|
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
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|
|
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 |