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Sample GSM1238604 Query DataSets for GSM1238604
Status Public on Mar 17, 2014
Title Ncrassa_glucose_rep1
Sample type SRA
 
Source name Mycelia
Organism Neurospora crassa
Characteristics strain: OR74A
carbon source: D-glucose
genotype: wild type
Growth protocol Conidia from 10-day-old agar culture were collected and counted by haemocytometer, then inoculated into 1×vogel's salts with 2% carbon source (D-glucose, D-xylose or L-arabinose) and grown for 16-26 hrs at 28 °C with constant light
Extracted molecule total RNA
Extraction protocol Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Neurospora crassa OR74A genome (version 12) using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count( v0.5.4p2).
The normalized expression values for each gene were calculated by the number of uniquely mapped reads per kilobase of exon region per million mapped reads (RPKM) and differential gene expression was determined by DESeq package (v1.5.1).
Genome_build: Neurospora crassa OR74A
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each sample.
 
Submission date Sep 23, 2013
Last update date May 15, 2019
Contact name Jingen Li
E-mail(s) li_jg@tib.cas.cn
Phone +86-02284861948
Organization name Tianjin institute of industrial biotechnology,Chinses Academy of Sciences
Street address Xiqi Dao 32, Tianjin Airport Economic Area
City Tianjin
ZIP/Postal code 300308
Country China
 
Platform ID GPL16164
Series (1)
GSE51091 Transcriptional comparison of the filamentous fungus Neurospora crassa growing on three major monosaccharides D-glucose, D-xylose and L-arabinose
Relations
BioSample SAMN02361131
SRA SRX357540

Supplementary file Size Download File type/resource
GSM1238604_Ncrassa_glucose_1_reads.txt.gz 40.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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