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| Status |
Public on Jun 05, 2021 |
| Title |
Young fruiting body stipe, replicate3 |
| Sample type |
SRA |
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| Source name |
Young fruiting body stipe
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| Organism |
Pleurotus ostreatus |
| Characteristics |
strain: N001
group: Po-YFB-S
tissue: Young fruiting body stipe
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| Treatment protocol |
We sampled vegetative mycelium (VM), six developmental stages and five tissue types, each in three biological replicates. Tissue from 3-8 individual fruiting bodies was pooled for each replicate of each sample type. Tissues were flash frozen in liquid nitrogen and kept at -80oC until futher extraction.
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| Growth protocol |
Dikaryotic strain N001 (CECT-20600) of Pleurotus ostreatus was grown in spawn culture (in 3kg PE bags) where conditions were 18-19 °C, relative humidity 80-85% and 8/16h light/dark period.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the four tissue types in three biological replicates, using the Quick-RNA Miniprep kit (Zymo Research, Irvine, CA, USA), following the manufacturer’s protocol.
Strand-specific cDNA libraries were constructed from poly(A)-captured RNA, using the Illumina TruSeq Stranded RNA-Seq library preparation kit, and sequenced on the Illumina HiSeq 4000/x platform in PE 2x150 format with 40 million reads per sample at OmegaBioservices (USA)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Po-YFB-S3
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| Data processing |
Reads were quality and adaptor trimmed using bbduk.sh and overlapping read pairs were merged with bbmerge.sh tools (part of BBMap/BBTools; http://sourceforge.net/projects/bbmap/) with the following parameters: qtrim=rl trimq=25 minlen=40.
A two-pass STAR alignment (Veeneman et al., 2015) was performed against reference genomes PleosPC15_2.
Counts were calculated using FeatureCounts (Liao et al 2014) with the following parameters: isGTFAnnotationFile=F, nthreads=ncpu, isPairedEnd=T, minFragLength=40, maxFragLength=600, strandSpecific=2, countChimericFragments=F,countMultiMappingReads=T, fraction=T, byReadGroup=F
Genes were filtered based on their expression levels in R (v. 3.0.2) keeping only those features that were detected by at least 5 mapped reads in at least 25% of the samples included in the study.
Trimmed mean of M values (TMM) scale normalization was used. Function: calcNormFactors, Package: edgeR, Version 3.4.2
Voom log2 transformation together with quantile normalization was applied. Function: voom normalize=quantile, Package: limma, Version: 3.18.13
Genome_build: JGI Mycocosm: Pleurotus ostreatus PC15 v2.0 (PleosPC15_2), PleosPC15_2_Assembly_scaffolds.fasta
Supplementary_files_format_and_content: Comma separated files containing raw count data
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| Submission date |
Jun 04, 2021 |
| Last update date |
Jun 06, 2021 |
| Contact name |
Laszlo G. Nagy |
| E-mail(s) |
[email protected]
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| Phone |
003662599600
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| Organization name |
Biological Research Centre, Hungarian Academy of Sciences
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| Department |
Institute of Biochemistry, Synthetic and Systems Biology Unit
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| Lab |
Laboratory of Fungal Genomics and Evolution
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| Street address |
Temesvari krt 62
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| City |
Szeged |
| State/province |
Csongrad |
| ZIP/Postal code |
6726 |
| Country |
Hungary |
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| Platform ID |
GPL30229 |
| Series (2) |
| GSE176179 |
Gene age predicts the transcriptional landscape of sexual morphogenesis in multicellular fungi [Pleos] |
| GSE176181 |
Gene age predicts the transcriptional landscape of sexual morphogenesis in multicellular fungi |
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| Relations |
| BioSample |
SAMN19572900 |
| SRA |
SRX11070711 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5359478_Po.YFB.S3_rawcount.csv.gz |
51.6 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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