will provide means to control tissue inflammation without compromising the physiological functions of Th17 cells. Here, we identified TCF1 as the key regulator that determines Th17 cell state. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21626

13 Samples

Download data: BW

(Submitter supplied) Groundbreaking research in the last decade has definitively established human pluripotent stem cells (hPSCs) as a powerful source for the unlimited generation of dopamine (DA) neurons used in cell-based therapy in Parkinson’s disease (PD). However, DA neurons constitute a heterogeneous group of cells with different molecular identities and, consequently, different functions and innervation targets. Moreover, the inaccessibility of the human brain has so far hindered our understanding of the highly complex human DA system and, therefore, the design of DA neuron subtype-specific differentiation protocols for more effective cell replacement therapies. Currently, DA neurons – located in human ventral midbrain – can only be reliably distinguished based on their projection patterns. Here, we used hPSCs to derive and then transplant DA neurons into a rat model of PD. After one year of transplantation, we performed single nucleus RNA sequencing (snRNAseq) of ~80,000 human nuclei to transcriptionally define cell type composition and obtained a comprehensive map of DA neuron molecular identities. Exploiting the fact that transplanted DA neurons innervated and integrated within the host circuitry, we then combined snRNAseq with axonal retrograde AAV barcoding to trace the projection patterns of molecularly distinct human DA neuron subtypes in the grafts. We thus defined human DA neuron transcriptional profiles based on their target-specific outgrowth in the host brain. The resulting datasets provide an unprecedented resource both for elucidating the molecular basis of human DA neuron diversity as well as for developing more targeted cell-based therapies, with major implications for outcomes of PD patients.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

21 Samples

Download data: RDS

(Submitter supplied) Transgenic mice and organoid models, such as three-dimensional tumoroid cultures, have emerged as powerful tools for investigating cancer development and targeted therapies. Yet, the extent to which these preclinical models recapitulate the cellular identity of heterogeneous malignancies, such as neuroblastoma (NB), remains to be validated. Here we characterize the transcriptional landscape of TH-MYCN tumors by single-cell RNA sequencing (scRNA-seq) and developed novel ex vivo tumoroids. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

14 Samples

Download data: CSV

(Submitter supplied) The efficacy of hepatic arterial infusion chemotherapy (HAIC) with oxaliplatin (OXA) and 5-fluorouracil (5-Fu) for treating advanced perihilar cholangiocarcinoma (pCCA) has been demonstrated, yet the survival benefits of HAIC for pCCA patients vary. Here, we aimed to screen out HAIC resistance-related bile microRNAs (miRNAs) and explore the functions of specific bile miRNAs in pCCA based on high-throughput sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: XLSX

(Submitter supplied) To analyze gene expression profiles at the single-cell level in pigs infected with PRRSV (Porcine Reproductive and Respiratory Syndrome Virus), aiming to understand the dynamic changes in gene expression, immune responses, and cellular interactions during PRRSV infection, and identify potential targets for intervention or prevention

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26351

36 Samples

Download data: MTX, TSV

(Submitter supplied) Epithelial-mesenchymal transition (EMT) is driven by transcriptional and epigenetic reprogramming. However, it is now well established that the final step of gene expression, translation, is also key to the establishment of physiopathological phenotypes, and one of its regulators is the ribosomes themselves. Using genome-wide analyses, we report on how the translational landscape evolves and how the translational machinery rearranges itself during EMT. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18573

12 Samples

Download data: TXT

(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) Epigenetic macromolecular enzyme complexes tightly regulate gene expression at the chromatin level and have recently been found to colocalize with RNA splicing machinery during active transcription1; however, the precise functional consequences of these interactions are uncertain. Here, we identify unique interactions of the CoREST repressor complex (LSD1-HDAC1-CoREST) with components of the RNA splicing machinery and their functional consequences in tumorigenesis. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: MTX, TSV

(Submitter supplied) We used CUT&RUN to evaluate the genome-wide mapping of human SMYD3 and H3K4me3 in HN-6 and 5-3 (SMYD3 KO) cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30173

