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Items: 1 to 20 of 1131

  • The following terms were not found in GEO DataSets: beta-D-Galactose, pentapivalate.
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1.

DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Saccharomyces cerevisiae
Type:
Other; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform:
GPL31112
82 Samples
Download data: BED, BIGWIG, COOL, MATRIX, TXT
Series
Accession:
GSE242400
ID:
200242400

PubMed Full text in PMC Similar studies

2.

DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions (MeDIP)

(Submitter supplied) Here, we present Methyltransferase Targeting-based chromosome Architecture Capture (MTAC), a method that maps the contacts between a target site (viewpoint) and the rest of the genome with high resolution and sensitivity. By targeting M.CviPI DNA methyltransferase to the viewpoint and by detecting differentially methylated regions, MTAC detects hundreds of intra- and inter-chromosomal interactions in the budding yeast genome that cannot be captured by 4C, Hi-C, or Micro-C.
Organism:
Saccharomyces cerevisiae
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL31112
66 Samples
Download data: BIGWIG, XLSX
Series
Accession:
GSE242398
ID:
200242398

PubMed Full text in PMC Similar studies

3.

Condition-specific 3’ mRNA isoform half-lives and stability elements in yeast

(Submitter supplied) Alternative polyadenylation generates numerous 3’ mRNA isoforms that can differ in their stability, structure, and function. These isoforms can be used to map mRNA stabilizing and destabilizing elements within 3’ untranslated regions (3’UTRs). Here, we examine how environmental conditions affect 3’ mRNA isoform turnover and structure in yeast cells on a transcriptome scale. Isoform stability broadly increases when cells grow more slowly, with relative half-lives of most isoforms being well correlated across multiple conditions. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL17342
12 Samples
Download data: TXT, XLSX
Series
Accession:
GSE228123
ID:
200228123

PubMed Full text in PMC Similar studies

4.

OXPHOS Promotes Apoptotic Resistance and Persistence in T­H17 cells

(Submitter supplied) Apoptotic cell death is a cell-intrinsic, immune tolerance mechanism that regulates the magnitude and resolution of T cell-mediated responses. Evasion of apoptosis is critical for the generation of memory T cells, as well as autoimmune T cells, and knowledge of the mechanisms that enable resistance to apoptosis will provide insight into ways to modulate their activity during protective and pathogenic responses. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24247
6 Samples
Download data: TXT
Series
Accession:
GSE185478
ID:
200185478

PubMed Full text in PMC Similar studies SRA Run Selector

5.

The presence of plasmids in L. lactis IL594 determines changes in host phenotype and expression of chromosomal genes

(Submitter supplied) The L. lactis IL594 strain contains seven plasmids (pIL1 to pIL7) and is the parental strain of the plasmid-free L. lactis IL1403, one of the most studied lactic acid bacteria (LAB) strain. The genetic sequences of pIL1 to pIL7 plasmids have been recently described, however the knowledge of global changes in host phenotype and transcriptome remains poor. In presented study, global phenotypic analyses were combined with transcriptomic studies to evaluate a potential influence of plasmidic genes on overall gene expression in industrially important L. more...
Organism:
Lactococcus lactis
Type:
Expression profiling by array
Platform:
GPL32506
12 Samples
Download data: TXT
Series
Accession:
GSE209756
ID:
200209756

PubMed Full text in PMC Similar studies Analyze with GEO2R

6.

Ageing transcriptomes of selected mutants on different carbon sources

(Submitter supplied) Here we show that an unrestricted galactose diet in early life minimises pathology during replicative ageing in budding yeast, irrespective of diet later in life. Lifespan and average mother cell division rate are comparable between glucose and galactose diets, but markers of senescence and the progressive dysregulation of gene expression observed on glucose are minimal on galactose, showing these to be facets of ageing pathology rather than intrinsic parts of the replicative ageing process. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19756
118 Samples
Download data: TXT
Series
Accession:
GSE207503
ID:
200207503

PubMed Full text in PMC Similar studies

7.

Copra β-mannooligosaccharide utilization by Bifidobacterium adolescentis ATCC 15703

(Submitter supplied) In order to understand gene expression profile of Bifidobacterium adolescentis ATCC 15703, it was grown in minimal media upto late log phase in the presence of β-mannooligosaccharide from copra till OD A600 = 0.800
Organism:
Bifidobacterium adolescentis ATCC 15703; Bifidobacterium adolescentis
Type:
Expression profiling by array
Platform:
GPL30400
8 Samples
Download data: TXT
Series
Accession:
GSE180349
ID:
200180349

Analyze with GEO2R

8.

