|
| Status |
Public on Jul 12, 2021 |
| Title |
Δcys-3 24uM Sulfate Biological Replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Δcys-3 24uM Sulfate
|
| Organism |
Neurospora crassa |
| Characteristics |
genotype: {delta}cys-3
medium: Vogel's minimal medium with 24uM sulfate
tissue: mycelia
|
| Treatment protocol |
Mycelia were washed in media lacking sulfur and then transferred to 3ml of Vogel's minimal media with either 24uM sulfate or no sulfur source and incubated at 25C in constant light with constant shaking at 200rpm for 4h prior to harvesting for RNAseq.
|
| Growth protocol |
N. crassa conidia were inoculated into 3ml of Vogel's minimal media + 500mg/L methionine and incubated at 25C in constant light with constant shaking at 200rpm for 24h
|
| 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 3000 |
| |
|
| 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 v2.1.0 with the parameters --max-intronlen 5000 --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-unstranded -u -b -G --compatible-hits-norm --max-bundle-frags=10000000
FPKMs in the FPKM_Metafile.xlsx were generated by running all samples through cuffmerge v2.2.1; then cuffquant v2.2.1 with the parameters --library-type fr-unstranded --max-bundle-frags=10000000; then cuffnorm v2.2.1 with the parameters --library-type fr-unstranded.
Genome_build: Neurospora crassa OR74A genome v12
Supplementary_files_format_and_content: tab-deliminated text files include FPKM values for each sample
|
| |
|
| Submission date |
May 05, 2021 |
| Last update date |
Jul 12, 2021 |
| 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 |
GPL30082 |
| Series (1) |
| GSE173890 |
Aspects of the Neurospora crassa sulfur starvation response are revealed by transcriptional profiling and DNA affinity purification sequencing |
|
| Relations |
| BioSample |
SAMN19021843 |
| SRA |
SRX10779321 |
