NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6921746 Query DataSets for GSM6921746
Status Public on Dec 06, 2023
Title ∆clr5_Avicel_1
Sample type SRA
 
Source name ∆clr5_Avicel
Organism Neurospora crassa
Characteristics strain: {delta}clr5
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 SAMN32628942
SRA SRX18965825

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap