GEO DataSets

(Submitter supplied) Proteostasis is vital for cellular health, with disruptions leading to pathologies including aging, neurodegeneration and metabolic disorders. Traditionally, proteotoxic stress responses were studied as acute reactions to various noxious factors; however, recent evidence reveals that many stress-response genes exhibit ~12-hour ultradian rhythms under physiological conditions in mammals. These rhythms, driven by an XBP1s-dependent 12h oscillator, are crucial for managing proteostasis. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: BIGWIG

(Submitter supplied) The balk RNA-seq in PBS- and αSyn pre-formed fibril (PFF)-treated neurons was done to investigate the expression levels of gene transcripts enriched in both BG4- and pS129-RIP-seq (GSE234238). Analysis of RNA-seq revealed that the expression levels of these common enriched RNAs in mPFF-treated neurons were little changed in comparison to vehicle-treated neurons.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: CSV

(Submitter supplied) Treatment with the toll-like receptor (TLR) 4 agonist monophosphoryl lipid A (MPLA) conditions innate immunocytes to respond robustly to subsequent infection, a phenotype termed innate immune memory. Our published studies show that metabolic reprogramming of macrophages is a prominent feature of the memory phenotype. We undertook studies to define the functional contributions of tricarboxylic acid (TCA) reprogramming to innate immune memory. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

26 Samples

Download data: TXT

(Submitter supplied) To better understand host/phage interactions and the genetic bases of phage resistance in a model system relevant to potential phage therapy, we isolated several spontaneous mutants of the USA300 S. aureus clinical isolate NRS384 that were resistant to phage K. Six of these had a single missense mutation in the host rpoC gene, which encodes the RNA polymerase beta prime subunit. To examine the hypothesis that the mutations in the host RNA polymerase affect the transcription of phage genes, we performed RNA-seq analysis on total RNA samples collected from NRS384 wild-type (WT) and rpoC G17D mutant cultures infected with phage K, at different time points after infection. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27158

56 Samples

Download data: XLSX

(Submitter supplied) The mouse uterine gene expressions during peri-implantation period at pregnancy day 4 and 6 was investigated by Visium spatial transcriptome.

Organism:

Mus musculus

Type:

Other

Platform:

GPL28457

2 Samples

Download data: CSV, H5, JPG, JSON, MTX, PNG, TSV

(Submitter supplied) Glucocorticoids are an essential part of many multi-agent treatment regimens for lymphoid malignancies where the emergence of glucocorticoid resistance is a significant barrier to a cure. We have previously identified that aberrant chromatin accessibility, at lymphocyte-specific glucocorticoid-response elements (GREs), is associated with drug resistance in acute lymphoblastic leukaemia (ALL). To gain a deeper understanding of regulatory mechanisms leading to these epigenetic alterations, we conducted a multi-omics study, to examine changes in chromatin conformation, following the in-vivo treatment of patient-derived xenografts (PDXs) with glucocorticoid i.e., dexamethasone (DEX). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL16791 GPL28038

21 Samples

Download data: BED, BW, HIC

(Submitter supplied) Non-conventional methylotrophic yeast Komagataella phaffii is an important production host in biotechnology and an emerging model organism. In this work, we studied K. phaffii response to nitrogen starvation during cultivation in media with methanol as the sole carbon source. The results were compared with well-established model yeast Saccharomyces cerevisiae. Some of the observed effects of nitrogen starvation in K. more...

Organism:

Komagataella phaffii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27930

6 Samples

Download data: TXT

(Submitter supplied) Emerging evidence suggest that mitochondrial reactive oxygen species (mROS) production is tightly controlled by electron transport chain (ETC), and increased levels of ROS production is linked to cancer development. The ETC therefore represents a promising way of cancer treatment. However, the epigenetic mechanisms governing the transcription of ETC genes to drive mROS production and cell proliferation remain to be fully characterized in cancer cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: BIGWIG

(Submitter supplied) Mesencephalic astrocyte-derived neurotrophic factor (MANF) is the only neurotrophic factor to be conserved between C. elegans and humans. MANF is a unique neutrotophic factor, as it is a resident ER protein in cells that express it and has a role in regulating ER stress response to tunicamycin exposure and pathogenic Pseudomonas exposure. We sought to further understand the role of MANF by comparing a deletion allele, an overexpression line, and the wild-type in this RNAseq experiment.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18245

9 Samples

Download data: TXT, XLSX

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

Organism:

Homo sapiens; Mus musculus; synthetic construct

Type:

Other

Platforms:

GPL26697 GPL21273 GPL20795

27 Samples

Download data

(Submitter supplied) RNA binding proteins can modulate RNA secondary structures, thus participating in post-transcriptional regulation. The DEAH-box helicase 36 (DHX36) has a remarkable ability to bind and unwind RNA G-quadruplex (rG4) and duplex. However, the transcriptome-wide RNA structure dynamic induced by DHX36 and how structure change subsequently influences RNA fate remain poorly understood. Here, we first identify the endogenous binding sites and specificity of DHX36 based on binding profiles. more...

