|
| Status |
Public on Mar 17, 2014 |
| Title |
Ncrassa_glucose_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Mycelia
|
| Organism |
Neurospora crassa |
| Characteristics |
strain: OR74A
carbon source: D-glucose
genotype: wild type
|
| Growth protocol |
Conidia from 10-day-old agar culture were collected and counted by haemocytometer, then inoculated into 1×vogel's salts with 2% carbon source (D-glucose, D-xylose or L-arabinose) and grown for 16-26 hrs at 28 °C 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( v0.5.4p2).
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 DESeq package (v1.5.1).
Genome_build: Neurospora crassa OR74A
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each sample.
|
| |
|
| Submission date |
Sep 23, 2013 |
| Last update date |
May 15, 2019 |
| 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) |
| GSE51091 |
Transcriptional comparison of the filamentous fungus Neurospora crassa growing on three major monosaccharides D-glucose, D-xylose and L-arabinose |
|
| Relations |
| BioSample |
SAMN02361133 |
| SRA |
SRX357541 |
