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| Status |
Public on Mar 17, 2022 |
| Title |
N. crassa 15min [B1-3] |
| Sample type |
SRA |
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| Source name |
conidia germination_PDA
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| Organism |
Neurospora crassa |
| Characteristics |
strain: FGSC2489
time point: 15 minutes after inoculation
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| Growth protocol |
The project was set to compare fungal conidial germination on different culture media and at different growth temperatures. For this set of expriment the N. crassa conidial germination was sampled on Bird medium at 37C. CULTURES were performed by applying 2 ml of the suspension of conidia in 1.5% Tween 60 (105 - 106 conidia/ml) to the surface of medium plates that were covered with cellophane membranes. Conidia germination were monitored with microscope, and roughly over 70% individual conidia showing same development stage were used to decide the sampling time points (15, 120, 240, and 360 minutes).
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| Extracted molecule |
total RNA |
| Extraction protocol |
For transcriptomic analysis, all tissues and perithecia were immediately and rapidly frozen in liquid nitrogen as they were sampled, then stored at -80°C. RNA was isolated from homogenized mycelia with TRI REAGENT (Invitrogen) and mRNA was purified using Dynabeads oligo(dT) magnetic separation (Invitrogen)
For purified total RNA collected from samples, strand-specific sequencing libraries were produced following the Illumina TruSeq stranded protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
replicate 3
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| 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
For each read, the first 6 and the last nucleotides were trimmed to the point where the Phred score of an examined base fell below 20 using in-house scripts. If, after trimming, the read was shorter than 45 bp, the whole read was discarded.
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
Genome_build: Neurospora crassa OR74A (FungiDB release 43)
Supplementary_files_format_and_content: CSV and tab delimited text files including raw counts and LOX output. LOX provides relative gene expression levels standardized by the lowest sample, with credible intervals
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| Submission date |
Mar 16, 2021 |
| Last update date |
Mar 17, 2022 |
| Contact name |
Francesc Lopez |
| E-mail(s) |
francesc.lopez@yale.edu
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| Organization name |
Yale University
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| Department |
Department of Genetics
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| Lab |
YCGA
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| Street address |
P.O. Box 27386
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| City |
West Haven |
| State/province |
CT |
| ZIP/Postal code |
06516 |
| Country |
USA |
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| Platform ID |
GPL26551 |
| Series (2) |
| GSE168991 |
Gene expression during conidia germination in Neurospora crassa on Bird medium at 37C |
| GSE168995 |
Gene expression during conidia germination in Neurospora crassa |
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| Relations |
| BioSample |
SAMN18319114 |
| SRA |
SRX10354684 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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