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Sample GSM2688554

Query DataSets for GSM2688554

Status

Public on Oct 08, 2018

Title

tmk1glycerol3

Sample type

SRA

Source name

mycelia

Organism

Trichoderma reesei

Characteristics

strain/genotype: mutant tmk1
treatment: glycerol

Treatment protocol

For gene expression assays, a spore suspension containing approximately 107 cells mL-1 was inoculated into 200 mL of Mandels-Andreotti medium (Schmollet al. 2009) containing 2% of glucose as the carbon source, and 1% of sugarcane bagasse or 1% of glycerol. Cultures on glucose were incubated at 30º C for 48h. For sugarcane bagasse cultures, strains were first growth on MEX medium 1% glycerol for 24 h, then transferred to sugarcane bagasse media for 48h.

Growth protocol

The parental and mutant strains were grown in MEX medium at 30°C for 7-10 days for complete sporulation.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted using the TRIzol kit (Invitrogen) according to manufacture's instructions.
RNA-seq libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA Library Prep Kit.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

Base calls and demultiplexing was performed with Illumina bcl2fastq version 1.8.4
The Illumina HiSeq 2500 system was used to sequence the transcriptome of Trichoderma reesei, yielding approximately 10 - 15 million 100-bp paired-end reads per sample. These sequences were firstly quality checked and filtered using FASTQC and Trimommatic v.0.32 (Bolger, et al, 2014).
Trimmed reads were mapped to the Trichoderma reesei 2.0 reference genome available the JGI Genome Portal (http://genome.jgi-psf.org/Trire2/Trire2.home.html) using Tohat2 v2.0.4 (Kim et al, 2013), allowing two mismatches and only unique alignments.
Samtools version 0.1.18 (Li et al., 2009) was used to process the alignments files which were visualized using the Integrative Genomics Viewer (Thorvaldsdottir et al., 2012).
Aligned reads were quantified using htseq-count v0.6.0 (Anders et al 2105) with Trichoderma reesei gene modes, that includes 9129 genes models.
Bioconductor DESeq2 package version v 1.6.3 (Love et al, 2014) was employed to perform the differential expression analysis, using two-fold change, i.e., log2 fold change ≥ 1 or ≤ -1 and adjusted p-value ≤ 0.05 as thresholds.
Genome_build: http://genome.jgi-psf.org/Trire2/Trire2.home.html
Supplementary_files_format_and_content: Processed data files are presented as tab delimited txt format. Raw count and TPM data are provided, being expressed as “Protein ID” “Sample ID”
Supplementary_files_format_and_content: Gene expression results are expressed as Log 2 Fold Change between indicated samples and the respective adjusted p-value calculated by DESeq2.

Submission date

Jun 28, 2017

Last update date

May 15, 2019

Contact name

Gabriela F Persinoti

E-mail(s)

[email protected]

Phone

551935175165

Organization name

Brazilian Center for Research in Energy and Materials CNPEM