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Sample GSM2526314 Query DataSets for GSM2526314
Status Public on Apr 11, 2017
Title Mclr-2Δsah-2 replicate 3
Sample type SRA
 
Source name Mycelia
Organism Neurospora crassa
Characteristics strain: FGSC 2489
genotype/variation: Mclr-2deltasah-2
Growth protocol Vogel’s minimal medium (VMM)(38) was used to grow N. crassa. Conidia were inoculated into 100 mL liquid media at 10^6 conidia/mL and grown at 25°C on a rotary shaker (200 rpm) for 16 hrs and than transfer into anothrer 100mL fresh VMM media for 24 hrs.
Extracted molecule total RNA
Extraction protocol Mycelia was filtered and frozen in liquid nitrogen, and RNA was harvested using Trizol reagent and purified using Qiagen RNeasy Mini Kit (Cat # 74104).
RNA libraries 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: N. crassa OR74A genome (v12)
Supplementary_files_format_and_content: fpkm_tracking
 
Submission date Mar 08, 2017
Last update date May 15, 2019
Contact name Lina Qin
E-mail(s) [email protected]
Phone 4156874329
Organization name University of Carlifornia
Street address 2151 Berkeley way
City Berkeley
State/province California
ZIP/Postal code 94720
Country USA
 
Platform ID GPL23150
Series (1)
GSE95807 Deciphering the Regulatory Network between the SREBP pathway and Protein Secretion in Neurospora crassa
Relations
BioSample SAMN06546985
SRA SRX2619904

Supplementary file Size Download File type/resource
GSM2526314_LQ12_genes.fpkm_tracking.gz 260.9 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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