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Sample GSM4544372 Query DataSets for GSM4544372
Status Public on Mar 09, 2021
Title Wild type 50mM Isoleucine Biological Replicate 1
Sample type SRA
 
Source name Neurospora crassa mycelia
Organism Neurospora crassa
Characteristics genotype: FGSC 2489
media: Vogel's minimal medium with 2% Sucrose and 50mM Isoleucine
Treatment protocol Mycelia were washed in media lacking a carbon source (for mannose or carbon starvation) or media lacking a nitrogen source (for all others) and then transferred to 3ml of Vogel's minimal media with thie indicated carbon or nitrogen source and incubated at 25C in constant light with constant shaking at 200rpm for 4h prior to harvesting for RNAseq.
Growth protocol N. crassa conidia were inoculated into 3ml of Vogel's minimal media + 2% sucrose and incubated at 25C in constant light with constant shaking at 200rpm for 24h
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 v2.1.0 with the parameters --max-intronlen 5000 --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-unstranded -u -b -G --compatible-hits-norm --max-bundle-frags=10000000
FPKMs in the FPKM_Metafile.txt were generated by running all samples through cuffmerge v2.2.1; then cuffquant v2.2.1 with the parameters --library-type fr-unstranded --max-bundle-frags=10000000; then cuffnorm v2.2.1 with the parameters --library-type fr-unstranded.
Genome_build: Neurospora crassa OR74A genome v12
Supplementary_files_format_and_content: tab-deliminated text files include FPKM values for each sample
 
Submission date May 11, 2020
Last update date Mar 09, 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
 
Platform ID GPL23150
Series (1)
GSE150256 DNA affinity purification sequencing and transcriptional profiling reveal new aspects of nitrogen regulation in a filamentous fungus
Relations
BioSample SAMN14886632
SRA SRX8321402

Supplementary file Size Download File type/resource
GSM4544372_WT_Ile_1.fpkm.txt.gz 259.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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