|
| Status |
Public on Sep 25, 2017 |
| Title |
[delta]clr-3 10h Starvation Biological Replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Neurospora crassa mycelia
|
| Organism |
Neurospora crassa |
| Characteristics |
genotype: [delta]clr-3
media: Vogel's minimal media lacking a carbon source
time: 10h
|
| Treatment protocol |
Mycelia were washed in media lacking a carbon source and then transferred to 100ml of Vogel's minimal media without a carbon source or Vogel's minimal media+2%Avicel and incubated at 25C in constant light with constant shaking at 200rpm for the indicated amount of time
|
| Growth protocol |
N. crassa conidia were inoculated into 100ml of Vogel's minimal media + 2% sucrose and incubated at 25C in constant light with constant shaking at 200rpm for 16h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mycelia were filtered using Whatman paper #1 and flash frozen using liquid nitrogen. RNA was isolated by bead beating in Trizol reagent and then cleaned up using the Qiagen RNeasy kit.
RNA 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: Neurospora crassa OR74A genome v12
Supplementary_files_format_and_content: tab-deliminated text files include FPKM values for each sample
|
| |
|
| Submission date |
Mar 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Lori B Huberman |
| Organization name |
University of California Berkeley
|
| Department |
Plant and Microbial Biology
|
| Lab |
Glass Lab
|
| Street address |
2151 Berkeley Way
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94708 |
| Country |
USA |
| |
|
| Platform ID |
GPL23150 |
| Series (1) |
| GSE95681 |
Network of nutrient sensing pathways and a conserved kinase cascade integrates osmolarity and carbon sensing in Neurospora crassa |
|
| Relations |
| BioSample |
SAMN06477534 |
| SRA |
SRX2612130 |
