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Sample GSM3565043 Query DataSets for GSM3565043
Status Public on Mar 16, 2019
Title PC_FB_R2
Sample type SRA
 
Source name fruiting body
Organism Phanerodontia chrysosporium
Characteristics strain: RP-78
group: PC_FB
flowcell_id: CALKCANXX
tissue: fruiting body
Growth protocol Phanerochaete chrysosporium RP-78 was fruited on YMPG media (10 g glucose, 10 g malt extract, 2 g peptone, 2 g yeast extract, 1 g asparagine, 2 g KH2PO4, 1 g MgSO4 x 7 H2O, 20 g agar for 1L with 1 mg thiamine added after cooling) covered with cellophane for 7 days at 37 °C in the dark, then placed in a moist growth chamber at 25 °C in an area with dimmed ambient light conditions, following the recommendations of Jill Gaskell (US Forest Products Laboratory, Washington, D. C., USA). Vegetative mycelium, young fruiting body and fruiting body stages were harvested for RNA extraction. Young fruiting body stage was defined as fruiting body initials that forms a compact mat well-delimited from the surrounding vegetative mycelium, while the fruiting bodies were harvested just after they started releasing spores (visible on the lids of Petri dishes).
Extracted molecule polyA RNA
Extraction protocol After harvesting, samples were immediately placed on liquid nitrogen and stored at -80 °C until use. 10-20 mg frozen tissue was placed in a pre-chilled mortar and ground to a fine powder. Quick-RNA Miniprep Kit (Zymo Research) was used according to manufacturer«s instructions.
Whole transcriptome sequencing was performed using the TrueSeq RNA Library Preparation Kit v2 (Illumina) according to the manufacturer’s instructions. Briefly, RNA quality and quantity measurements were performed using RNA ScreenTape and Reagents on TapeStation (all from Agilent) and Qubit (ThermoFisher); only high quality (RIN >8.0) total RNA samples were processed. Next, RNA was DNaseI (ThermoFisher) treated and the mRNA was purified and fragmented. First strand cDNA synthesis was performed using SuperScript II (ThermoFisher) followed by second strand cDNA synthesis, end repair, 3’-end adenylation, adapter ligation and PCR amplification. All of the purification steps were performed using AmPureXP Beads (Backman Coulter). Final libraries were quality checked using D1000 ScreenTape and Reagents on TapeStation (all from Agilent). Concentration of each library was determined using either the QPCR Quantification Kit for Illumina (Agilent) or the KAPA Library Quantification Kit for Illumina (KAPA Biosystems)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Reads were quality trimmed using CLC Genomics Workbench Tool (v. 10.0.1). Ambiguous base limit=0, Error probability cutoff value=0.05.
Reads were mapped using RNA-Seq analysis package v. 2.15 of CLC Genomics Workbench Tool (v. 10.0.1) allowing intergenic mapping. Parameters: min. read length fraction = 0.8, min. read similarity fraction = 0.8. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=30, Count paired reads as two=no, Expression value= Total counts.
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
Linear modeling with empirical Bayes moderation was built in limma. Package: limma, Version: 3.18.13
Supplementary_files_format_and_content: Comma separated files containing RNA-Seq count data, exported from CLC Genomics Workbench Tool
 
Submission date Jan 16, 2019
Last update date Mar 17, 2019
Contact name Laszlo G. Nagy
E-mail(s) lnagy@fungenomelab.com
Phone 003662599600
Organization name Biological Research Centre, Hungarian Academy of Sciences
Department Institute of Biochemistry, Synthetic and Systems Biology Unit
Lab Laboratory of Fungal Genomics and Evolution
Street address Temesvari krt 62
City Szeged
State/province Csongrad
ZIP/Postal code 6726
Country Hungary
 
Platform ID GPL25555
Series (2)
GSE125199 Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi [Phanerochaete chrysosporium]
GSE125200 Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi
Relations
BioSample SAMN10756509
SRA SRX5255320

Supplementary file Size Download File type/resource
GSM3565043_PC_FB_R2.CLC.RNA-Seq.csv.gz 336.3 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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