|
Status |
Public on Mar 29, 2023 |
Title |
WT_xylose_4h_2 |
Sample type |
SRA |
|
|
Source name |
Mycelium
|
Organism |
Thermothelomyces thermophilus |
Characteristics |
strain: ATCC 42464 genotype: WT treatment: xylose_4h tissue: Mycelium cell type: fungal cell
|
Growth protocol |
Precultured mycelium from M. thermophila WT strain (ATCC42464) were shifted into 1×Vogel’s salt with 2% D-glucose, 2% D-xylose, 2% L-arabinose, arabinan, or no carbon for the induciton of additional 4 h.
|
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
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|
|
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 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(version 0.13.5). Assembly: Myceliophthora thermophila ATCC 42464(https://genome.jgi.doe.gov/Spoth2/Spoth2.home.html) Supplementary files format and content: tab-delimited text files including Reads count for each sample.
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|
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Submission date |
Dec 20, 2022 |
Last update date |
Mar 29, 2023 |
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 |
GPL27455 |
Series (1) |
GSE221464 |
The arabinose transporter MtLat-1 is involved in hemicellulase induction in Myceliophthora |
|
Relations |
BioSample |
SAMN32337848 |
SRA |
SRX18797654 |