GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Cryptococcus neoformans var. grubii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25340

881 Samples

Download data

(Submitter supplied) Cryptococcus neoformans is a fungal pathogen with a polysaccharide capsule that becomes greatly enlarged in the mammalian host and during in vitro growth in response to host-like conditions. To understand how individual host-like signals affect capsule size and gene expression, we grew wild-type cells and cells lacking components of the cAMP pathway: Pde1, Pde2, Pkr1. We also took samples for RNA-Seq at 30, 90, 180, 1440 minutes and carried out RNA-Seq in quadruplicate. more...

Organism:

Cryptococcus neoformans var. grubii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25340

90 Samples

Download data: TSV

(Submitter supplied) Cryptococcus neoformans is a fungal pathogen with a polysaccharide capsule that becomes greatly enlarged in the mammalian host and during in vitro growth in response to host-like conditions. To understand how individual host-like signals affect capsule size and gene expression, we grew cells wild-type KN99 cells with either no added cyclic AMP (cAMP), 1.1 mM, 1.8 mM, 3.3 mM, 11 mM, or 20 mM cAMP. capsule thickness at 1440 min. more...

Organism:

Cryptococcus neoformans var. grubii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25340

71 Samples

Download data: TSV

(Submitter supplied) Cryptococcus neoformans is a fungal pathogen with a polysaccharide capsule that becomes greatly enlarged in the mammalian host and during in vitro growth in response to host-like conditions. To understand how individual host-like signals affect capsule size and gene expression, we grew cells with and without all combinations of 5 signals suspected of affecting capsule size: Tissue-culture medium (DMEM or RPMI), temperature (37°C), CO2 (5%), and the addition of HEPES buffer. more...

Organism:

Cryptococcus neoformans var. grubii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25340

720 Samples

Download data: TSV

(Submitter supplied) Cryptococcus neoformans is a fungal pathogen of immunocompromised people that causes fatal meningitis. The fungal cell wall is essential to viability and pathogenesis of C. neoformans, and biosynthesis and repair of the wall is primarily controlled by the cell wall integrity (CWI) signaling pathway. Previous work by us and others have shown that deletion of genes encoding the four major kinases in the CWI signaling pathway, namely PKC1, BCK1, MKK2 and MPK1 results in severe cell wall phenotypes, sensitivity to a variety of cell wall stressors and, for Mpk1, reduced virulence in a mouse model. more...

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14571

12 Samples

Download data: GTF, TXT

(Submitter supplied) Cryptococcus neoformans is an opportunistic basidiomycete pathogen that is a major etiological agent of fungal meningoencephalitis leading to more than 180,000 deaths worldwide annually. For this pathogen, the polysaccharide capsule is a key virulence factor, which interferes with the phagocytosis by host innate immune cells, but its complex signaling networks remain elusive. In this study, we systematically analyzed capsule biosynthesis and signaling networks by using C. more...

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32481

30 Samples

Download data: XLSX

(Submitter supplied) We report on our study the role of C. neoformans transcription factor Pdr802, whose expression is highly induced under host-like conditions in vitro and is critical for C. neoformans dissemination and virulence in a mouse model of infection. We found that direct targets of Pdr802 include the calcineurin targets Had1 and Pmc1, which are important for C. neoformans virulence, the transcription factor Bzp4, which promotes cryptococcal melanization and capsule thickness, and 35 transmembrane transporters. more...

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27451

56 Samples

Download data: CSV

(Submitter supplied) We report on our study the role of C. neoformans transcription factor Pdr802, whose expression is highly induced under host-like conditions in vitro and is critical for C. neoformans dissemination and virulence in a mouse model of infection. We found that direct targets of Pdr802 include the calcineurin targets Had1 and Pmc1, which are important for C. neoformans virulence, the transcription factor Bzp4, which promotes cryptococcal melanization and capsule thickness, and 35 transmembrane transporters. more...

Organism:

Cryptococcus neoformans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27451

12 Samples

Download data: BED, NARROWPEAK

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Cryptococcus neoformans; Cryptococcus neoformans var. neoformans

Type:

Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL14571 GPL4009 GPL14564

54 Samples

Download data: BED, CSV, CUFF, SAM, WIG

(Submitter supplied) SAGA member Ada2 is required for the majority of H3K9 acetylation in C. neoformans. To identify specific genomic loci that exhibit Ada2-dependent H3K9 acetylation, we performed ChIP-Seq against H3K9ac in wildtype and ada2Δ cells.

