|
| Status |
Public on Apr 11, 2017 |
| Title |
Wild type replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Mycelia
|
| Organism |
Neurospora crassa |
| Characteristics |
strain: FGSC 2489
genotype/variation: wildtype
|
| Growth protocol |
Vogel’s minimal medium (VMM)(38) was used to grow N. crassa. Conidia were inoculated into 100 mL liquid media at 10^6 conidia/mL and grown at 25°C on a rotary shaker (200 rpm) for 16 hrs and than transfer into anothrer 100mL fresh VMM media for 24 hrs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mycelia was filtered and frozen in liquid nitrogen, and RNA was harvested using Trizol reagent and purified using Qiagen RNeasy Mini Kit (Cat # 74104).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina Casava1.8 software used for base calling
Sequence reads were trimmed for adaptor sequence and aligned to the predicted transcripts from the N. crassa OR74A genome (v12) with HiSat2 v2.0.5 with the parameters --max-intronlen 5000 --rna-strandness R --dta-cufflinks
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using Cufflinks v2.2.1 with the parameters --library-type fr-firststrand -u -b -G --compatible-hits-norm --max-bundle-frags=10000000
Genome_build: N. crassa OR74A genome (v12)
Supplementary_files_format_and_content: fpkm_tracking
|
| |
|
| Submission date |
Mar 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Lina Qin |
| E-mail(s) |
[email protected]
|
| Phone |
4156874329
|
| Organization name |
University of Carlifornia
|
| Street address |
2151 Berkeley way
|
| City |
Berkeley |
| State/province |
California |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL23150 |
| Series (1) |
| GSE95807 |
Deciphering the Regulatory Network between the SREBP pathway and Protein Secretion in Neurospora crassa |
|
| Relations |
| BioSample |
SAMN06546983 |
| SRA |
SRX2619893 |
