|
| Status |
Public on Mar 18, 2021 |
| Title |
Mtclr-4_4h_2 |
| Sample type |
SRA |
| |
|
| Source name |
ΔMtclr-4
|
| Organism |
Thermothelomyces thermophilus |
| Characteristics |
strain: ATCC 42464
genotype/variation: {delta}Mtclr-4
|
| Growth protocol |
M. thermophila strains were inoculated into 1×Vogel’s salt with 2% glucose and cultivated at 45 °C for 16h. Mycelia were collected and washed three times with 1×Vogel’s salt, and then transferred into the medium with 2% Avicel as the carbon source for an additional 4 h of cultivation. N. crassa strains were inoculated into 1×Vogel’s salt with 2% sucrose and grown for 16 h at 25 °C. Mycelia of the N. crassa were collected and washed with 1×Vogel’s salt several times, and transferred into the medium with 2% Avicel as the carbon source for an additional 4 h of cultivation.
|
| 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 Myceliophthora thermophila ATCC 42464 or Neurospora crassa FGSC 2489 genome 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).
Genome_build: Myceliophthora thermophila ATCC 42464(https://genome.jgi.doe.gov/Spoth2/Spoth2.home.html) and Neurospora crassa OR74A genome (version 12)
Supplementary_files_format_and_content: tab-delimited text files including Reads count for each sample.
|
| |
|
| Submission date |
Mar 19, 2018 |
| Last update date |
Mar 18, 2021 |
| 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 |
GPL24572 |
| Series (1) |
| GSE111986 |
A novel conserved transcription factor CLR-4 regulates cellulase genes expression through controlling the intracellular cAMP level in ascomycete fungi |
|
| Relations |
| BioSample |
SAMN08731611 |
| SRA |
SRX3809736 |
