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Sample GSM2521542 Query DataSets for GSM2521542
Status Public on Sep 25, 2017
Title [delta]clr-3 10h Starvation Biological Replicate 2
Sample type SRA
 
Source name Neurospora crassa mycelia
Organism Neurospora crassa
Characteristics genotype: [delta]clr-3
media: Vogel's minimal media lacking a carbon source
time: 10h
Treatment protocol Mycelia were washed in media lacking a carbon source and then transferred to 100ml of Vogel's minimal media without a carbon source or Vogel's minimal media+2%Avicel and incubated at 25C in constant light with constant shaking at 200rpm for the indicated amount of time
Growth protocol N. crassa conidia were inoculated into 100ml of Vogel's minimal media + 2% sucrose and incubated at 25C in constant light with constant shaking at 200rpm for 16h
Extracted molecule total RNA
Extraction protocol Mycelia were filtered using Whatman paper #1 and flash frozen using liquid nitrogen. RNA was isolated by bead beating in Trizol reagent and then cleaned up using the Qiagen RNeasy kit.
RNA were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Illumina Casava1.8 software used for base calling
Sequence reads were trimmed for adaptor sequence and aligned to the predicted transcripts from the N. crassa OR74A genome (v12) with HiSat2 v2.0.5 with the parameters --max-intronlen 5000 --rna-strandness R --dta-cufflinks
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using Cufflinks v2.2.1 with the parameters --library-type fr-firststrand -u -b -G --compatible-hits-norm --max-bundle-frags=10000000
Genome_build: Neurospora crassa OR74A genome v12
Supplementary_files_format_and_content: tab-deliminated text files include FPKM values for each sample
 
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
 
Platform ID GPL23150
Series (1)
GSE95681 Network of nutrient sensing pathways and a conserved kinase cascade integrates osmolarity and carbon sensing in Neurospora crassa
Relations
BioSample SAMN06477535
SRA SRX2612129

Supplementary file Size Download File type/resource
GSM2521542_LH05.fpkm.txt.gz 260.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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