|
| Status |
Public on Mar 05, 2022 |
| Title |
Mycelia_WT_1D_2 |
| Sample type |
SRA |
| |
|
| Source name |
Mycelia
|
| Organism |
Neurospora crassa |
| Characteristics |
genotype: Wild type
tissue: Mycelia
time (culture): 1D
|
| Growth protocol |
Conidia of △stk-12 and wild-type (WT) strains were separately inoculated into Avicel medium (1×Vogel's salt, 2% w/v crystalline cellulose) and batch cultured for 5 days at 25 ℃ with constant light.
|
| 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 Neurospora crassa OR74A genome (version 12) 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( v0.5.4p3).
The normalized expression values for each gene were calculated by the number of uniquely mapped reads per kilobase of exon region per million mapped reads (RPKM) and differential gene expression was determined by NOISeq package (v2.6.0).
Genome_build: NC12 (Neurospora crassa OR74A)
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each sample.
|
| |
|
| Submission date |
Apr 05, 2019 |
| Last update date |
Mar 05, 2022 |
| Contact name |
liangcai lin |
| E-mail(s) |
[email protected]
|
| Organization name |
Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences
|
| Street address |
32 West 7th Avenue, Tianjin Airport Economic Area
|
| City |
Tianjin |
| ZIP/Postal code |
300308 |
| Country |
China |
| |
|
| Platform ID |
GPL16164 |
| Series (1) |
| GSE129410 |
Disruption of serine/threonine protein kinase STK-12 increases cellulase expression in Neurospora crassa |
|
| Relations |
| BioSample |
SAMN11351712 |
| SRA |
SRX5648342 |
