txid40674[Organism:exp] - GEO DataSets

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Select item 2002673101.

Microenvironment Shapes Small Cell Lung Cancer Neuroendocrine States and Presents Therapeutic Opportunities

(Submitter supplied) Small-cell lung cancer (SCLC) is the most fatal form of lung cancer. Intra-tumoral heterogeneity, marked by neuroendocrine (NE) and non-neuroendocrine (non-NE) cell states, defines SCLC, but the drivers of SCLC plasticity are poorly understood. To map the landscape of SCLC tumor microenvironment (TME), we apply spatially resolved transcriptomics and quantitative mass spectrometry-based proteomics to metastatic SCLC tumors obtained via rapid autopsy. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21290
12 Samples

Download data: XLSX

Series

Accession:: GSE267310

ID:: 200267310

Select item 2002672952.

Microneedle-mediated Delivery of Immunomodulators Restores Immune Privilege in Hair Follicles and Reverses Immune-Mediated Alopecia

(Submitter supplied) Disorders in the regulatory arm of the adaptive immune system result in autoimmune-mediated diseases. While systemic immunosuppression is the prevailing approach to manage them, it fails to achieve long-lasting remission due to concomitant suppression of the regulatory arm and carries the risk of heightened susceptibility to infections and malignancies. Alopecia Areata is a condition characterized by localized hair loss due to autoimmunity. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24247
9 Samples

Download data: TXT

Series

Accession:: GSE267295

ID:: 200267295

Select item 2002672433.

Compressed phenotypic screening empowers scalable biological discovery (PDAC screens)

(Submitter supplied) High-throughput phenotypic screens leveraging biochemical perturbations and high-content readouts are poised to advance therapeutic discovery, yet they remain constrained by limitations of scale. To address this, we establish a method of pooling exogenous perturbations followed by computational deconvolution to compress a screen’s required sample, labor, and financial input. We benchmark the approach with a bioactive small molecule library and a high-content imaging readout, demonstrating the feasibility and increased efficiency of compressed experimental designs compared to conventional approaches. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL18573
54 Samples

Download data: MTX, TSV

Series

Accession:: GSE267243

ID:: 200267243

Select item 2002671724.

Endothelial Pd1 orchestrates cerebrovasculature homeostasis and oligodendrogenesis during brain development

(Submitter supplied) Purpose: To explore further into the mechanisms by which endothelial PD1 controls cerebrovascular development and oligodendrogenesis, we employed RNA-seq to examine genome-wide alterations in endothelial cells from P0 conditional PD1 knockout mice, comparing them with their wild-type littermates. Methods: mRNA was extracted from P0 isolated endothelial cells of Pd1fl/fl and Pd1cKO-Tie2 mice, and the quality and quantity were assessed using the Agilent 2100 Bioanalyzer. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
4 Samples

Download data: XLS

Series

Accession:: GSE267172

ID:: 200267172

Select item 2002671505.

Cancer-associated MDM2 W329G mutant attenuates ribosomal stress-mediated p53 responses to promote cell survival and glycolysis

(Submitter supplied) Although amplification/overexpression is the predominant mechanism for the oncogenic properties of MDM2, an increasing number of MDM2 somatic missense mutations were identified in cancer patients with the recent advances in sequencing technology. Here, we characterized an MDM2 cancer-associated mutant variant W329G identified from patient samples that contain a wild-type p53 gene. We found that the MDM2 W329G mutant was resistant to the inhibitory effect of ribosomal protein L11 (RPL11) on MDM2-mediated p53 ubiquitination and degradation, in line with its defect on RPL11 binding. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
16 Samples

Download data: TXT

Series

Accession:: GSE267150

ID:: 200267150

Select item 2002670876.

Real-time quantitative PCR analysis of human CRC patients tumor tissues and compared normal tissues

(Submitter supplied) Tumor tissues and compared normal tissues were collected from 3 CRC patients. The nrStar™ Human snoRNA PCR Array was used to analyze the differentially expressed snoRNAs associated with colorectal cancer.

Organism:: Homo sapiens

Type:: Other

Platform:: GPL30066
6 Samples

Download data: TXT

Series

Accession:: GSE267087

ID:: 200267087

Select item 2002670727.

Platform-based gene regulation by an endoderm-specific lncRNA via stabilizing nuclear speckles

(Submitter supplied) Nuclear speckles (NSs), one of the key non-membrane nuclear bodies, participate in transcription, RNA processing, and chromatin organization, yet their precise functions and mechanisms in vivo remain elusive. Here we show that Falcor, an endoderm-specific long non-coding RNA (lncRNA), is necessary and sufficient for maintaining structural integrity of NSs in mouse liver cells. Disruption and reinstatement of NSs by Falcor coordinately regulate more than one thousand genes, including those related to metabolic processes. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL21103
46 Samples

Download data: TXT

Series

Accession:: GSE267072

ID:: 200267072

Select item 2002670478.

Transthyretin orchestrates vitamin B12-induced stress resilience

(Submitter supplied) Background: Chronic stress significantly contributes to mood- and anxiety disorders. Previous data suggest a correlative connection between vitamin B12 supplementation, depression, and stress resilience. However, the underlying mechanisms are still poorly understood. Methods: Using the chronic variable stress mouse model coupled with RNA-sequencing, we determined vitamin B12-induced transcriptional changes related to stress resilience. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24247
12 Samples

Download data: TSV

Series

Accession:: GSE267047

ID:: 200267047

Select item 2002670389.

