|
| Status |
Public on Mar 23, 2023 |
| Title |
64_2_2 |
| Sample type |
SRA |
| |
|
| Source name |
crossed mutant protoperithecia
|
| Organism |
Neurospora crassa |
| Characteristics |
strain: FGSC#4564, mat a[m1]s-3B cyh-1
time point: 2 hr after crossing
morphology: crossed protoperithecia
Stage: stage2
|
| Treatment protocol |
Protoperithecia from mat 1-2-1 muant were crossing with conidia from wild type FGSC#2489
|
| Growth protocol |
Conidia of N. crassa mat 1-2-1 mutant (FGSC#4564, mat a[m1]s-3B cyh-1) were harvested from cultures on Bird medium. 2 ml filtrate conidia spore was plated out on cellophane membrane covering solid SCM in petri dish (9cm in diameter) and incubated were incubated in a refrigerated incubator (VWR Signature™ Diurnal Growth for 6 days until abundant protoperithecia appear.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cellophane membranes with fungal tissues were collected at protoperithecial stage (0 time point right before the crossing) and 2h after crossing. Tissue samples were flash frozen in liquid nitrogen and stored at ﹣80 C. All tissues/perithecia that were collected from a single plate were counted as one biological replicate. At least three biological replicates were prepared for each sampled time-point.
Total RNA was extracted from homogenized tissue with TRI REAGENT (Molecular Research Center) as in Clark et al. (2008).
Sequencing libraries were produced from purified total RNA samples by the Illumina TruSeq stranded protocol. The libraries underwent 101 bp paired-end sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
replicate 2
|
| Data processing |
According to Illumina protocol, the libraries underwent 101-bp paired-end sequencing using an Illumina NovaSeq (S4). Basecalls performed using CASAVA version 1.8.2
Trimming of the reads for the presence of adapters and low quality bases was performed with fastp with default parameters.
Trimmed reads were mapped to the Neurospora crassa OR74A reference genome (FungiDB release 43) with hisat2 v2.1.0 indicating that reads correspond to the reverse complement of the transcripts. Alignments with quality score below 20 were excluded from further analysis.
Gene counts were produced with stringtie v1.3.3b and the python script “prepde.py” provided in the package. Stringtie was limited to reads matching the reference annotation.
LOX v1.4 was applied to the tallies for each sample for each gene to estimate gene expression levels and credible intervals across developmental stages. LOX provides relative gene expression levels standardized by the lowest sample, with credible intervals
Assembly: Neurospora crassa OR74A (FungiDB release 43)
Supplementary files format and content: Tab delimited and CSV text files including raw counts and LOX output, respectively. LOX provides relative gene expression levels standardized by the lowest sample, with credible intervals
|
| |
|
| Submission date |
Mar 23, 2022 |
| Last update date |
Mar 23, 2023 |
| Contact name |
Francesc Lopez |
| E-mail(s) |
francesc.lopez@yale.edu
|
| Organization name |
Yale University
|
| Department |
Department of Genetics
|
| Lab |
YCGA
|
| Street address |
P.O. Box 27386
|
| City |
West Haven |
| State/province |
CT |
| ZIP/Postal code |
06516 |
| Country |
USA |
| |
|
| Platform ID |
GPL26551 |
| Series (1) |
| GSE199259 |
Orphan elements are clustered with allorecognition loci and likely involved in incompatibility and speciation in Neurospora |
|
| Relations |
| BioSample |
SAMN26897898 |
| SRA |
SRX14588059 |
