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Series GSE173890 Query DataSets for GSE173890
Status Public on Jul 12, 2021
Title Aspects of the Neurospora crassa sulfur starvation response are revealed by transcriptional profiling and DNA affinity purification sequencing
Organism Neurospora crassa
Experiment type Expression profiling by high throughput sequencing
Summary Accurate nutrient sensing is important for rapid fungal growth and exploitation of available resources. Sulfur is an important nutrient source found in a number of biological macromolecules, including proteins and lipids. The model filamentous fungus Neurospora crassa is capable of utilizing sulfur found in a variety of sources from amino acids to sulfate. During sulfur starvation, the transcription factor CYS-3 is responsible for upregulation of genes involved in sulfur uptake and assimilation. Using a combination of RNA sequencing and DNA affinity purification sequencing, we performed a global survey of the N. crassa sulfur starvation response and the role of CYS-3 in regulating sulfur responsive genes. Along with genes known to be involved in sulfur metabolism, the CYS-3 transcription factor also directly activated the expression of a number of uncharacterized transporter genes, suggesting that regulating sulfur import is an important aspect of regulation by CYS-3. Additionally, CYS-3 directly regulated the expression of genes involved in mitochondrial electron transfer. During sulfur starvation, genes involved in nitrogen metabolism, such as amino acid and nucleic acid metabolic pathways, along with genes encoding proteases and nucleases that are necessary for scavenging nitrogen, were activated. Sulfur starvation also caused changes in the expression of genes involved in carbohydrate metabolism, such as those encoding glycosyl hydrolases. Thus, our data suggest a connection between sulfur metabolism and other aspects of cellular metabolism.
Overall design mRNA profiles of wild type N. crassa cells and N. crassa cells with a cys-3 partial deletion exposed to media with 24uM sulfate and sulfur starvation for 4 hours. Each of the two strains (mutant and wild type control) was exposed to both sulfur conditions for 4 total experiments, each done in biological triplicate. There are a total of 12 samples.
Contributor(s) Huberman LB, Wu VW, O'Malley RC, Glass NL
Citation(s) 34523983
Submission date May 05, 2021
Last update date Oct 12, 2021
Contact name Lori B Huberman
Organization name University of California Berkeley
Department Plant and Microbial Biology
Lab Glass Lab
Street address 2151 Berkeley Way
City Berkeley
State/province CA
ZIP/Postal code 94708
Country USA
Platforms (1)
GPL30082 Illumina HiSeq 3000 (Neurospora crassa)
Samples (12)
GSM5282408 Wild type 24uM Sulfate Biological Replicate 1
GSM5282409 Wild type 24uM Sulfate Biological Replicate 2
GSM5282410 Wild type 24uM Sulfate Biological Replicate 3
BioProject PRJNA727482
SRA SRP318535

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Supplementary file Size Download File type/resource
GSE173890_FPKM_Metafile.xlsx 1.1 Mb (ftp)(http) XLSX
GSE173890_RAW.tar 3.0 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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