Genomewide identification of replication fork stalling/pausing sites and the interplay between RNA Pol II transcription and DNA replication progression

(Submitter supplied) DNA replication progression can be affected by the presence of physical barriers on the DNA, like the RNA Polymerases, leading to replication stress and DNA damage. Nonetheless, we do not know the overall influence of transcription on DNA replication progression. To characterize what happens at sites where DNA replication forks stall and pause, we establish a genome-wide approach to identify them. This approach uses multiple timepoints to identify replication fork/stalling hotspots as the replication progresses through the genome. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL21697
4 Samples

Download data: TXT

Series

Accession:: GSE267038

ID:: 200267038

Select item 20026703610.

Trefoil factor 2 expressed by the murine pancreatic acinar cells is required for the development of islets and for beta cell function during aging

(Submitter supplied) Exocrine-to-endocrine crosstalk in the pancreas is crucial to maintain beta cell function. However, the molecular mechanisms underlying this crosstalk are largely undefined. Trefoil factor 2 (Tff2) is a secreted factor known to promote the proliferation of beta cells in vitro, but its physiological role in vivo in the pancreas is unknown. Also, it remains unclear which pancreatic cell type expresses Tff2 protein. more...

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24247
16 Samples

Download data: TXT

Series

Accession:: GSE267036

ID:: 200267036

Select item 20026701411.

Spermine-induced DNA methylation change in human macrophages

(Submitter supplied) Polyamines, crucial molecules involved in cell proliferation and growth, play a pivotal role in cancer development and progression. Within the tumor microenvironment, macrophages, key components of the immune system, exhibit a complex relationship with polyamines. Evidence suggests that polyamines can modulate macrophage polarization, influencing their functional phenotypes. Here, we detected the gene DNA methylation changes in spermine-stimulated human macrophages isolated from PBMCs and TAMs.

Organism:: Yersinia enterocolitica; Toxoplasma gondii; Salmonella enterica subsp. enterica serovar Typhimurium; Mammarenavirus choriomeningitidis; Orthohantavirus puumalaense; Leptospira interrogans; Rickettsia typhi; Mycobacterium tuberculosis variant bovis; Mycobacterium tuberculosis; Mycobacterium tuberculosis variant microti; Mycobacterium canetti; Orthohantavirus seoulense; Yersinia pseudotuberculosis; Rickettsia prowazekii; Bartonella quintana; Mycobacterium avium; Homo sapiens; Streptobacillus moniliformis; Bartonella henselae; Francisella tularensis subsp. tularensis; Francisella tularensis subsp. holarctica; Campylobacter jejuni; Francisella tularensis subsp. novicida; Yersinia pestis; Staphylococcus aureus; Mycobacterium avium subsp. paratuberculosis; Cowpox virus; Escherichia coli O157:H7; Francisella tularensis subsp. mediasiatica; Paslahepevirus balayani

Type:: Methylation profiling by array

Platform:: GPL21445
4 Samples

Download data: IDAT, TXT

Series

Accession:: GSE267014

ID:: 200267014

Select item 20026701212.

Effect of over-expression of SNORA28 on gene expression in HCT116 cells

(Submitter supplied) SNORA28 is highly expressed in CRC and associated with poor prognosis of patients. HCT116 cells were transfected with lentivirus overexpressing SNROA28 and then performed RNA-seq analysis to provide a molecular basis for further exploring the SNORA28 function in CRC.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL20301
6 Samples

Download data: TXT

Series

Accession:: GSE267012

ID:: 200267012

Select item 20026699013.

Haploinsufficient phenotypes promote selection of PTEN and ARID1A deficient clones in human colon.

(Submitter supplied) Normal human tissues are known to be composed of a pactchwork of mutant clones but with limited implications on cancer risk. PTEN and ARID1A deficient clones were detected in the human colon using immunohistrochemistry and were found to be the product of monoallelic loess. They were associated with a bias in clone dynamics which resulted in positive selection in the tissue. Heterozygous mutations were introduced in intestinal organoids which were subjected to bulk RNA-seq to describe the molecular mechanisms behind their positive selection. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL24676
16 Samples

Download data: CSV

Series

Accession:: GSE266990

ID:: 200266990

Select item 20026697914.

Ubiquitylation of Pol II controls early stages of the transcription cycle.

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

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:: GPL30173
54 Samples

Download data: BW

Series

Accession:: GSE266979

ID:: 200266979

Select item 20026697315.

Ubiquitylation of Pol II controls early stages of the transcription cycle [TT-seq]

(Submitter supplied) Control of RNA Polymerase II (Pol II) through ubiquitylation is essential for the DNA-damage response. Here we reveal a distinct ubiquitylation pathway in human cells that targets excessive and defective Pol II molecules at the initial stages of the transcription cycle. This pathway, mediated by ARMC5CUL3 ubiquitin ligase, drives homeostatic Pol II turnover, and is further enhanced when early stages of transcription - initiation and pausing - are perturbed. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL30173
18 Samples

Download data: BW

Series

Accession:: GSE266973

ID:: 200266973

Select item 20026697216.

Ubiquitylation of Pol II controls early stages of the transcription cycle [ChIP-seq]

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL30173
36 Samples

Download data: BW

Series

Accession:: GSE266972

ID:: 200266972

Select item 20026692317.

RNA-seq expression analysis of liver, adipose, skeletal muscle, heart, and pancreatic islets from DO founder strain mice fed high-fat, high-sugar diet. [liver]

(Submitter supplied) RNA-seq was performed on samples of frozen tissue (liver, adipose, skeletal muscle, heart, and pancreatic islets) from the eight founder stains for the Diversity Outbred mice. The mice were fed a high-fat, high-sugar diet to sensitize them to the development of diabetes.