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GenomicsPING 2.0: An R/Bioconductor package for nucleosome positioning using next-generation sequencing data
MNase-Seq and ChIP-Seq have evolved as popular techniques to study chromatin and histone modification. Although many tools have been developed to identify enriched regions, software tools for nucleosome positioning are still limited. We introduce a flexible and powerful open-source R package, PING 2...
ORGANISM(S): Saccharomyces cerevisiae 
2013-07-11 | E-GEOD-47073 | biostudies-arrayexpress
OtherComprehensive temporal protein dynamics during the diauxic shift in Saccharomyces cerevisiae
Data from ProteomeXchange, PXD ID: PXD002093. File: m04675.mzml. Published as part of Mol Cell Proteomics. 2015 Jun 15 . From the Abstract: {{i}} Yeast (Saccharomyces cerevisiae) has served as a key model system in biology and as a benchmark for omics technology. Although near-complete proteomes of...
ORGANISM(S): Yeast 
GPM11210039772 | GPMDB
Resource Reanalysis 
OtherComprehensive temporal protein dynamics during the diauxic shift in Saccharomyces cerevisiae
Data from ProteomeXchange, PXD ID: PXD001338. File: Hap2_fraction_5.mzml. Published as part of Mol Cell Proteomics. 2015 Jun 15 . From the Abstract: {{i}} Yeast (Saccharomyces cerevisiae) has served as a key model system in biology and as a benchmark for omics technology. Although near-complete pro...
ORGANISM(S): Yeast 
GPM32320015932 | GPMDB
Resource Reanalysis 
UnknownInfluence of Inhaled Amiloride on Lung Fluid Clearance in Response to Normobaric Hypoxia in Healthy Individuals.
Not available
S-EPMC5743027 | biostudies-literature
TranscriptomicsKey Role of MicroRNA in the Regulation of Granulocyte Macrophage Colony-stimulating Factor Expression in Murine Alveolar Epithelial Cells (AEC) during Oxidative Stress
A genome wide microarray identified 19 candidate miRNA altered in primary AEC during oxidative stress with reversal by treatment with GM-CSF. Three of these microRNA (miR 133a, miR133a* and miR133b) are also predicited to bind the GM-CSF 3 UTR. 4 samples. Primary murine alveolar epithelial cells wer...
ORGANISM(S): Mus musculus 
2014-04-11 | E-GEOD-56687 | biostudies-arrayexpress
TranscriptomicsControl of chromatin structure by Spt6 has different consequences in coding and regulatory regions
Spt6 is a highly conserved factor that carries out important functions in transcription and chromatin structure. To gain new insights into Spt6, we measured nucleosome occupancy along Saccharomyces cerevisiae chromosome III in an spt6 mutant and found that the level of nucleosomes is greatly reduced...
ORGANISM(S): Saccharomyces cerevisiae 
2010-12-01 | E-GEOD-21787 | biostudies-arrayexpress
TranscriptomicsIncreased hemoglobin expression in NASH livers
BACKGROUND & AIMS: Recent studies revealed that hemoglobin is expressed in some non-erythrocytes and it suppresses oxidative stress when overexpressed. Oxidative stress plays a critical role in the pathogenesis of non-alcoholic steatohepatitis (NASH). This study was to investigate whether hemoglobin...
ORGANISM(S): Homo sapiens 
2010-10-20 | E-GEOD-24807 | biostudies-arrayexpress
TranscriptomicsMycobacterium tuberculosis transcriptional responses to acidic pH and carbon source
The purpose of this study was to examine how Mtb integrates acidic pH and available carbon sources as environmental cues to regulate its metabolism and growth rate. RNA-seq transcriptional profiling of M. tuberculosis growing at acidic or neutral pH, in pyruvate or glycerol, was examined. These stu...
ORGANISM(S): Mycobacterium tuberculosis 
2014-07-07 | E-GEOD-52020 | biostudies-arrayexpress
TranscriptomicsInfluence of BrpA on critical virulence attributes of Streptococcus mutans
Streptococcus mutans, the primary etiological agent of human dental caries, has developed multiple mechanisms to colonize and form biofilms on the tooth surface. The brpA gene codes for a predicted surface-associated protein with apparent roles in biofilm formation, autolysis, and cell division. In ...
ORGANISM(S): Streptococcus mutans 
2008-08-30 | E-GEOD-11773 | biostudies-arrayexpress
MetabolomicsExtreme genome diversity and cryptic speciation in a harmful algal bloom forming eukaryote

Harmful algal blooms (HABs) of the toxic haptophyte Prymnesium parvum are a recurrent problem in many inland and estuarine waters around the world. Strains of P. parvum vary in the toxins they produce and in other physiological traits associated with HABs, but the genetic basis ...

2023-04-26 | MTBLS5893 | MetaboLights
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