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GenomicsGenome-wide profiling of p63 binding sites identifies genes and regulatory elements for p63-related disorders
We identified p63 target genes and binding sites responsible for ectodermal defects by genome-wide profiling of p63 binding using ChIP-seq and expression analysis in human primary keratinocytes from patients with p63 mutations. As proof of principle, we identified a novel de novo microdeletion causi...
ORGANISM(S): Homo sapiens 
2010-08-15 | E-GEOD-17611 | biostudies-arrayexpress
TranscriptomicsTranscription start site identification in wild type Escherichia coli
RNAseq was used to map transcription start sites globally in wild type Escherichia coli. Total RNA was isolated from cells grown in LB media until exponential phase.
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2021-04-16 | E-MTAB-9655 | biostudies-arrayexpress
MetabolomicsA cytochrome P450 CYP87A4 imparts sterol side-chain cleavage in digoxin biosynthesis
Digoxin extracted from the foxglove plant is a widely prescribed natural product for treating heart failure. It is listed as an essential medicine by the World Health Organization. However, how the foxglove plant synthesizes digoxin is mostly unknown, especially the cytochrome P450 sterol side chain...
2025-07-03 | MTBLS7993 | MetaboLights
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
TranscriptomicsTranscription start site identification in Bacillus subtilis
Cappable-seq was used to map transcription start sites globally in wild type Bacillus subtilis. Total RNA was isolated from cells grown in LB media until exponential phase. RNA corresponding to transcription start sites was capped with a 5' biotin tag, which was used for enrichment via a pull down w...
ORGANISM(S): Bacillus subtilis subsp. subtilis str. 168 
2021-04-16 | E-MTAB-8582 | biostudies-arrayexpress
TranscriptomicsATAC-seq data of Amphimedon queenslandica (Demosponge species) through eight developmental stages, from white stage (cleavage) to adult
We report a comprehensive DNA accessibility profile of the Demosponge species Amphimedon queenslandica using Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) through six embryonic developmental stages, a larval stage and adult stage. We assessed the dynamics of chromatin accessi...
ORGANISM(S): Amphimedon queenslandica 
2021-10-10 | E-MTAB-10203 | biostudies-arrayexpress
GenomicsHigh definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing
DNA methylation stabilizes developmentally programmed gene expression states. Aberrant methylation is associated with disease progression and is a common feature of cancer genomes. Presently, few methods enable quantitative, large-scale, single-base resolution mapping of DNA methylation states in d...
ORGANISM(S): Homo sapiens 
2009-07-08 | E-GEOD-17001 | biostudies-arrayexpress
TranscriptomicsMAFB ChIPseq in Human EndoCBH2 cells
The intent of this experiment was to determine MAFB binding sites in human pancreatic beta cells. This is particularly relevant as MAFB is not expressed in mature rodent beta cells; thus, it may perform unique functions in human. Sequencing was performed following IP with an anti-MAFB antibody using...
ORGANISM(S): Homo sapiens 
2020-03-17 | E-MTAB-8612 | biostudies-arrayexpress
TranscriptomicsThe dsRBP and inactive editor, ADR-1, utilizes dsRNA binding to regulate A-to-I RNA editing across the C. elegans transcriptome
Purpose: The purpose of this experiment is to expand the repertoire of C. elegans edited transcripts and identify the roles of ADR-1 as indirect regulator of editing and ADR-2 as the only active deaminase in vivo. Methods: Strand-specific RNA sequencing of wild-type and adr mutant worms, followed by...
ORGANISM(S): Caenorhabditis elegans 
2014-01-20 | E-GEOD-51556 | biostudies-arrayexpress
ProteomicsAn aspartyl pseudoprotease dominates the secretory hydrolase landscape of the skin commensal Malassezia in situ
Malassezia globosa is abundant and prevalent on sebaceous areas of the human skin. Genome annotation reveals that M. globosa possesses a repertoire of secreted hydrolytic enzymes relevant for lipid and protein metabolism on the skin. In-gel proteomics identifies a predicted aspartyl protease, MGL_33...
ORGANISM(S): Cellular Organisms 
2023-11-23 | PXD042508 | JPOST Repository
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