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Sample GSM6873682 Query DataSets for GSM6873682
Status Public on Mar 29, 2023
Title WT_arabinose_4h_1
Sample type SRA
 
Source name Mycelium
Organism Thermothelomyces thermophilus
Characteristics strain: ATCC 42464
genotype: WT
treatment: arabinose_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
 
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.
 
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 SAMN32337847
SRA SRX18797655

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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