GEO DataSets

(Submitter supplied) Background The safety of CRISPR-based gene editing methods is of the utmost priority in clinical applications. Previous studies have reported that Cas9 cleavage induced frequent aneuploidy in primary human T cells, but whether cleavage-mediated editing of base editors would generate off-target structure variations remains unknown. Here, we investigated the potential off-target structural variations associated with CRISPR/Cas9, ABE and CBE editing in mouse embryos and primary human T cells by whole-genome sequencing and single-cell RNA-seq analyses. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: MTX, TSV

(Submitter supplied) Transcriptome profiling of WT, mbd1, pyl5 and mbd1 pyl5 knock-out mutants in response to Abscisic acid (ABA) was done using Affymetrix GenechipTM Arabidopsis ATH1 Genome Array.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

20 Samples

Download data: CEL

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17021

10 Samples

Download data

(Submitter supplied) We designed CRISPR-Cas9 whole genome screens to identify and rank critical genes for cholesterol metabolism in modified LDL treated BMDMs

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

22 Samples

Download data: CSV

(Submitter supplied) Alcohol-associated liver disease (ALD) results from excessive alcohol consumption and is more severe in females. The prenane X receptor (PXR), a xenobiotic nuclear receptor essential for toxin defense, has been implicated in ALD, but the underlying mechanisms remain unclear. Due to species differences in ligand specificty, humanized PXR (hPXR) mouse models are necessary to investigate its role in the sexual dimorphism of ALD in humans. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL20775

32 Samples

Download data: CEL

(Submitter supplied) Glioblastoma (GBM) is defined by heterogenous and resilient cell populations that closely reflect neurodevelopmental cell types. While it is clear that GBM echoes early and immature cell states, identifying the specific developmental programs disrupted in these tumors has been hindered by a lack of high-resolution trajectories of glial and neuronal lineages. Here, we delineate the course of human astrocyte maturation to uncover discrete developmental stages and attributes mirrored by GBM. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL34284

101 Samples

Download data: XLSX

(Submitter supplied) Glioblastoma (GBM) is defined by heterogenous and resilient cell populations that closely reflect neurodevelopmental cell types. While it is clear that GBM echoes early and immature cell states, identifying the specific developmental programs disrupted in these tumors has been hindered by a lack of high-resolution trajectories of glial and neuronal lineages. Here, we delineate the course of human astrocyte maturation to uncover discrete developmental stages and attributes mirrored by GBM. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

50 Samples

Download data: BW

(Submitter supplied) Bacterial non-coding RNAs fulfill a variety of cellular functions, for example as catalysts, as structural components in multiprotein complexes or as regulators of gene expression at the transcriptional and post-transcriptional level. Some RNAs display exceptionally broad conservation across bacterial phyla and are involved in fundamental and unique cellular functions. Hence, the characterization of new RNA families with deep sequence and/or structure conservation has the potential to reveal new molecular and biological RNA functions. more...

Organism:

Clostridioides difficile

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25258

12 Samples

Download data: WIG

(Submitter supplied) Bacterial non-coding RNAs fulfill a variety of cellular functions, for example as catalysts of chemical reactions, as structural components in multiprotein complexes or as regulators of gene expression at the transcriptional and post-transcriptional level. Some RNAs, such as ribosomal RNAs, display exceptionally broad conservation across bacterial phyla and are involved in fundamental and unique cellular functions. more...

Organism:

Clostridioides difficile

Type:

Other

Platform:

GPL30071

28 Samples

Download data: RC, XML

(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:

GPL32159 GPL19057

34 Samples

Download data: BW

(Submitter supplied) Exhausted CD8 T cells result from chronic antigen stimulation and have reduced ability to clear disease. The epigenetic regulation of the dysfunctional phenotype of exhausted CD8 T cells is a promising avenue for therapies aimed at reversing or preventing CD8 T cell exhaustion. Here, utilizing an in vitro model, we show global increase of the repressive histone modification H3K27me3 in CD8 T cell exhaustion as well as increased gene expression of the subunits of PRC2, the complex responsible for H3K27me3 deposition. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

14 Samples

Download data: BW

(Submitter supplied) Exhausted CD8 T cells result from chronic antigen stimulation and have reduced ability to clear disease. The epigenetic regulation of the dysfunctional phenotype of exhausted CD8 T cells is a promising avenue for therapies aimed at reversing or preventing CD8 T cell exhaustion. Here, utilizing an in vitro model, we show global increase of the repressive histone modification H3K27me3 in CD8 T cell exhaustion as well as increased gene expression of the subunits of PRC2, the complex responsible for H3K27me3 deposition. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32159 GPL19057

20 Samples

Download data: TXT

(Submitter supplied) We recently established ACSS2 as a potential candidate for therapeutic interventions in alcohol use disorders (AUD), in which memory of alcohol-associated environmental cues is a primary driver of craving and relapse. Prior research, however, has been limited to passive exposure to ethanol and the importance of this pathway in models of voluntary drinking that better approximate human alcohol consumption remains unknown. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

78 Samples

Download data: TXT

(Submitter supplied) We performed RNA-seq to determine the differential expression genes from undifferentiated trophoblast stem cells (TSCs) and 7-days differentiated trophoblast giant cells (TGCs). We performed RNA-seq to determine the differential expression genes from undifferentiated trophoblast stem cells (TSCs) and 7-days differentiated trophoblast giant cells (TGCs). mTSCs were nurtured in a stem cell medium specifically designed for their growth. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TXT, XLSX

(Submitter supplied) We found that Histone Deacetylase 4 is the target of human miR-122b-5p using transcriptome approach and report thst HDAC4 is downregulated in CHIKV infected human macrophages through global transcriptome profiling

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15520

18 Samples

Download data: TAB, TXT

(Submitter supplied) To investigate the impact caused by miR-155 ablation, B cells from miR-155-sufficient and -deficient mice were cultured in hypoxic conditions and analyzed for profiling the binding of a miR-155 target, Kdm2a, to genomic loci and the distribution pattern of H3K36me2, which Kdm2a demethylates.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

18 Samples

Download data: BIGWIG, BROADPEAK

(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: SF

(Submitter supplied) In multiple sclerosis (MS), microglia and macrophages within the central nervous system (CNS) play an important role in determining the balance between myelin repair and demyelination/neurodegeneration. Phagocytic and regenerative functions of these CNS innate immune cells support remyelination, whereas chronic and maladaptive inflammatory activation promotes lesion expansion and disability, particularly in the progressive forms of MS. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: SF

(Submitter supplied) The histone variant H3.3 facilitates mRNA transcription activation and suppression at cis-regulatory elements such as promoters and enhancers, with histone epigenetic modifications including acetylation or methylation as context-defining features. Canonical histone H3 and histone variant H3.3 are post-translationally modified with the genomic distribution of these marks denoting transcription features and with more recent evidence suggesting that these modifications may influence transcription. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

28 Samples

Download data: BED, BW

(Submitter supplied) The histone variant H3.3 facilitates mRNA transcription activation and suppression at cis-regulatory elements such as promoters and enhancers, with histone epigenetic modifications including acetylation or methylation as context-defining features. Canonical histone H3 and histone variant H3.3 are post-translationally modified with the genomic distribution of these marks denoting transcription features and with more recent evidence suggesting that these modifications may influence transcription. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

8 Samples

Download data: BW, TXT