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GenomicsTET1 is a maintenance DNA demethylase that prevents methylation spreading in adult cells [DREAM]
We report that full length TET1 (TET1-FL) overexpression fails to induce global DNA demethylation in HEK293T cells. The preferential binding of TET1-FL to hypomethylated CpG islands (CGIs) through its CXXC domain leads to its inhibited 5-hydroxymethylcytosine (5hmC) production as methylation level i...
ORGANISM(S): Homo sapiens 
2014-06-04 | E-GEOD-44038 | biostudies-arrayexpress
GenomicsTET1 is a maintenance DNA demethylase that prevents methylation spreading in adult cells [MeDIP-Seq]
We report that full length TET1 (TET1-FL) overexpression fails to induce global DNA demethylation in HEK293T cells. The preferential binding of TET1-FL to hypomethylated CpG islands (CGIs) through its CXXC domain leads to its inhibited 5-hydroxymethylcytosine (5hmC) production as methylation level i...
ORGANISM(S): Homo sapiens 
2014-06-04 | E-GEOD-44036 | biostudies-arrayexpress
TranscriptomicsGenome-Wide Transcriptional Effects of the Anti-Cancer Agent Camptothecin
The anti-cancer drug camptothecin inhibits replication and transcription by trapping DNA topoisomerase I (Top1) covalently to DNA in a M-bM-^@M-^\cleavable complexM-bM-^@M-^]. To examine the effects of camptothecin on RNA synthesis genome-wide we used Bru-Seq and show that camptothecin treatment aff...
ORGANISM(S): Homo sapiens 
2013-10-29 | E-GEOD-48678 | biostudies-arrayexpress
TranscriptomicsTET1 is a maintenance DNA demethylase that prevents methylation spreading in adult cells [RNA-seq]
We report that full length TET1 (TET1-FL) overexpression fails to induce global DNA demethylation in HEK293T cells. The preferential binding of TET1-FL to hypomethylated CpG islands (CGIs) through its CXXC domain leads to its inhibited 5-hydroxymethylcytosine (5hmC) production as methylation level i...
ORGANISM(S): Homo sapiens 
2014-06-04 | E-GEOD-49833 | biostudies-arrayexpress
TranscriptomicsRate of elongation by RNA polymerase II is influenced by specific gene features and histone modifications
The rate of transcription elongation plays important roles in the timing of expression of full-length transcripts as well as for the regulation of alternative splicing. In this study we coupled Bru-Seq technology with 5,6-dichlorobenzimidazole 1-M-NM-2-D-ribofuranoside (DRB) to estimate the elongati...
ORGANISM(S): Homo sapiens 
2014-04-01 | E-GEOD-55534 | biostudies-arrayexpress
TranscriptomicsMolecular characterization of tumor cells from the cerebrospinal fluid and matched primary tumors from metastatic breast cancer patients with leptomeningeal disease
We purified tumor cells in the CSF (M-bM-^@M-^\CSFTCM-bM-^@M-^]) from 15 metastatic breast cancer patients diagnosed with leptomeningeal disease using a two-step method involving immunomagnetic enrichment and fluorescence-activated cell sorting (IE/FACS). Magnetic beads coated with mAb to the epithe...
ORGANISM(S): Homo sapiens 
2014-01-09 | E-GEOD-46068 | biostudies-arrayexpress
TranscriptomicsIdentifying transcription start sites and active enhancer elements using BruUV-seq
BruUV-seq utilizes UV light to introduce transcription-blocking DNA lesions randomly in the genome prior to bromouridine-labeling and deep sequencing of nascent RNA. By inhibiting transcription elongation, but not initiation, pre-treatment with UV light leads to a redistribution of transcription rea...
ORGANISM(S): Homo sapiens 
2015-12-21 | E-GEOD-75398 | biostudies-arrayexpress
GenomicsDNA-seq of differentially induced promoter regions in E. coli UTI89 strain grown in either J82 bladder epithelial cells, urine, DMEM or LB medium.
The method DFI-seq was developed to enable identification of differentially expressed genes in uropathogenic E. coli strain UTI89 during growth in human urine and in bladder epithelial cells. By utilising this new method, the aim was to identify novel virulence genes in UTI89. DFI-seq is a combinati...
ORGANISM(S): Escherichia coli UTI89 
2017-05-01 | E-MTAB-5657 | biostudies-arrayexpress
ProteomicsIdentification of candidate circulating glucocorticoid response biomarkers in humans using a proteomic approach
Glucocorticoids used in pharmacological doses for the treatment of a variety of medical conditions, and endogenous glucocorticoid excess – Cushing’s syndrome, may result in several adverse effects, but currently there is no clinically useful biomarker of glucocorticoid activity. A three-phase prote...
ORGANISM(S): Homo sapiens (Human) 
2021-03-14 | PXD019945 | Pride
Pbmc Glucocorticoid Proteomics Dexamethasone Biomarker 
Transcriptomics16S rDNA sequencing of BALB/c and C57BL/7 mouse gut microbiomes
Age-dependent changes of the gut-associated microbiome have been linked to increased frailty and systemic inflammation. This study found that age-associated changes of the gut microbiome of BALB/c and C57BL/6 mice could be reverted by co-housing of aged (22 months old) and adult (3 months old) mice ...
ORGANISM(S): Mus musculus 
2019-05-08 | E-MTAB-7750 | biostudies-arrayexpress
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