Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mar1 deletion and RNA enrichment in Cryptococcus neoformans: pilot data for a high-throughput sequencing course

ABSTRACT: Mar1 deletion and RNA enrichment in Cryptococcus neoformans: pilot data for a high-throughput sequencing course. The goal of this project was to generate pilot data in preparation for a summer course on high-throughput sequencing where participants prepared their own RNA-Seq libraries and analyzed the resulting data. This pilot experiment addressed two questions: 1. Does this experimental system (Cryptococcus neoformans H99 wildtype and mar1 deletion mutant grown in YPD and tissue culture media) provide a good dataset for course participants to analyze. 2. Which rRNA depletion method is best to use in the wetlab component of the course. This data was generated in preparation for the intensive summer course on high-throughput sequencing, funded by NIH grant 5R25EB023928-03 "A hands-on, integrative next-generation sequencing course: design, experiment, and analysis".

ORGANISM(S): Cryptococcus neoformans

PROVIDER: GSE160397 | GEO | 2021/02/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Nutritional regulation of pathogenesis gene expression in Pseudomonas syringae

Project description:Pseudomonas syringae was grown on minimal media and King's B medium. The goal of this project was to generate pilot data in preparation for a summer course on high-throughput sequencing where participants prepared their own RNA-Seq libraries and analyzed the resulting data. The summer course was funded by NIH grant 5R25EB023928-03 "A hands-on, integrative next-generation sequencing course: design, experiment, and analysis".

2021-02-22 | GSE160315 | GEO

Mar1 deletion and RNA enrichment in Cryptococcus neoformans: pilot data for a high-throughput sequencing course

Project description:Mar1 deletion and RNA enrichment in Cryptococcus neoformans: pilot data for a high-throughput sequencing course

| PRJNA673133 | ENA

Epigenetic stabilization of DC and DC precursor classical activation by TNFalpha drives protective T-cell polarization

Project description:We report that TNFalpha mediated dendritic cell priming via alterations in histone 3 lysine 4 trimethylation (H3K4me3) sustains lasting protective Th1/Th17 responses during invasive Cryptococcus neoformans pulmonary infection. Cryptococcus neoformans pulmonary infection results in increased global lung dendritic cell H3K4me3 over naive lung dendritic cells. Blockage of TNFalpha during Cryptococcus neoformans pulmonary infection results in decreased H3K4me3 at sites crucial to protective Th1/Th17 responses.

2018-08-15 | GSE118543 | GEO

Ribosome profiling of Cryptococcus neoformans H99

Project description:We measured protein translation (by ribosome profiling) and RNA levels (by polyA-enriched RNA-seq) in Cryptococcus neoformans strain H99 and Cryptococcus neoformans strain JEC21. This is the first transcriptome-wide map of translation in this species complex.

2019-06-22 | GSE133125 | GEO

Whole genome sequencing of amphotericin B adaptors in Cryptocooccus neoformans

Project description:We exposed Cryptococcus neoformans lab strain H99 to amphtericin B and obtained some adaptors. We did sequencing of these adaptors.

2021-03-12 | E-MTAB-10172 | biostudies-arrayexpress

Whole genome sequecing of Cryptococcus neoformans treated with tunicamycin adaptors

Project description:We exposed Cryptococcus neoformans lab strain H99 to tunicamycin and obtained some adaptors. We did whole genome sequencing of these adaptors as well as the parent.

2021-04-29 | E-MTAB-10356 | biostudies-arrayexpress

Whole genome sequencing of flucytosine adaptors in Cryptocooccus neoformans

Project description:We exposed Cryptococcus neoformans lab strain H99 to SD plate supplemented with 1 µg/ml flucytosine, and obtained 54 adaptors. We did sequencing of these adaptors.

2021-06-17 | E-MTAB-10538 | biostudies-arrayexpress

Temporal and thermal optimization of trypsin digestion for the cryptococcal proteome

Project description:Mass spectrometry-based proteomics supports investigation into diverse biological systems, providing insights into regulation, signaling, modifications, and interactions. Optimized sample preparation is critical to ensure robust and reproducible analyses balanced with time and cost. In this article, we evaluated trypsin digestion parameters for the human fungal pathogen, Cryptococcus neoformans, and determined conditions for optimal peptide identification

2024-10-12 | PXD056755 | Pride

Characterizing the transcriptional role of L-DOPA and antimycin A on mitichondrial regulation in Cryptococcus neoformans using a cir1 knockout strain

Project description:Proper mitochondrial function is critical for the ability of the fungal pathogen Cryptococcus neoformans to cause disease. Mitochondrial dysfunction of WT cells treated with antimycin A or L-DOPA, or on cells lacking Cir1 is evident from this dataset. These experiments revealed influences on transcript levels of genes encoding Fe-S cluster assembly components and the response to oxidative stress in Cryptococcus neoformans.

2024-04-07 | GSE222564 | GEO

Expression profiles of circRNAs in peripherial blood mononuclear cells from cryptococcal meningitis and healthy individuals.

Project description:CircRNAs are a recently well-known regulator that mediates a variety of biological processes. Cryptococcus neoformans is an environmental fungal pathogen that can cause fatal cryptococcal meningitis in immunocompromised individuals. However, the involvement of circRNA in cryptococcal infection remains unclear. In this study, high‐throughput microarray was performed to identify the circRNA expression profile in cryptococcal meningitis patients.

2020-12-07 | GSE159601 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data