Loss of Mitochondrial Fatty Acid Beta-Oxidation Protein Short Chain Enoyl-CoA Hydratase Disrupts Oxidative Phosphorylation Protein Complex Stability and Function

(Submitter supplied) Short chain enoyl-CoA hydratase 1 (ECHS1) is involved in the second step of mitochondrial fatty acid β-oxidation (FAO), catalysing the hydration of short chain enoyl-CoA esters to short chain 3-hyroxyl-CoA esters. Genetic deficiency in ECHS1 (ECHS1D) is associated with a specific subset of Leigh Syndrome, a disease typically caused by defects in oxidative phosphorylation (OXPHOS). Here, we examined the molecular pathogenesis of ECHS1D using a CRISPR/Cas9 edited human cell ‘knockout’ model and fibroblasts from ECHS1D patients. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16791
8 Samples
Download data: TSV
Series
Accession:
GSE200252
ID:
200200252

PubMed Full text in PMC Similar studies Analyze with GEO2R

9.

Longitudinal DNA methylation and RNA-seq datasets in primary human fibroblasts with mitochondrial genetic, metabolic, and endocrine perturbations

(Submitter supplied) The current RNA sequencing and DNA methylation datasets provide an epigenomic map across the entire replicative lifespan of primary human fibroblast cell lines from n=6 healthy male and female donors and n=3 donors with lifespan-altering mitochondrial disease caused by mutations in the SURF1 gene. These datasets can be integrated with other measures collected in parallel along the lifespan, including cytological (cell size, morphology), bioenergetic (energy expenditure, derived ATP synthesis rates from Seahorse), secreted proteins, telomere length, and whole-genome sequencing (WGS) data. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Methylation profiling by array
Platforms:
GPL21145 GPL20301
824 Samples
Download data: IDAT
Series
Accession:
GSE179849
ID:
200179849

PubMed Full text in PMC Similar studies

10.

A longitudinal RNA sequencing dataset in primary human fibroblasts with mitochondrial genetic, metabolic, and endocrine perturbations

(Submitter supplied) The current RNA sequencing dataset (n=345) provides a transcriptional map of cultured primary human fibroblasts (in vitro) aged through the cellular lifespan. The dataset was generated from paired-end (150bp) Illumina HiSeq sequencing, with an average coverage of 38.3million reads per sample. These data contain gene expression trajectories collected at high temporal frequency (every 11 days, ~7timepoints per donor) across the replicative lifespan of primary human fibroblast cell lines from n=4 healthy male and female donors, and n=3 donors with lifespan-altering mitochondrial disease caused by mutations in the SURF1 gene. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20301
345 Samples
Download data: CSV
Series
Accession:
GSE179848
ID:
200179848

PubMed Full text in PMC Similar studies Analyze with GEO2RSRA Run Selector

11.

A longitudinal DNA methylation dataset in primary human fibroblasts with mitochondrial genetic, metabolic, and endocrine perturbations

(Submitter supplied) The current DNA methylation dataset (n=479) provides an epigenetic map of cultured primary human fibroblasts (in vitro) aged through the cellular lifespan. The dataset was generated using the Illumina EPIC bead array, which includes DNA methylation levels (0-1.0) at 866,091 CpG sites. This provides DNA methylation trajectories collected at high temporal frequency (every 8 days, ~7timepoints per a donor) across the entire replicative lifespan of primary human fibroblast cell lines from n=6 healthy male and female donors and n=3 donors with lifespan-altering mitochondrial disease caused by mutations in the SURF1 gene. more...
Organism:
Homo sapiens
Type:
Methylation profiling by array
Platform:
GPL21145
479 Samples
Download data: CSV, IDAT
Series
Accession:
GSE179847
ID:
200179847

PubMed Full text in PMC Similar studies

12.

An alternative transcriptome shapes cell fate transitions in yeast (TIF-seq)

(Submitter supplied) Alternative mRNA isoforms and long noncoding RNAs (lncRNA) make up a large fraction of the transcriptome and play key functions in cell-fate programming. These transcripts often initiate upstream of coding gene promoters from alternative transcription start sites (TSS) where they can regulate gene expression in cis through transcription-coupled chromatin alterations. How, when and where transcription of alternative cis-acting RNAs regulates local gene expression remains poorly understood. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing; Other
Platform:
GPL19756
8 Samples
Download data: BEDPE
Series
Accession:
GSE141269
ID:
200141269

PubMed Full text in PMC Similar studies SRA Run Selector

13.

An alternative transcriptome shapes cell fate transitions in yeast (MNase-seq)

(Submitter supplied) Alternative mRNA isoforms and long noncoding RNAs (lncRNA) make up a large fraction of the transcriptome and play key functions in cell-fate programming. These transcripts often initiate upstream of coding gene promoters from alternative transcription start sites (TSS) where they can regulate gene expression in cis through transcription-coupled chromatin alterations. How, when and where transcription of alternative cis-acting RNAs regulates local gene expression remains poorly understood. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17342
36 Samples
Download data: BED, BW
Series
Accession:
GSE137709
ID:
200137709

PubMed Full text in PMC Similar studies SRA Run Selector

14.

