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Sample GSM8119574

Query DataSets for GSM8119574

Status

Public on Jul 19, 2024

Title

QM9414 SESp-cbh1 wtXYR1, batch lactose day 2, rep1

Sample type

SRA

Source name

mycelia

Organism

Trichoderma reesei

Characteristics

strain: QM9414
tissue: mycelia
genotype: wild-type XYR1 under pdc1 promoter, SESp-cbh1
condition: fed-batch: batch lactose
time: day 2

Growth protocol

Trichoderma reesei trains were grown in 250 mL Ambr bioreactors (Sartorius), first with batch lactose as the carbon source, then with glucose feed.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted from mycelia using TRIzol (Thermo Fisher Scientific) according to manufacturer’s instructions with small modifications. Mycelium samples were ground using cooled mortars under liquid nitrogen into fine powder and about 50 µL of powder was transferred into a 2 mL tube, after which 1 mL of TRIzol was immediately added. Mixture was vortexed and incubated at room temperature for 5 minutes, after which it was centrifuged (12000 x g, 4 °C, 10 minutes) and the supernatant was transferred to a new tube. After this, the protocol was continued according to manufacturer’s instructions. RNA was then purified using RNeasy Mini kit (Qiagen) according to manufacturer’s instructions, except that 950 µl of 94 vol-% ethanol was added instead of 250 µl during the second step.
Extracted and purified RNA samples were sent for RNA-sequencing in Source BioScience (Cambridge, UK). rRNA depletion libraries were prepared using Next Ultra II Directional RNA Library Prep kit (New England Biolabs). Sequencing of the rRNA libraries was done using Illumina NovaSeq 6000.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

wtXYR1 lac d2 rep1

Data processing

Reads were quality filtered and trimmed using FastP v0.20.0 and the quality of the raw sequence data was evaluated using FastQC v0.11.8. Reads were then aligned to T. reesei genome version 2.0 with GFF annotations using HISAT2 v2.1.0. Sam-files were sorted and compressed with SAMtools v1.9 and the alignments were assembled and quantified using StringTie v2.0.4. Downstream analyses were carried out in R v4.2.2. Differential gene expression analysis was carried out with R package DESeq2 v1.34.0.
Assembly: JGI Trichoderma reesei QM6a v2.0
Supplementary files format and content: tab-delimited text file includes DESeq2-normalized counts for each sample
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

Submission date

Feb 29, 2024

Last update date

Jul 19, 2024

Contact name

Emmi Sveholm

E-mail(s)

[email protected]

Organization name

VTT Technical Research Centre of Finland

Street address

Tekniikantie 21