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Sample GSM4681832 Query DataSets for GSM4681832
Status Public on May 06, 2023
Title Mycelium of 1 gram Mutant Ku70 were solid-static cultured 24h in a medium of straw plus wheat bran [POXKu70S_SWT]
Sample type SRA
 
Source name Mycelium
Organism Penicillium oxalicum
Characteristics strain: Ku70
Growth protocol Fresh spores of the MuKu70 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with % (w/v) Avicel, and incubated in a shaker at 180 rpm and 28°C for 24 h.
Extracted molecule total RNA
Extraction protocol Total RNA were extracted using TRIzol RNA Kit
A cDNA library with 100 bp of length was constructed using the extracted total RNA, and assessed with the ABI StepOnePlus Real-Time PCR System and the Agilent 2100 Bioanalyzer. The eligible cDNA library was sequenced via the Illumina HiSeq 4000 system
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model BGISEQ-500
 
Data processing Remove reads with adapters;Remove reads in which unknown bases are more than 10%;Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 10).
The clean reads mapped onto the genome of P. oxalicum wild type strain HP7-1 to functional annotation, susing the software BWA v0.7.10-r789 and Bowtie2 v2.1.0.
FPKM, representing gene expression levels, was calculated with the software RSEM v1.2.12
DEGs were screened with NOISeq or DESeq2 tools
Genome_build: GenBank database under accession number JRVD00000000
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.
 
Submission date Jul 22, 2020
Last update date May 06, 2023
Contact name Li ChengXi
E-mail(s) Chengxi-Li@hotmail.com
Organization name Bengbu Medical College
Department Affiliated Sixth People’s Hospital
Street address 2600 Donghai Avenue, Bengbu, Anhui, China
City bengbu
State/province Anhui
ZIP/Postal code 233000
Country China
 
Platform ID GPL24231
Series (2)
GSE154712 Effect of gene deletion on gene expression of Penicillium oxalicum
GSE154882 Effects of transcription factor POX04513 on the transcription of cellulase genes and xylanase genes in Penicillium oxalicum
Relations
BioSample SAMN15595180
SRA SRX8787083

Supplementary file Size Download File type/resource
GSM4681832_POXKu70_04513S_SW_24hT.gene.FPKM.txt.gz 51.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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