GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Series GSE95681

Query DataSets for GSE95681

Status

Public on Sep 25, 2017

Title

Network of nutrient sensing pathways and a conserved kinase cascade integrates osmolarity and carbon sensing in Neurospora crassa

Organism

Neurospora crassa

Experiment type

Expression profiling by high throughput sequencing

Summary

Identifying nutrients available in the environment and utilizing them in the most efficient manner is a challenge common to all organisms. The model filamentous fungus Neurospora crassa is capable of utilizing a variety of carbohydrates, from simple sugars to the complex carbohydrates found in plant cell walls. The zinc binuclear cluster transcription factor CLR-1 is necessary for utilization of cellulose, a major, recalcitrant component of the plant cell wall; however, expression of clr-1 in the absence of an inducer is not sufficient to induce cellulase gene expression. We performed a screen for unidentified actors in the cellulose-response pathway and identified a gene encoding a hypothetical protein (clr-3) that is required for repression of CLR-1 activity in the absence of an inducer. Using clr-3 mutants, we implicated the hyperosmotic-response pathway in the tunable regulation of glycosyl hydrolase production in response to changes in osmolarity. The role of the hyperosmotic-response pathway in nutrient sensing may indicate that cells use osmolarity as a proxy for the presence of free sugar in their environment. These signaling pathways form a nutrient-sensing network that allows N. crassa cells to tightly regulate gene expression in response to environmental conditions.

Overall design

mRNA profiles of wild type and mutant N. crassa cells exposed to carbon starvation and cellulose. There are 14 different strains and conditions each done in biological triplicate, which includes wild type controls for a total of 42 samples.

Contributor(s)

Huberman LB, Coradetti ST, Glass NL

Citation(s)

Submission date

Mar 03, 2017

Last update date

May 15, 2019

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 (2)

GPL16164	Illumina HiSeq 2000 (Neurospora crassa)
GPL23150	Illumina HiSeq 4000 (Neurospora crassa)

Samples (42)

More...

GSM2521538	Wild type 10h Starvation Biological Replicate 1
GSM2521539	Wild type 10h Starvation Biological Replicate 2
GSM2521540	Wild type 10h Starvation Biological Replicate 3

GSM2521541	[delta]clr-3 10h Starvation Biological Replicate 1
GSM2521542	[delta]clr-3 10h Starvation Biological Replicate 2
GSM2521543	[delta]clr-3 10h Starvation Biological Replicate 3
GSM2521544	[delta]os-1 10h Starvation Biological Replicate 1
GSM2521545	[delta]os-1 10h Starvation Biological Replicate 2
GSM2521546	[delta]os-1 10h Starvation Biological Replicate 3
GSM2521547	[delta]os-2 10h Starvation Biological Replicate 1
GSM2521548	[delta]os-2 10h Starvation Biological Replicate 2
GSM2521549	[delta]os-2 10h Starvation Biological Replicate 3
GSM2521550	[delta]cre-1 10h Starvation Biological Replicate 1
GSM2521551	[delta]cre-1 10h Starvation Biological Replicate 2
GSM2521552	[delta]cre-1 10h Starvation Biological Replicate 3
GSM2521553	[delta]os-1[delta]clr-3 10h Starvation Biological Replicate 1
GSM2521554	[delta]os-1[delta]clr-3 10h Starvation Biological Replicate 2
GSM2521555	[delta]os-1[delta]clr-3 10h Starvation Biological Replicate 3
GSM2521556	[delta]os-2[delta]clr-3 10h Starvation Biological Replicate 1
GSM2521557	[delta]os-2[delta]clr-3 10h Starvation Biological Replicate 2
GSM2521558	[delta]os-2[delta]clr-3 10h Starvation Biological Replicate 3
GSM2521559	[delta]cre-1[delta]clr-3 10h Starvation Biological Replicate 1
GSM2521560	[delta]cre-1[delta]clr-3 10h Starvation Biological Replicate 2
GSM2521561	[delta]cre-1[delta]clr-3 10h Starvation Biological Replicate 3
GSM2521562	[delta]clr-3 4h Starvation Biological Replicate 1
GSM2521563	[delta]clr-3 4h Starvation Biological Replicate 2
GSM2521564	[delta]clr-3 4h Starvation Biological Replicate 3
GSM2521565	[delta]clr-1 4h Avicel Biological Replicate 1
GSM2521566	[delta]clr-1 4h Avicel Biological Replicate 2
GSM2521567	[delta]clr-1 4h Avicel Biological Replicate 3
GSM2521568	[delta]clr-2 4h Avicel Biological Replicate 1
GSM2521569	[delta]clr-2 4h Avicel Biological Replicate 2
GSM2521570	[delta]clr-2 4h Avicel Biological Replicate 3
GSM2521571	Pccg1-clr-2 4h Starvation Biological Replicate 1
GSM2521572	Pccg1-clr-2 4h Starvation Biological Replicate 2
GSM2521573	Pccg1-clr-2 4h Starvation Biological Replicate 3
GSM2521574	Wild type 4h Avicel Biological Replicate 1
GSM2521575	Wild type 4h Avicel Biological Replicate 2
GSM2521576	Wild type 4h Avicel Biological Replicate 3
GSM2521577	Wild type 4h Starvation Biological Replicate 1
GSM2521578	Wild type 4h Starvation Biological Replicate 2
GSM2521579	Wild type 4h Starvation Biological Replicate 3

Relations

BioProject

SRA

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE95681_FPKM_Metafile.txt.gz	1.4 Mb	(ftp)(http)	TXT
GSE95681_RAW.tar	10.8 Mb	(http)(custom)	TAR (of TXT)
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |