GEO DataSets

(Submitter supplied) Diffuse intrinsic pontine gliomas (DIPG) are paediatric malignant gliomas developing in the brainstem, where resection is unattainable, leaving palliative radiotherapy as the major standard of care. Patients with DIPG have dismal prognosis of 9-12 months of survival and currently there is no effective therapy. Over 80% of DIPGs harbour a mutation in histone 3 (H3.3 or H3.1) resulting in a lysine to methionine substitution (H3K27M). more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL24676 GPL11154

47 Samples

Download data: TSV, WIG

(Submitter supplied) The utilization of single-cell resolved spatial transcriptomics to delineate immune responses during SARS-CoV-2 infection was able to identify macrophages to have elevated expression of IFI27 in areas of infection.

Organism:

Homo sapiens; Mus musculus

Type:

Other

Platform:

GPL33484

116 Samples

Download data: CSV, TXT

(Submitter supplied) Ferroptosis is a form of regulated cell death characterized by iron-dependent overaccumulation of lipid peroxides. It can be prevented by cellular mechanisms such as GPX4-mediated elimination of the lipid peroxides at the cost of glutathione (GSH). Since originally being discovered as a property of RAS-mutant cancer cells, ferroptosis has been shown to be regulated by several important oncogenes and tumor suppressors. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

5 Samples

Download data: TXT

(Submitter supplied) Chromatin landscapes are disrupted during DNA replication and must be restored faithfully to maintain genome regulation and cell identity. The H3-H4 modification landscape is restored by parental histone recycling and post-replication modification of new histone H3-H4. How DNA replication impact on histone H2A-H2B is unknown. Here, we track H2A-H2B modifications and H2A.Z during DNA replication and across the cell cycle using quantitative genomics. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30172 GPL30173 GPL19057

156 Samples

Download data: BW

(Submitter supplied) Chromatin landscapes are disrupted during DNA replication and must be restored faithfully to maintain genome regulation and cell identity. The H3-H4 modification landscape is restored by parental histone recycling and post-replication modification of new histone H3-H4. How DNA replication impact on histone H2A-H2B is unknown. Here, we track H2A-H2B modifications and H2A.Z during DNA replication and across the cell cycle using quantitative genomics. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30173 GPL30172 GPL19057

54 Samples

Download data: BED, BW

(Submitter supplied) We present MultiEditR, the first algorithm specifically designed to detect and quantify RNA editing from Sanger sequencing (z.umn.edu/multieditr). Although RNA editing is routinely evaluated by measuring the heights of peaks from in Sanger sequencing traces, the accuracy and the precision of this approach has yet to be evaluated against gold-standards next-generation sequencing methods. Through a comprehensive comparison to RNA-seq and amplicon based deep sequencing, we show that MultiEditR is accurate, precise, and reliable for detecting endogenous and programmable RNA editing.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: TXT

(Submitter supplied) Methanogenesis allows methanogenic archaea (methanogens) to generate cellular energy for their growth while producing methane. Hydrogenotrophic methanogens thrive on carbon dioxide and molecular hydrogen as sole carbon and energy sources. Thermophilic and hydrogenotrophic Methanothermobacter spp. have been recognized as robust biocatalysts for a circular carbon economy and are now applied in power-to-gas technology. more...

Organism:

Methanothermobacter thermautotrophicus; Methanothermobacter marburgensis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32859 GPL32860

12 Samples

Download data: SF

(Submitter supplied) Background: Poor nutrition during development programs kidney function. No studies on postnatal consequences of decreased perinatal nutrition exist in nonhuman primates (NHP) for translation to human renal disease. Our baboon model of moderate maternal nutrient restriction (MNR) produces intrauterine growth restricted (IUGR) and programs renal fetal phenotype. We hypothesized that the IUGR phenotype persists postnatally influencing responses to a high-fat, high-carbohydrate, high-salt (HFCS) diet. more...

Organism:

Homo sapiens; Papio hamadryas

Type:

Expression profiling by array

Platform:

GPL10558

24 Samples

Download data: TXT

(Submitter supplied) We used a highly sensitive nano-5hmC-Seal method and profiled the genome-wide distribution of 5-hydroxymethylcytosine (5hmC) in plasma cell-free DNA (cfDNA) from 384 patients with bladder, breast, colorectal, kidney, lung, or prostate cancer and 221 controls. We used machine learning and developed plasma cfDNA 5hmC signatures that are highly sensitive for cancer detection and cancer origin determination. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL24676 GPL21697