Organism:

Cryptococcus neoformans

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL14571

12 Samples

Download data: BED, SAM

(Submitter supplied) To contextualize the cryptococcal Spt-Ada-Gcn5 Acetyltransferase (SAGA) member Ada2 in the capsule regulatory network, RNA-Seq was performed on wildtype, ada2Δ and two other transcription factors, nrg1Δ and cir1Δ, which like ada2Δ are also defective for capsule formation, virulence and filamentation.

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14564

20 Samples

Download data: BED, CUFF, WIG

(Submitter supplied) To understand the relationship between gene expression and capsule formation, H99 cells were cultured overnight at 37ºC in the following eight conditions: low iron medium with or without both 500 mM ethylenediaminetetraacetic acid (EDTA) and 10 mM bathophenanthroline disulfonate (BPDS); phosphate-buffered saline (PBS) with or without 10% v/v fetal bovine serum; Dulbecco's Modified Eagle's Medium (from Sigma) in ambient air or 5% CO2; and Littman's medium with either 0.01 µg/ml or 1 µg/ml thiamine.

Organism:

Cryptococcus neoformans; Cryptococcus neoformans var. neoformans

Type:

Expression profiling by array

Platform:

GPL4009

22 Samples

Download data: CSV

(Submitter supplied) Purpose: To examine the comparative transcriptional profiles of WT and rim101 mutant cells in host-mimicking in vitro conditions to determine genes that are responsible for the increased virulence of the rim101 strain. The rim101 mutant is able to trigger an overactive inflammatory response, presumably by exposing an antigenic trigger. Using transcriptional profiling, we determined that many genes involved in cell wall processes were differentially transcribed between the wild type and the mutant strain.

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16431

2 Samples

Download data: CSV

(Submitter supplied) Cryptococcus neoformans is a prevalent human fungal pathogen that must survive within various tissues in order to establish a human infection. We have identified the C. neoformans Rim101 transcription factor, a highly conserved pH-response regulator in many fungal species. The rim101- mutant strain displays growth defects similar to other fungal species in the presence of alkaline pH, increased salt concentrations, and iron limitation. more...

Organism:

Cryptococcus neoformans var. grubii; Cryptococcus neoformans var. neoformans

Type:

Expression profiling by array

Platform:

GPL4009

1 Sample

Download data: GPR

(Submitter supplied) Cryptococcus neoformans is a fungal pathogen responsible for hundreds of thousands of deaths per year. Its critical virulence factor is a polysacharride capsule which grows large upon entry into a mammalian host. We previously identified USV101 as a transcription factor whose deletion results in enlarged capsules. Here, we characterize strains lacking or overexpressing USV101 in terms of their virulence-related phenotypes, the altered course of infection by them and immune response to them in a mouse model, the relationship of Usv101 to other transcription factors involved in capsule regulation, and the changes in Usv101 activity during capsule induction.

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19081

46 Samples

Download data: CUFF, TXT

(Submitter supplied) Purpose: Key steps in understanding a biological process include identifying genes that are involved and determining how they are regulated. We developed a novel method for identifying TFs involved in a specific process and used it to map regulation of the key virulence factor of Cryptococcus neoformans, its capsule. Results: The map, built from expression profiles of 41 TF mutants, includes 20 TFs not previously known to regulate virulence attributes. more...

Organism:

Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19081 GPL14571

320 Samples

Download data: BED, CUFF, TXT

(Submitter supplied) We compared the expression profile of titan-like cells with cells of regular size in C. neoformans. This was investigated at different time points of the transition: 7 and 24 h

Organism:

Cryptococcus neoformans var. grubii H99

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24689

10 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Cryptococcus neoformans var. grubii H99

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21548 GPL23176

26 Samples

Download data

(Submitter supplied) Purpose: Understanding the iron-responsive regulatory networks in Cryptococcus neoformans. Methods: The transcriptome profiles of the wild-type, cir1 mutant and hapX mutant were generated by RNA-seq using Illumina Hiseq, in triplicate. The transcriptome profiles of each mutant was compared with that of the wild-type strain. Results: The iron-responsive transcription factors, Cir1 and HapX, are major regulators for iron acquisition and metabolism in C. more...

Organism:

Cryptococcus neoformans var. grubii H99

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21548

18 Samples

Download data: XLSX

(Submitter supplied) Purpose: Defining the regulatory role of the transcription factors, Cir1 and HapX, in C. neoformans. Methods: Chromatin immunoprecipitation followed by high-throughput sequencing was performed using chromatin immunoprecipitated DNA from the strains Cir1-Flag and HapX-Flag grown in low- and high-iron condition. Results: Cir1 and HapX bind to the promoter region of the genes involved in iron acquisition and metabolism in C. more...

Organism:

Cryptococcus neoformans var. grubii H99

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23176

8 Samples

Download data: XLSX