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Sample GSM8678031 Query DataSets for GSM8678031
Status Public on Jan 17, 2025
Title Korasit dilution 18,000X B
Sample type SRA
 
Source name Mycelium
Organism Phanerodontia chrysosporium
Characteristics tissue: Mycelium
treatment: Korasit dilution 18,000X
batch: 10_23
Treatment protocol Stock solutions of Tanalith E3474 and Korasit KS2 were prepared by diluting them by 145 fold in pure water. These stock solutions were then filtered using a 0.22 µM filter and used to reach final dilutions of 37,000X and 18,000X in the culture medium. For Tanalith E3474, a dilution of 37,000X corresponds to 3 mg/L of copper and to 59 ng/mL of each azole (i.e 0.19 µM of tebuconazole and 0.17 µM of propiconazole). This dilution was chosen because the concentration of copper is in line with the amount of copper we measured in the 24h water-leachate of Tanalith E3474 treated wood (personal data) and with the one measured in the 24h water-leachate of wood vacuum-pressure impregnated using a commercial copper ethanolamine solution. For Korasit KS2, a dilution of 37 000X corresponds to 2.75 mg/L of copper and 4.9 mg/L of quaternary ammonium compounds (QAC).
Growth protocol Phanerochaete chrysosporium RP78 was cultivated on solid 1% malt 3% agar plates at 37°C with or without Tanalith E3474 and Korasit KS2.
Extracted molecule total RNA
Extraction protocol The fungal mycelium was harvested post 3 days fungal growth on both formulation at two different concentrations using a scalpel, and was immediately snap-frozen in liquid nitrogen. From harvested sample, total RNA from P. chrysosporium was extracted using the RNeasy Plant Mini Kit (Qiagen), following the standard protocol of the provider, with additional Dnase treatment and LiCl precipitation.
cDNA libraries were prepared for sequencing using standard Illumina protocols by IGA Technology Services (Udine, Italy)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Library name: NAK18B
This sample is from mycelium grown with Korasit diluted 18000X. It is the second of three biological replicates used in this experiment.
Data processing Illumina sofware was used by IGA to generate fastq raw data files
raw reads were paired, trimmed (quality limit=0.05, automatic read through adapter trimming, discard short reads) and mapped against Phanerochaete chrysosporium RP78 v4.0 transcripts (https://mycocosm.jgi.doe.gov/Phchr4_2/Phchr4_2.home.html) using CLC Genomics Workbench v23.0.5 (Qiagen, Courtaboeuf, France).
For mapping, the minimum length fraction was 0.9, the minimum similarity fraction 0.9, and the maximum number of hits for a read was set to 10.
Differentially expressed genes (DEGs) were calculated using DESeq2 (v1.32) and unique mapped gene reads as entry .
Condition-specific differentially expressed genes (DEGs) were identified for each pairwise condition, using a false discovery rate (FDR) < 0.05 and a log2 fold-change (Log2FC) ≥ |1| as cut-off.
Assembly: Phanerochaete chrysosporium RP78 v4.0 transcripts (https://mycocosm.jgi.doe.gov/Phchr4_2/Phchr4_2.home.html)
Supplementary files format and content: tab-delimited text files include Protein ID, raw counts, RPKM, TPM and CPM values for each sample
 
Submission date Dec 12, 2024
Last update date Jan 17, 2025
Contact name Annegret Kohler
E-mail(s) annegret.kohler@inrae.fr
Phone +33 (0)383 394072
Organization name INRAE
Department UMR 1136
Lab Interactions Arbres/Micro-organismes
Street address Centre INRAE Grand Est Nancy
City Champenoux
ZIP/Postal code 54280
Country France
 
Platform ID GPL35189
Series (1)
GSE284110 Mycoremediation of copper-azole wood preservatives by Phanerochaete chrysosporium with a focus on resistance mechanisms and azole detoxification
Relations
BioSample SAMN45788856
SRA SRX27056665

Supplementary file Size Download File type/resource
GSM8678031_NAK18B.txt.gz 256.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA

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