605 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL24676

69 Samples

Download data: BROADPEAK, NARROWPEAK, TAB

(Submitter supplied) Background: SWI/SNF (BAF) chromatin remodeling complexes regulate lineage-specific enhancer activity by promoting accessibility for diverse DNA-binding factors and chromatin regulators. Additionally, they are known to modulate the function of the epigenome through regulation of histone post-translational modifications and nucleosome composition, although the way SWI/SNF complexes govern the epigenome remains poorly understood. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

10 Samples

Download data: BROADPEAK, NARROWPEAK, TXT

(Submitter supplied) Here, we report that intranasal administration of MSCs to non-inflamed lung microenvironment changed transcriptomic profiles compared to control group. We found 674 differentially regulated genes unique for the short-term model, while only 75 genes were unique for the prolonged observations, suggesting waning of the low-grade inflammation and active resolution in the longer time point. Moreover, we evaluated the enrichment of differentially expressed genes (DEGs) in the gene ontologies, signaling pathways, and mapped predicted interactions using clusterProfiler v.4.0.0. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

15 Samples

Download data: XLSX

(Submitter supplied) A reliable animal model that can mimic the GBM intracranial infiltration and Blood-brain barrier (BBB) interaction is necessary for effective therapeutics development. Here, we report a zebrafish-based orthotopic GBM xenograft model, in which GBM cells from different species and even patients, can robustly propagate and faithfully reproduce their histological characteristics. Single-cell RNA-seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. more...

Organism:

Homo sapiens; Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20795 GPL23085

34 Samples

Download data: CSV

(Submitter supplied) In this study, we utilize the RNA-seq of germ cell to uncover the early germ cell development. To obtain fish with defined sex, we crossed domesticated zebrafish with the Nadia strain that has a female-dominant W segment. These fish were placed on a ziwi:GFP background to facilitate sorting of fluorescent germ cells for transcriptomic analysis. We analyzed the transcriptomes of germ cells at 10 to 14 days postfertilization (dpf), when sex dimorphic changes started to appear.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

22 Samples

Download data: TSV

(Submitter supplied) We ablated RBM24 from human embryonic stem cells (hESCs) using CRISPR/Cas9 techniques. Although RBM24-/- hESCs still differentiated into sarcomere-hosting cardiomyocytes, they exhibited disrupted sarcomeric structures with punctate Z-lines due to impaired myosin replacement during early myofibrillogenesis. Transcriptomics revealed >4000 genes regulated by RBM24. Among them, core myofibrillogenesis proteins (e.g. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL17021

6 Samples

Download data: TXT, XLSX

(Submitter supplied) Several genome-wide CRISPR knockout screens have been conducted to identify host factors regulating SARS-CoV-2 replication, but the models used have often relied on overexpression of ACE2 receptor and didn’t express TMPRSS2 protease, known to be important for viral entry at the plasma membrane. Here, we conducted a meta-analysis of these screens and showed a high level of cell-type specificity of the identified hits, arguing for the necessity to pursue efforts to uncover the full landscape of SARS-CoV-2 regulators. more...

Organism:

Homo sapiens; Chlorocebus sabaeus

Type:

Other; Third-party reanalysis

Platforms:

GPL16791 GPL18770

24 Samples

Download data: XLSX

(Submitter supplied) The site-specific chromatin incorporation of eukaryotic histone variant H2A.Z is driven by the multi-component chromatin remodeling complex SWR1/SRCAP/ p400. The budding yeast SWR1 complex replaces the H2A-H2B dimer in the canonical nucleosome with the H2A.Z-H2B dimer, but the mechanism governing the directionality of H2A-to-H2A.Z exchange remains elusive. Here, we use single-molecule force spectroscopy to dissect the disassembly/ reassembly of H2A-nucleosome and H2A.Z-nucleosome. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

6 Samples

Download data: BIGWIG

(Submitter supplied) Little is known about the role of the three Jumonji C (JmjC) enzymes in Plasmodium falciparum (Pf). Here, we show that JIB-04 and other established inhibitors of mammalian JmjC histone demethylases kill asexual blood stage parasites and are even more potent at blocking gametocyte development and gamete formation. In late stage parasites, JIB-04 increased levels of trimethylated lysine residues on histones, suggesting the inhibition of P. more...

Organism:

Plasmodium falciparum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21298

16 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; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL16417 GPL11002

23 Samples

Download data: BEDGRAPH, FPKM_TRACKING

(Submitter supplied) The faithful transmission of genome information is fundamental to the germline stem cell cycle. One exception to this is meiosis when active recombination takes place. This study aims to understand how dna damage responses and meiotic recombination mechanisms are properly coordinated with developmental programs of germ cells by comparing transcriptomic and epigenetic profiles of germline competent pluripotent stem cells, germline stem cells and somatic cells etc. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL16417 GPL11002

12 Samples

Download data: BEDGRAPH