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| Status |
Public on Mar 16, 2019 |
| Title |
CC_H_R2 |
| Sample type |
SRA |
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| Source name |
secondary hyphal knot
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| Organism |
Coprinopsis cinerea |
| Characteristics |
strain: #326 (A43mut B43mut pab 1-1)
group: CC_H
flowcell_id: C86GRANXX
tissue: secondary hyphal knot
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| Growth protocol |
For fruiting Coprinopsis cinerea strain #326 (A43mut B43mut pab 1-1) an agar disk (5 mm in diameter) was placed on the center of YMG/T agar media (4 g yeast extract, 10 g malt extract, 4 g glucose, 10 g agar media with 100 mg tryptophane added after cooling at 37 °C for five days in the dark. When the colonies reached the 1-2 mm distance from the edge of Petri dishes they were placed into 25 °C for one week in a 12 hrs light/12 hrs dark cycle for fruiting
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| 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 to extract RNA 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)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Reads were quality trimmed using CLC Genomics Workbench Tool (v 9.5.3). Ambiguous base limit=0, Error probability cutoff value=0.05.
Reads were mapped using RNA-Seq analysis package 2.1 of CLC Genomics Workbench Tool (v. 9.5.3) 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
Genome_build: Coprinopsis cinerea AmutBmut pab1-1 v1.0 (Copci_AmutBmut1) JGI Project Id: 1004746
Supplementary_files_format_and_content: Comma separated files containing RNA-Seq count data, exported from CLC Genomics Workbench Tool
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| Submission date |
Jan 16, 2019 |
| Last update date |
Mar 17, 2019 |
| Contact name |
Laszlo G. Nagy |
| E-mail(s) |
lnagy@fungenomelab.com
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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 |
GPL26053 |
| Series (2) |
| GSE125184 |
Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi [Coprinopsis cinerea] |
| GSE125200 |
Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi |
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| Relations |
| BioSample |
SAMN10756293 |
| SRA |
SRX5255164 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3564747_CC_H_R2.CLC_RNA-Seq.csv.gz |
329.1 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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