An alternative transcriptome shapes cell fate transitions in yeast (TES-seq)

(Submitter supplied) Alternative mRNA isoforms and long noncoding RNAs (lncRNA) make up a large fraction of the transcriptome and play key functions in cell-fate programming. These transcripts often initiate upstream of coding gene promoters from alternative transcription start sites (TSS) where they can regulate gene expression in cis through transcription-coupled chromatin alterations. How, when and where transcription of alternative cis-acting RNAs regulates local gene expression remains poorly understood. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21656
81 Samples
Download data: BW
Series
Accession:
GSE137708
ID:
200137708

PubMed Full text in PMC Similar studies SRA Run Selector

15.

An alternative transcriptome shapes cell fate transitions in yeast (TSS-seq)

(Submitter supplied) Alternative mRNA isoforms and long noncoding RNAs (lncRNA) make up a large fraction of the transcriptome and play key functions in cell-fate programming. These transcripts often initiate upstream of coding gene promoters from alternative transcription start sites (TSS) where they can regulate gene expression in cis through transcription-coupled chromatin alterations. How, when and where transcription of alternative cis-acting RNAs regulates local gene expression remains poorly understood. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21656
82 Samples
Download data: BW
Series
Accession:
GSE137707
ID:
200137707

PubMed Full text in PMC Similar studies SRA Run Selector

16.

An alternative transcriptome shapes cell fate transitions in yeast (mRNA-seq)

(Submitter supplied) Alternative mRNA isoforms and long noncoding RNAs (lncRNA) make up a large fraction of the transcriptome and play key functions in cell-fate programming. These transcripts often initiate upstream of coding gene promoters from alternative transcription start sites (TSS) where they can regulate gene expression in cis through transcription-coupled chromatin alterations. How, when and where transcription of alternative cis-acting RNAs regulates local gene expression remains poorly understood. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21656
81 Samples
Download data: BW
Series
Accession:
GSE137706
ID:
200137706

PubMed Full text in PMC Similar studies SRA Run Selector

17.

Gene expression analysis of dissociated and FDG FACS-sorted mammary glands of 16 week old nulliparous AXL +/LacZ and AXL LacZ/LacZ mice (B6.129P2-AXLtm1Dgen strain, Jackson Labs)

(Submitter supplied) The receptor tyrosine kinase AXL is associated with epithelial plasticity in several solid tumors including breast cancer and AXL-targeting agents are currently in clinical trials. We hypothesized that AXL is a driver of stemness traits in cancer by co-option of a regulatory function normally reserved for stem cells. AXL-expressing cells in human mammary epithelial ducts co-expressed markers associated with multipotency, and AXL inhibition abolished colony-formation and self-maintenance activities while promoting terminal differentiation in vitro. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6885
8 Samples
Download data: IDAT
Series
Accession:
GSE156662
ID:
200156662

PubMed Full text in PMC Similar studies Analyze with GEO2R

18.

Elucidating the molecular determinants of Aβ aggregation with deep mutational scanning

(Submitter supplied) Despite the importance of Aβ aggregation in Alzheimer’s disease etiology, our understanding of the sequence determinants of aggregation is sparse and largely derived from in vitro studies. For example, in vitro proline and alanine scanning mutagenesis of Aβ40 proposed core regions important for aggregation. However, we lack even this limited mutagenesis data for the more disease-relevant Aβ42. Thus, to better understand the molecular determinants of Aβ42 aggregation in a cell-based system, we combined a yeast DHFR aggregation assay with deep mutational scanning. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL18573
18 Samples
Download data: TSV
Series
Accession:
GSE139122
ID:
200139122

SRA Run Selector

19.

Locust bean gum derived galacto-manno-oligosaccharides utilization by Lactobacillus plantarum WCFS1

(Submitter supplied) In order to understand LBG derived galacto-manno-oligosaccharides utilization by a probiotic bacterium, Lactobacillus plantarum WCFS1, we have grown Lactobacillus plantarum WCFS1 (in duplicates) till mid log phase (OD600nm ~0.5, 10 h) in carbon free MRS (de Man, Rogosa Sharpe ) media containing either galacto-manno-oligosaccharides, mannose, glucose or galactose (1% w/v) as the sole carbon source.
Organism:
Lactiplantibacillus plantarum WCFS1
Type:
Expression profiling by array
Platform:
GPL25372
8 Samples
Download data: TXT
Series
Accession:
GSE117591
ID:
200117591

Analyze with GEO2R

20.

Transcriptomic Signature of Right Ventricular Failure in Experimental Pulmonary Arterial Hypertension: Deep Sequencing Demonstrates Mitochondrial, Fibrotic, Inflammatory and Angiogenic Abnormalities

(Submitter supplied) Abstract: Right ventricular failure (RVF) remains the leading cause of death in pulmonary arterial hypertension (PAH). We investigated the transcriptomic signature of RVF in hemodynamically well-phenotyped monocrotaline (MCT)-treated, male, Sprague-Dawley rats with severe PAH and decompensated RVF (increased right ventricular (RV) end diastolic volume (EDV), decreased cardiac output (CO), tricuspid annular plane systolic excursion (TAPSE) and ventricular-arterial decoupling). more...
Organism:
Rattus norvegicus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25029
11 Samples
Download data: CSV
Series
Accession:
GSE119754
ID:
200119754

SRA Run Selector

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