GEO DataSets

(Submitter supplied) The effectiveness of antibacterial agents is strongly influenced by its antibacterial mechanism, which, in turn, is dependent on the agent’s topological structure. In addition to oxidative stress (especially caused by reactive oxygen species), known to be a key mechanism for 2D phosphorene structures, physical penetration of bacterial cell membranes is predicted for violet phosphorene nanosheets. In this study, we demonstrate that violet phosphorus (VP) and its exfoliated product, violet phosphorene nanosheets (VPNS), have superior antibacterial capability against pathogens.A series of antibacterial tests and theoretical calculations show that VPNS can inactivate >99.9% of two common pathogens (Escherichia coli and Staphylococcus aureus) and >99% of two “superbugs” (i.e., antibiotic-resistant bacteria, Escherichia coli pUC19 and methicillin-resistant Staphylococcus aureus) via oxidative stress combined with cell membrane penetration by VPNS Moreover, VPNS have higher antibacterial activity than black phosphorene nanosheets in vitro and in vivo. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

6 Samples

Download data: TXT

(Submitter supplied) Neutrophils can efficiently trigger cytotoxicity towards tumor cells and other target cells upon engagement of the IgA receptor CD89. However, the cell-intrinsic factors that influence the induction of cell death upon exposure to neutrophil effector mechanisms in vivo remain largely unknown. To uncover genetic regulators that influence target cell sensitivity to IgA-induced neutrophil-mediated killing, we used a human CD89 (hCD89) transgenic mouse model in which IgA-mediated killing of Her2-positive CD47-deficient murine target cells is mediated by neutrophils. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL16417

18 Samples

Download data: TXT

(Submitter supplied) The key role of tertiary lymphoid structures in autoimmune and non-autoimmune conditions has been recently appreciated. While many of the molecular mechanisms involved in tertiary lymphoid structure formation have been identified, their cellular sources and temporal and spatial relationship remain unknown. Using single-cell RNA-sequencing, spatial transcriptomics and proteomics of minor salivary glands of patients with Sjogren’s disease and Sicca Syndrome, ex-vivo and in vivo functional studies, we construct a cellular and spatial map of key components involved in the formation and function of tertiary lymphoid structures. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

73 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

33 Samples

Download data

(Submitter supplied) How cellular diversity is created is a key question in biology. Embryonic stem cells (ESCs) are pluripotent cells that can develop into any cell type in the body. Yet, the regulatory mechanisms that govern cell fate decisions remain largely unknown. Moreover, although genetically identical, individual ESCs are strikingly heterogeneous regarding their differentiation capacity but the molecular basis for this phenotypic heterogeneity is unclear. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: TXT

(Submitter supplied) To investigate the effect of cholic acid sulfate to MAIT cells, PBMCs were stimulated with each antigen (5-OP-RU, cholic acid sulfates; CA3S and CA7S) and scRNA sequencing was performed. the homeostatic related genes expressed in cholic acid sulfate stimulation, while the inflammatory related gene expressed in 5-OP-RU stimulation. This analysis showed that cholic acid sulfate contributes to maintenance of MAIT cells.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

3 Samples

Download data: CSV

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL24247 GPL17021

52 Samples

Download data: XLSX

(Submitter supplied) Transfer RNAs (tRNAs) play a central and well recognized role in protein synthesis. Recent studies revealed that these molecules can be cleaved to generate tRNA fragments (tRFs) with regulatory functions. Here, we studied the contribution of tRFs to pancreatic β-cell loss during the initial phases of type 1 diabetes (T1D), an autoimmune disorder characterized by the invation of immune cells in the pancreas and progressive loss of insulin-secreting cells. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24247

10 Samples

Download data: XLSX

(Submitter supplied) Slow-cycling cells (SCCs) are a heterogeneous subpopulation of tumor cells. They pre-exist in tumor tissues and evade killing by chemotherapeutics that target mitosis due to their dormant nature. We here utilized varieties of fluorescent dyes or proteins (Claret, H2BeGFP, and Violet) retaining method to label and isolate SCCs, and RNA-seq was performed to understand the gene expression characteristics of subpopulations of SCCs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: TXT

(Submitter supplied) Coordination of cell activity trough Ca2+ waves enables pancreatic β-cells to secrete precise quantities of insulin in response to blood sugar. However, how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging using CaMPARI and single-molecule RNA detection, we reveal a gene-signature depicting a molecularly and metabolically distinct state of first responder β-cells. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

