|
Status |
Public on Dec 06, 2023 |
Title |
WT_His_1 |
Sample type |
SRA |
|
|
Source name |
WT_His
|
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× No-nitrogen Vogel’s salt with 2% Avicel, and 50 mM Histidine 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 |
SAMN32628936 |
SRA |
SRX18965831 |