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Links from GEO DataSets

Items: 20

1.

Toward an integrated model of capsule regulation in Cryptococcus neoformans

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Cryptococcus neoformans var. neoformans; Cryptococcus 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
Series
Accession:
GSE32228
ID:
200032228
2.

ChIP-Seq of H3K9 acetylation for wildtype and ada2Δ cells in Cryptococcus neoformans

(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
Series
Accession:
GSE32075
ID:
200032075
3.

RNA-Seq analysis of ada2Δ, nrg1Δ and cir1Δ and KN99α wildtype cells in capsule inducing and non-inducing conditions

(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
Series
Accession:
GSE32049
ID:
200032049
4.

Cryptococcal H99 cells grown in 8 conditions for capsule induction

(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
Series
Accession:
GSE31911
ID:
200031911
5.

ChIP-Seq and RNA-Seq analysis of the iron regulatory transcription factors in Cryptococcus neoformans in response to iron availability

(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:
GPL23176 GPL21548
26 Samples
Download data
Series
Accession:
GSE126314
ID:
200126314
6.

Transcriptome analysis of the iron regulatory transcription factors in Cryptococcus neoformans in response to iron availability

(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
Series
Accession:
GSE126313
ID:
200126313
7.

ChIP-Seq analysis of the iron regulatory transcription factors in Cryptococcus neoformans in response to iron availability

(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
Series
Accession:
GSE126312
ID:
200126312
8.

Unraveling capsule biosynthesis and signaling networks in Cryptococcus neoformans

(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
Series
Accession:
GSE208163
ID:
200208163
9.

HapX positively and negatively regulates the transcriptional response to iron deprivation in Cryptococcus neoformans

(Submitter supplied) Analysis of the transcriptional response of C. neoformans WT, cir1 mutant, hap3 mutant and hapX mutant to different iron sources.
Organism:
Cryptococcus neoformans
Type:
Expression profiling by array
Platform:
GPL10700
48 Samples
Download data: TXT
Series
Accession:
GSE22988
ID:
200022988
10.

WT vs gcn5 mutant gene expression under capsule inducing conditions

(Submitter supplied) Cryptococcus neoformans is an environmental fungus and an opportunistic human pathogen. Previous studies have demonstrated major alterations in its transcriptional profile as this microorganism enters the hostile environment of the human host. To assess the role of chromatin remodeling in host-induced transcriptional responses, we identified the C. neoformans Gcn5 histone acetyltransferase and demonstrated its function by complementation studies of Saccharomyces cerevisiae. more...
Organism:
Cryptococcus neoformans; Cryptococcus neoformans var. grubii
Type:
Expression profiling by array
Platform:
GPL10872
1 Sample
Download data: GPR
Series
Accession:
GSE23948
ID:
200023948
11.

Usv101 is a key regulator of cryptococcal virulence and determinant of host response

(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
Series
Accession:
GSE69532
ID:
200069532
12.

Model-driven mapping of transcriptional networks reveals the circuitry and dynamics of virulence regulation

(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
Series
Accession:
GSE60398
ID:
200060398
13.

The transcription factor Pdr802 regulates Titan cell production and Cryptococcus neoformans pathogenicity (RNA-Seq)

(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
Series
Accession:
GSE162851
ID:
200162851
14.

The transcription factor Pdr802 regulates Titan cell production and Cryptococcus neoformans pathogenicity

(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
Series
Accession:
GSE153134
ID:
200153134
15.

ChIP-chip of the Cryptococcus neoformans transcription factor GAT201 and expression profiling of gat201KO

(Submitter supplied) identify binding sites of Gat201 in C. neoformans cells grown in DMEM at 37C in 5% CO2 The anti-phagocytic polysaccharide capsule of the yeast C. neoformans is a major virulence attribute. However, previous studies of the pleiotropic virulence determinant Gat201, a GATA-family transcription factor, suggested that capsule-independent antiphagocytic mechanisms exist. We have determined that Gat201 controls the mRNA levels of ~1100 genes (16% of the genome) and binds the upstream regions of ~130 genes. more...
Organism:
Cryptococcus neoformans; Cryptococcus neoformans var. grubii
Type:
Genome binding/occupancy profiling by genome tiling array; Expression profiling by array
Platforms:
GPL13228 GPL4522
12 Samples
Download data: GPR
Series
Accession:
GSE27660
ID:
200027660
16.

Cryptococcus neoformans 243K tiling chip

(Submitter supplied) standard Agilent protocol
Organism:
Cryptococcus neoformans
1 Series
4 Samples
Download data
Platform
Accession:
GPL13228
ID:
100013228
17.

Differentially expressed genes of cir1 mutants in low iron or high iron medium

(Submitter supplied) Iron overload is known to exacerbate many infectious diseases and, conversely, iron withholding is an important defense strategy for mammalian hosts. The mechanisms by which fungal pathogens sense iron in the mammalian host environment are poorly understood. The AIDS-associated pathogen Cryptococcus neoformans provides a unique opportunity to explore iron sensing in the context of infection because iron levels control elaboration of the polysaccharide capsule that is the major virulence factor of the fungus. more...
Organism:
Cryptococcus neoformans var. neoformans; Cryptococcus neoformans var. neoformans B-3501A
Type:
Expression profiling by array
Platform:
GPL4009
4 Samples
Download data: TXT
Series
Accession:
GSE5341
ID:
200005341
18.

C. neoformans gene expression in DMEM of WT and rim101 mutant cells

(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
Series
Accession:
GSE43189
ID:
200043189
19.

The role of the central region of Ada2 in gene regulation

(Submitter supplied) The SAGA complex of Saccharomyces cerevisiae contains greater than 20 components that acetylate and deubiquitylate nucleosomal histones. Its acetyltransferase, Gcn5 preferentially acetylates histones H3 and H2B and is regulated through interactions with Ada2 and Ngg1/Ada3. The N-terminal region of Ada2 contains a SANT domain that contacts Gcn5 near its catalytic site. Sequence alignments of Ada2 homologues indicate a conserved ~120 amino acid residue central region that interacts with Ngg1.To examine the function of this central region, we constructed ada2 alleles with mutations of clustered conserved residues. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by array; Expression profiling by genome tiling array
Platforms:
GPL4131 GPL884
6 Samples
Download data: TXT
Series
Accession:
GSE11377
ID:
200011377
20.

WT vs rim101 mutant gene expression under capsule inducing conditions

(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
Series
Accession:
GSE23929
ID:
200023929
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