|
| Status |
Public on Dec 06, 2023 |
| Title |
WT_Avicel_2 |
| Sample type |
SRA |
| |
|
| Source name |
WT_Avicel
|
| Organism |
Neurospora crassa |
| Characteristics |
strain: FGSC 2489
cell type: Mycelium
|
| Growth protocol |
Precultured mycelium from N. crassa WT strain or ∆clr5 strain were shifted into 1×Vogel’s salt with 2% Avicel for the induciton of additional 8 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 Neurospora crassa OR74A 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: Neurospora crassa OR74A (https://fungidb.org/fungidb/app/downloads/release-61/NcrassaOR74A/)
Supplementary files format and content: tab-delimited text files including Reads count for each sample.
|
| |
|
| Submission date |
Jan 07, 2023 |
| Last update date |
Dec 06, 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 |
GPL16164 |
| Series (1) |
| GSE222372 |
The transcriptional factor Clr-5 is involved in cellulose degradation through regulation of amino acid metabolism in Neurospora crassa |
|
| Relations |
| BioSample |
SAMN32628939 |
| SRA |
SRX18965828 |
