GEO DataSets

(Submitter supplied) Tissue damage and repair are hallmarks of inflammation. Despite a wealth of information on the mechanisms that govern tissue damage, mechanistic insight on how inflammation affects repair is lacking. Here, we investigated how interferons influence tissue repair after damage to the intestinal mucosa. We found that type III, not type I or II, interferons delay epithelial cell regeneration by inducing the upregulation of Z-DNA-binding protein 1 (ZBP1). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: CSV, H5, H5AD, XLSX

(Submitter supplied) In this study we compared the effects of ALK inhibitor on the gene expression, activation of cell signaling pathways, and functional properties of cells derived from a patient with Anaplastic Large Cell Lymphoma. we used microarrays to map the genome-wide gene expression patterns in ALK+TCL cells in response to ALK inhibition.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

24 Samples

Download data: CEL

(Submitter supplied) Analysis of single cell RNA-seq, CITE-seq data and bulk RNA-seq data on cells isolated from the livers of mice following PBS and APAP (paracetamol/acetaminophen) administration. Spatial Transcriptomics analysis was performed using 10x Visium platform on mouse livers 48hrs post PBS or APAP administration. We also analysed single cell RNA-seq data on CD64+F4/80+ macrophages isolated from the livers of Trem2 fl/fl mice and CD64CRE Trem2 fl/fl mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24247 GPL21103

42 Samples

Download data: CSV, H5

(Submitter supplied) Temozolomide kills cancer cells by forming O6-methylguanine (O6-MeG), which leads to cell cycle arrest and apoptosis. However, O6-MeG repair by O6-methylguanine-DNA methyltransferase (MGMT) contributes to drug resistance. Characterizing genomic profiles of O6-MeG could elucidate how O6-MeG accumulation is influenced by repair, but there are no methods to map genomic locations of O6-MeG. Here, we developed an immunoprecipitation- and polymerase-stalling-based method, termed O6-MeG-seq, to locate O6-MeG across the whole genome at single-nucleotide resolution. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL34281

36 Samples

Download data: TSV

(Submitter supplied) Glioblastoma is incurable and in urgent need of improved therapeutics. We identify a small compound, Gliocidin, that kills glioblastoma cells while sparing nontumor replicative cells. Gliocidin activity targets a de novo purine synthesis vulnerability in glioblastoma through indirect inhibition of inosine monophosphate dehydrogenase 2 (IMPDH2). IMPDH2 blockade reduces intracellular guanine nucleotide levels causing nucleotide imbalance, replication stress, and tumor cell death. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL24676

16 Samples

Download data: CSV, RDS

(Submitter supplied) The mRNA-binding protein KSRP (KH-type splicing regulatory protein) is known to modulate immune cell functions post-transcriptionally e.g. by reducing the mRNA stability of cytokines. It is known that KSRP binds AU-rich motifs (ARE) within the 3´-untranslated region of mRNA spe-cies, which in many cases encode dynamically regulated proteins like cytokines. Innate myeloid immune cells, such as polymorphonuclear neutrophils (PMN) or macrophages (MAC) eliminate pathogens by multiple mechanisms, including phagocytosis, as well as secretion of chemo- and cytokines. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

12 Samples

Download data: TSV

(Submitter supplied) Intermittent fasting (IF) reduces the inflammatory symptoms of Rheumatoid Arthritis (RA); however, its anti-inflammatory underlying molecular mechanisms are unknown. Aim: To investigate the effect of IF on joint inflammatory molecular mechanisms in collagen-induced arthritis (CIA) through DNA microarray and clinical and histopathological evaluations. Methods: CIA was induced in sixteen male DBA/1 mice divided into two groups, one received every other day IF for four weeks. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL21877

4 Samples

Download data: CEL, CHP, XLSX

(Submitter supplied) Single-molecule correlated chemical probing (smCCP) is an experimentally concise strategy for characterizing higher-order structural interactions in RNA. smCCP data yield rich, but complex, structural information on base pairing, conformational ensembles, and tertiary interactions. To date, through-space communication specifically measuring RNA tertiary structure has been difficult to isolate from structural communication reflective of other interactions. more...

