|
| Status |
Public on Jul 23, 2020 |
| Title |
cpc-1KO-2%glu-3-AT_3 |
| Sample type |
SRA |
| |
|
| Source name |
mycelia
|
| Organism |
Neurospora crassa |
| Characteristics |
strain: cpc-1 deletion mutant (cpc-1delta)
tissue: mycelia
culture conditions: 2%glu-3-AT
|
| Treatment protocol |
For the samples cultured in 2% glucose medium or 0.1% glucose medium, no special treatment was performed. For the samples treated with 3-AT, the cultures were treated with 5 mM 3-AT for 8 h before sample collection.
|
| Growth protocol |
Fresh conidia (one week post inoculation on slants) of the WT strain and the cpc-1 deletion mutant were cultured in 2% glucose medium (1 × Vogel’s, 2% glucose) with or without 3-AT, or 0.1% glucose medium (1 × Vogel’s, 0.1% glucose and 0.17% arginine) at room temperate under constant light.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagents (Invitrogen) and treated with DNase (Turbo DNase, Ambion) accoding to standard RNA extraction protocal.
Libraries were constucted using Illumina TruSeq reagents. All RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing reads were mapped to reference sequences using tophat2 with parameters --min-intron-length 4 --max-intron-length 5000 --library-type fr-firststrand --max-multihits 20 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --mate-inner-dist 0 --mate-std-dev 50 --no-coverage-search.
Reads Per Kilobase Million (RPKM) were calculated using cufflinks with parameters --min-intron-length 4 --max-intron-length 5000 --library-type fr-firststrand --multi-read-correct --upper-quartile-norm --frag-bias-correct
Genome_build: The reference sequence is whole genome sequence (supercontigs) with gff annotation file from NCBI database (assembly NC12).
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample.
|
| |
|
| Submission date |
May 11, 2020 |
| Last update date |
Jul 23, 2020 |
| Contact name |
xueliang lyu |
| E-mail(s) |
lvxueliang0715@aliyun.com
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Physiology
|
| Lab |
Yi Liu
|
| Street address |
6001 Forest Park Road
|
| City |
Dallas |
| State/province |
Texas |
| ZIP/Postal code |
75235 |
| Country |
USA |
| |
|
| Platform ID |
GPL26551 |
| Series (1) |
| GSE150287 |
Effect of cpc-1 deletion in Neurospora crassa on transcriptome under different culture conditions |
|
| Relations |
| BioSample |
SAMN14888079 |
| SRA |
SRX8323522 |