9 Samples

Download data: BED, BIGWIG

(Submitter supplied) We used RNA-seq to evaluate the transcriptomic changes induced by permanent SMYD3 KO in the HPV-negative head and neck squamous cell carcinoma cell lines HN-6.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: CSV

(Submitter supplied) The vagus nerves are important carriers of sensory information from the viscera to the central nervous system. Emerging evidence suggests that sensory signaling through the right, but not the left, vagus nerve evokes striatal dopamine release and reinforces appetitive behaviors. However, the extent to which differential gene expression within vagal sensory neurons contributes to this asymmetric reward-related signaling remains unknown. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32190

8 Samples

Download data: CSV, XLSX

(Submitter supplied) We have previously demonstrated that preconditioning flap donor with electrical stimulation (ES) could increase the survival area of pedicled perforator flaps in a rat model. However, the detailed molecular mechanisms remain unclear. In this study, we first verified the effects of ES through in vivo and in vitro experiments. Then we explored the underlying mechanisms in vitro. The results indicated that preconditioning with ES could not only increase the flap survival area but mitigate human umbilical vein endothelial cells (HUVECs) dysfunction. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: TXT

(Submitter supplied) Background. The blood-brain barrier (BBB) regulates immune cell entry into the CNS, and various strategies have been developed to target this barrier in efforts to alleviate neuroinflammation in neurodegenerative diseases. α4β1 is crucial for T cell influx into the CNS. In the context of HIV, CD4 T cells drive viral infiltration, while CD8 T cells are essential for viral clearance. This dual role complicates strategies aimed at targeting T cell entry during HIV infection, yet it remains an area that has not been thoroughly explored. more...

Organism:

Macaca mulatta; blank sample

Type:

Other

Platforms:

GPL29487 GPL27943

288 Samples

Download data: DCC, PKC, TIFF

(Submitter supplied) After spinal cord injury (SCI), macrophages engage in the phagocytosis of myelin debris and dead cells, transforming into foam cells. Nevertheless, the ultimate fate and functional role of these foam cells remain unclear, while their inflammatory phenotype elicits ongoing controversy. We discovered that macrophages transform into foam cells through 3 stages, which were phagocytosis, digestion, and lipid overload. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

48 Samples

Download data: CSV, XLS

(Submitter supplied) Effect-based methods (EBM) are of growing interest in environmental monitoring programs. Few EBM have incorporated transcriptomics even though these provide a wealth of biological information and can be modeled to yield transcriptomic points of departure (tPODs). The study objectives were to: A) characterize cytotoxic effects of soil extracts on the rainbow trout RTgill-W1 and the human Caco-2 cell lines; B) measure gene expression changes and calculate tPODs; and C) compare in vitro responses to available measures of plastic-related compounds and metals. more...

Organism:

Oncorhynchus mykiss; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29994 GPL24676

552 Samples

Download data: TXT

(Submitter supplied) Glioblastoma (GBM) leads to severe systemic and local immunosuppression, and immunotherapies have had limited success. One of the hallmarks of GBM immunosuppression is poor T cell infiltration and significant intratumoral T cell dysfunction. IL-15 is a promising immunocytokine with the ability to stimulate T cell activation and proliferation. In this study, we evaluate the treatment efficacy of RLI (an IL-15 superagonist) delivered to tumor cells using a tumor-selective retroviral replicating vector (RRV) in the poorly immunogenic syngeneic murine SB28 and Tu2449 models of GBM. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL34328

8 Samples

Download data: CSV, MTX, TSV, TXT

(Submitter supplied) Effective therapies for pancreatic ductal adenocarcinoma (PDAC) have been largely elusive. Prior proteogenomic studies of PDAC have been limited to bulk samples limiting the ability to define tumor-intrinsic targets and understanding tumor heterogeneity. Here, we perform Multiplexed kinase Inhibitor Beads and Mass Spectrometry (MIB-MS) on 102 patient derived xenografts (PDX) derived from 14 unique primary PDAC to define the tumor-intrinsic kinome landscape. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL18573

88 Samples

Download data: CSV