Organism:

Enterococcus faecalis

Type:

Other

Platform:

GPL24867

15 Samples

Download data

(Submitter supplied) Allergic rhinitis (AR) is a typical allergic disease mediated by immunoglobulin E (IgE), which greatly affects the quality of life and is more sensitive to change of seasons due to various nasal symptoms. AR worsening symptoms can lead to more dangerous diseases, there is an urgent need to develop safe and effective treatments. Cirsium japonicum (CSJ) is a plant that has been used in traditional medicine due to its various efficacy and safety; so far, the effects and major mechanisms of CSJ on AR have not been reported. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30215

15 Samples

Download data: RESULTS, TXT

(Submitter supplied) The Open Problems Perurbation Prediction (OP3) dataset is to-date the largest single-cell small molecule perturbation dataset in primary tissue with multiple donor replicates. Compounds are dosed in cultured peripheral blood mononuclear cells (PBMCs), enabling the robust computation of perturbation effects on gene expression across four distinct cell type populations: T-cells, B-cells, NK cells, and Myeloid cells. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL24676

102 Samples

Download data: H5AD

(Submitter supplied) Activation of thyroid stimulating hormone receptor (TSHR) fundamentally leads to hyperthyroidism. To elucidate TSHR signaling, we conducted transcriptome analyses for hyperthyroid mice that we generated by overexpressing TSH. TSH overexpression drastically changed their thyroid transcriptome. In particular, enrichment analyses identified the cell cycle, phosphatidylinositol-3 kinase/Akt pathway, and Ras-related protein 1 pathway as possibly associated with goiter development. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

21 Samples

Download data: XLSX

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

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL16192 GPL17225

12 Samples

Download data: BW

(Submitter supplied) Genomes pervasively produce long non-coding RNAs (lncRNAs) of largely unknown functions. Some of these lncRNAs have been implicated in roles related to ageing and associated diseases. Here we characterize aal1 (ageing-associated lncRNA 1) which is induced in non-dividing, ageing cells of fission yeast. Deletion of aal1 shortens the chronological lifespan of non-dividing cells, while ectopic overexpression of aal1 from a plasmid prolongs their lifespan, indicating that this lncRNA acts in trans. more...

Organism:

Schizosaccharomyces pombe

Type:

Other

Platform:

GPL16192

6 Samples

Download data: BW, XLSX

(Submitter supplied) Cell death plasticity is crucial for modulating tissue homeostasis and immune responses, but our understanding of the molecular components that regulate cell death pathways to determine cell fate remains limited. Here, a CRISPR screen of acute myeloid leukemia cells identifies protein tyrosine phosphatase non-receptor type 23 (PTPN23) as essential for survival. Loss of PTPN23 activates nuclear factor-kappa B, apoptotic, necroptotic, and pyroptotic pathways by causing the accumulation of death receptors and toll-like receptors (TLRs) in endosomes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

76 Samples

Download data: CSV, TXT

(Submitter supplied) Phthalates are ubiquitous pollutants in the environment; however, the mechanisms of phthalate-associated reproductive disorders in men are not fully understood. The aim of this study is to investigate associations between urinary phthalate metabolite concentrations and sperm DNA methylation. The study was conducted on 697 men from three prospective pregnancy cohorts: Longitudinal Investigation of Fertility and the Environment (LIFE) Study, Sperm Environmental Epigenetics and Development Study (SEEDS), and Environment and Reproductive Health (EARTH) Study.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL29753

697 Samples

Download data: IDAT, TXT

(Submitter supplied) Single-cell nascent RNA sequencing is essential for understanding how a genome drives cell diversity. We developed scFLUENT-seq, a single-cell method that captures genome-wide transcription with brief metabolic labeling. Our analysis shows that only 3~6% of the genome is transcribed per cell in a 10-minute window, compared to over 80% in bulk, revealing significant variability in how individual cells interpret the genome. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

1 Sample

Download data: BW

(Submitter supplied) Nucleolar ribosomal DNA (rDNA) repeats control ribosome manufacturing. rDNA harbors a ribosomal RNA (rRNA) gene and an intergenic spacer (IGS). RNA polymerase (Pol) I transcribes rRNA genes yielding the rRNA components of ribosomes. Pol II at the IGS induces rRNA production by preventing Pol I from excessively synthesizing IGS non-coding RNAs (ncRNAs) that can disrupt nucleoli. At the IGS, Pol II regulatory processes and whether Pol I function can be beneficial remain unknown. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL28352

6 Samples

Download data: TDF

(Submitter supplied) Proneural gliomas are aggressive brain tumors characterized by enrichment of oligodendrocyte progenitor cell (OPC) transcripts and genetic alterations. In this study we sought to identify transcriptional and epigenetic differences between OPCs with Trp53 deletion and PDGF-BB overexpression (BB-p53n), which form aggressive gliomas when transplanted in mouse brains, and those carrying only p53 deletion (p53n), which do not. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

9 Samples

Download data: TXT

(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) Three Prime Repair Exonuclease 1 (TREX1) gene mutations have been associated with Aicardi-Goutières Syndrome (AGS) - a rare, severe pediatric autoimmune disorder that primarily affects the brain and has a poorly understood etiology. Microglia are brain-resident macrophages indispensable for brain development and implicated in multiple neuroinflammatory diseases. However, the role of TREX1 - a DNase that cleaves cytosolic nucleic acids, preventing viral- and autoimmune-related inflammatory responses - in microglia biology remains to be elucidated. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

5 Samples

Download data: MTX, TSV