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Series GSE52153 Query DataSets for GSE52153
Status Public on Jul 01, 2014
Title Transcriptional profiling of staurosporine-induced cell death in wild type versus Δczt-1 in Neurospora crassa
Organism Neurospora crassa
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: Compare the transcriptional profile of staurosporine-treated cells in Neurospora crassa wild type and Δczt-1 (ΔNCU09974) cells
Methods: Conidial suspensions were obtained and 1 x 106 cells/ml incubated in minimal medium for 6 hours (26ºC, 140 rpm, constant light) followed by the addition of staurosporine (or DMSO) and growth for 1 more hour. Cells were harvested using 0.45 μm filters and immediately frozen in liquid nitrogen. Total RNA was isolated by the Trizol-Phenol-Chloroform method. After digestion of 25 μg RNA with TURBO DNAse (Life Technologies), mRNA was purified using Dynabeads oligo(dT) magnetic beads (Life Technologies). The mRNA was chemically fragmented using the Ambion RNA fragmentation kit (Life Technologies). First and second strand cDNA synthesis was achieved using appropriate kits (Life Technologies). The illumina TruSeq kit was employed to generate the cDNA libraries with indexing adapters essentially following the manufacturer’s protocol. After purification of the libraries with AMPure XP beads (Roche), the quality of the libraries was analysed in a Agilent 2100 Bioanalyzer. The cDNA libraries were sequenced in a illumina HiSeq2000 and single reads of 50 bp were obtained. Sequencing data was handled essentially with Tophat, Cufflinks and Cuffdiff. Expression levels are presented as Fragments/Reads Per Kilobase of transcript per Million mapped reads (FPKM/RPKM).
Results: Transcriptional profiling of staurosporine-treated cells wild type by RNA-sequencing showed that genes encoding the machinery for protein synthesis are enriched among the genes repressed by the drug. Functional category enrichment analyses also show that genes encoding components of the mitochondrial respiratory chain are downregulated by staurosporine, whereas genes involved in endoplasmic reticulum activities are upregulated. In contrast, a staurosporine-treated czt-1 deletion strain is unable to repress the genes for the respiratory chain and to induce the genes related with the endoplasmic reticulum, indicating a role for CZT-1 on the regulation of activity of these organelles.
Conclusions: This transcriptional profiling study is framed in a comprehensive study on the role of the novel transcription factor CZT-1 (NCU09974) in Neurospora crassa.
 
Overall design Transcriptional profile of wild type and Δczt-1 cells staurosporine-treated cells in Neurospora crassa was compared using illumina HiSeq2000 and single reads of 50 bp.
 
Contributor(s) Gonçalves AP
Citation(s) 24717808
Submission date Nov 06, 2013
Last update date May 15, 2019
Contact name António Pedro Gonçalves
E-mail(s) antoniopedrocardoso@gmail.com
Organization name University of California, Berkeley
Department Plant and Microbial Biology
Lab Glass Lab
Street address 341A Koshland Hall
City Berkeley
ZIP/Postal code 94720
Country USA
 
Platforms (1)
GPL16164 Illumina HiSeq 2000 (Neurospora crassa)
Samples (4)
GSM1260334 Wild type DMSO
GSM1260335 Wild type Staurosporine
GSM1260336 Δczt-1 DMSO
Relations
BioProject PRJNA227035
SRA SRP032761

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE52153_czt-1DMSOvsczt-1STS.txt.gz 336.2 Kb (ftp)(http) TXT
GSE52153_wtDMSOvsczt-1DMSO.txt.gz 334.6 Kb (ftp)(http) TXT
GSE52153_wtDMSOvswtSTS.txt.gz 334.7 Kb (ftp)(http) TXT
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