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Sample GSM8550468 Query DataSets for GSM8550468
Status Public on Oct 09, 2024
Title tah-1_2
Sample type SRA
 
Source name Mycelia
Organism Curvularia clavata
Characteristics tissue: Mycelia
strain: J1
genotype: {delta}tah-1
time: 4 day
treatment: Lignosulfonate
Growth protocol Mycelia from the C. clavata strains were inoculated into 100 mL of Vogel’s minimal medium supplemented with 2% (w/v) glucose (MMG) or 2% lignosulfonate and 0.25% glucose (MML). The culture was incubated at 30°C with continuous shaking at 200 rpm for 4 days.
Extracted molecule total RNA
Extraction protocol 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 for RNA-seq were prepared using standard Illumina protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-T7
 
Description mRNA of the Δtah-1 mutant grown on lignosulfonate for 4 day, sample 2
Data processing Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v0.19.5.
Clear reads were mapped to Curvularia clavata YC1106 genome using HISAT2 (v2.1.0) with parameters --dta --phred64 unstranded --new-summary -x index -1 read_r1 -2 read_r2(PE).
The counts of reads uniquely mapped to only one gene for each gene were calculated by RSEM (v1.3.3) with default parameters.
The normalized expression values for each gene were calculated by the number of uniquely mapped transcripts per million (TPM) and differential gene expression was determined by DESeq2 package.
Assembly: ASM2392016v1
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample
 
Submission date Oct 02, 2024
Last update date Oct 09, 2024
Contact name Jinyang Li
E-mail(s) lijy@tib.cas.cn
Organization name Chinese Academy of Sciences
Street address No. 32, Xiqi Road, Tianjin Airport Economic Park
City Tianjin
ZIP/Postal code 300308
Country China
 
Platform ID GPL34958
Series (1)
GSE278592 Transcriptome insight into lignin utilization by Curvularia clavata and identification of regulators of laccase activity
Relations
BioSample SAMN43764483
SRA SRX26083820

Supplementary file Size Download File type/resource
GSM8550468_tah_L_2_FPKM.txt.gz 50.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA

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