Organism:

synthetic construct

Type:

Other

Platform:

GPL26697

11 Samples

Download data: TSV

(Submitter supplied) We performed multiomics analysis; single nucleus RNA-seq (snRNA-seq) combined with ATAC (snATAC-seq) with 10XGenomics Multiome platform to generate cell-type-specific gene expression and chromatin accessibility atlas of the mouse polycystic kidney disease on a time course.

Organism:

Mus musculus

Type:

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

Platform:

GPL24247

32 Samples

Download data: CSV, H5, RDS, TBI, TSV

(Submitter supplied) Background & Aims: The association between chronic inflammation and gastric carcinogenesis is well established, but it is not clear how immune cells and cytokines regulate this process. We investigated the role of interleukin 27 (IL27) in the development of gastric atrophy, hyperplasia, and metaplasia (preneoplastic lesions associated with inflammation-induced gastric cancer) in mice with autoimmune gastritis. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

2 Samples

Download data: MTX, TSV

(Submitter supplied) Antibiotic use can lead to expansion of multi-drug resistant pathobionts within the gut microbiome that can cause life-threatening infections. Selective alternatives to conventional antibiotics are in dire need. Here, we describe a Klebsiella PhageBank that enables the rapid design of antimicrobial bacteriophage cocktails to treat multi-drug resistant Klebsiella pneumoniae. Using a transposon library in carbapenem-resistant K. more...

Organism:

Klebsiella pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34705

4 Samples

Download data: CSV

(Submitter supplied) In recent years, microbiome studies revealed that Candida species are common colonisers of the human skin. The distribution of species however varies greatly. Although C. parapsilosis is more likely to resemble skin commensals, opinions are divided, and discrepancies are present regarding C. albicans, that is also often associated with cutaneous candidiasis. Therefore, we aimed to thoroughly assess the nature of skin epithelial cell - Candida interactions. more...

Organism:

Homo sapiens; Candida albicans

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL28323

30 Samples

Download data: CSV

(Submitter supplied) Background: Fetal Alcohol Spectrum Disorders (FASD) cause life-long cognitive and behavioral impairment and are highly prevalent across the world. The effects of developmental ethanol exposure on astrocyte functions in vivo are poorly understood. To fill this gap, we assessed changes in the astrocyte translatome following in vivo developmental ethanol exposure and mechanistically linked some of these changes to altered neuronal development. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

48 Samples

Download data: CSV

(Submitter supplied) Osteoporosis and other metabolic bone diseases are prevalent in the aging population. While bone has the capacity to regenerate throughout life, bone formation rates decline with age and contribute to reduced bone density and strength. Identifying mechanisms and pathways that increase bone accrual in adults could prevent fractures and accelerate healing. G protein-gated inwardly rectifying K+ (GIRK) channels are key effectors of G protein-coupled receptor signaling. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

8 Samples

Download data: CSV

(Submitter supplied) Mutations in RNA splicing factor genes (SF3B1, SRSF2, and U2AF1) are common in AML and MDS and recent studies demonstrate pharmacologic degradation of the RNA splicing factor RBM39 results in preferential killing of splicing factor mutant cells. We therefore conducted a phase II clinical trial (NCT05024994) of the oral RBM39 degrader E7820 at the recommended phase II dose in patients with R/R MDS/AML and a splicing factor mutation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

29 Samples

Download data: CSV

(Submitter supplied) We used RNA-Seq to annotate aberrantly changed biological processes and signaling pathways induced by Ythdf2 loss in microglia isolated from the Ythdf2-/- and the Ythdf2fl/fl mice at P7

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

5 Samples

Download data: TXT

(Submitter supplied) Background: MET inhibitors have demonstrated efficacy in treating patients with non-small cell lung cancer (NSCLC) harboring METex14 skipping alterations. Advancements in spatial profiling technologies have unveiled the complex dynamics of the tumor microenvironment, a crucial factor in cancer progression and therapeutic response. Using spatial profiling, this study investigates the effects of the MET inhibitor tepotinib on the TME in a case of locally advanced NSCLC with a METex14 skipping alteration. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL33991

94 Samples

Download data: DCC