191 Samples

Download data: CSV

(Submitter supplied) Certain cancers, such as acute myeloid leukemia (AML), are caused by malignant stem cells that fail maturation. We sought to mechanistically understand how metabolism might regulate cell fate decisions and to identify metabolic differentiation agents that might be leveraged therapeutically.  We find that nucleotide – purine, pyrimidine, and deoxynucleotide – depletion leads to AML differentiation by way of replication stress. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

158 Samples

Download data: CSV, TSV

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

Organism:

Homo sapiens; Mus musculus

Type:

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

5 related Platforms

284 Samples

Download data: BW, CSV, MTX, TXT

(Submitter supplied) Certain cancers, such as acute myeloid leukemia (AML), are caused by malignant stem cells that fail maturation. We sought to mechanistically understand how metabolism might regulate cell fate decisions and to identify metabolic differentiation agents that might be leveraged therapeutically.  We find that nucleotide – purine, pyrimidine, and deoxynucleotide – depletion leads to AML differentiation by way of replication stress. more...

Organism:

Mus musculus; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL18573

47 Samples

Download data: BW

(Submitter supplied) In this study we analyzed the effects of an altered Cas13a expression in vivo, in presence or absence of ectopically expressed protospacer RNA (plasmid pCV2_SB6), by RNA-sequencing. The genomic modification of the cas13a controlling promoter enables altered expression of cas13a by adding either subinhibitory crystal violet (CV) concentrations (for transcriptional repression of cas13a), or additionally IPTG (for transcriptional induction of cas13a), to the mutant cultures. more...

Organism:

Rhodobacter capsulatus SB 1003

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34167

21 Samples

Download data: WIG

(Submitter supplied) T-lymphocytes from visceral and subcutaneous white adipose tissue (vWAT and sWAT, respectively) can have opposing roles in the systemic metabolic changes associated with obesity. However, few studies have focused on this subject. Claudin-1 (CLDN1) is a protein involved canonically in Tight Junctions (TJs) and tissue paracellular permeability. We evaluated the gene expression in T lymphocytes from vWAT and sWAT and in the whole adipose depots.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23126

22 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23159

16 Samples

Download data: CEL

(Submitter supplied) In the last few years, pulsed electric fields have emerged as promising clinical tools for tumor treatments. This study highlights the distinct impact of a specific pulsed electric field protocol named PEF-5 (0.3 MV/m, 40 µs, 5 pulses) on astrocytes (NHA), medulloblastoma (D283) and gli-oblastoma (U87 NS) cancer stem-like cells. We pursued this goal performing ultrastructural analyses corroborated by molecular/omics approaches to understand the vulnerability or re-sistance mechanisms triggered by PEF-5 exposure in the different cell types. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23159

8 Samples

Download data: CEL

(Submitter supplied) In the last few years, pulsed electric fields have emerged as promising clinical tools for tumor treatments. This study highlights the distinct impact of a specific pulsed electric field protocol named PEF-5 (0.3 MV/m, 40 µs, 5 pulses) on astrocytes (NHA), medulloblastoma (D283) and gli-oblastoma (U87 NS) cancer stem-like cells. We pursued this goal performing ultrastructural analyses corroborated by molecular/omics approaches to understand the vulnerability or re-sistance mechanisms triggered by PEF-5 exposure in the different cell types. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23159

8 Samples

Download data: CEL

(Submitter supplied) The extent to which tissue-resident memory T (TRM) cells in transplanted organs possess alloreactivity is uncertain. This study investigates the alloreactive potential of TRM cells in kidney explants from four patients who experienced severe acute rejection leading to graft loss. Alloreactive T-cell receptors (TCRs) clones were identified in pre-transplant blood samples through mixed lymphocyte reactions, followed by single-cell RNA and TCR sequencing of the proliferated recipient T cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

8 Samples

Download data: CSV

(Submitter supplied) BAP1 is a deubiquitinase (DUB) of the Ubiquitin C-terminal Hydrolase (UCH) family that regulates gene expression and other cellular processes, through its direct catalytic activity on the repressive epigenetic mark histone H2AK119ub, as well as several other substrates. BAP1 is also a highly important tumor suppressor, expressed and functional across many cell types and tissues. In recent work, we demonstrated a cell intrinsic role of BAP1 in the B cell lineage development in murine bone marrow, however the role of BAP1 in the regulation of B cell mediated humoral immune response has not been previously explored. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

10 Samples

Download data: TXT