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| Status |
Public on Nov 14, 2023 |
| Title |
filamentous fungus reference strain, glucose, rep1 |
| Sample type |
SRA |
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| Source name |
mycelia
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| Organism |
Trichoderma reesei RUT C-30 |
| Characteristics |
strain: RutC30
cell type: mycelia
genotype: reference
treatment: glucose fed-batch
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| Extracted molecule |
total RNA |
| Extraction protocol |
8 mL samples were filtered and immediately frozen in liquid nitrogen. Frozen mycelia were ground by a Fastprep homogenizer for 2 x 40 sec at 6 m/s using Lysis matrix C (MP Bio) with 700 µL of RTL Buffer (Qiagen RNeasy Mini Kit) and 7 µL of β-mercaptoethanol. After removing cell debris by a QIAshredder column, RNA was extracted using the RNeasy Mini Kit and following the instructions of the manufacturer (Qiagen). The RNA concentration was measured with Qubit 2.0, and the quality of the extracted RNAs was evaluated on a Bioanalyzer (Agilent) and agarose gel electrophoresis.
Library preparation and Illumina sequencing were performed at the Ecole normale superieure genomics core facility (Paris, France). Messenger (polyA+) RNAs were purified from 1000 ng of total RNA using oligo(dT). Libraries were performed using the strand specific RNA-Seq library preparation Stranded mRNA Prep, Ligation kit (Illumina) and were multiplexed on two P2 flowcell. (Illumina). A 118 bp single-end read sequencing was performed on a NextSeq 2000 device (Illumina). A mean of 42 million ± 4 million passing Illumina quality filter reads was obtained for each of the 16 samples
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Description |
Rut GC1
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| Data processing |
The analyses were performed using the Eoulsan (version 2.5) pipeline, including read filtering, mapping, alignment filtering, read quantification, normalisation and differential analysis: Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the Trichoderma reesei QM6a genome (JGI version) using STAR (version 2.7.8a). Alignments from reads matching more than once on the reference genome were removed using htsjdk 1.118. To compute gene expression, a custom Trichoderma reesei QM6a annotation file was used. All overlapping regions between alignments and referenced CDS were counted using HTSeq-count 0.5.3. The sample counts were normalized using DESeq2 1.8.1. Statistical treatments and differential analyses were also performed using DESeq2 1.8.1.
Assembly: JGI Trichoderma reesei QM6a genome, 2019 version
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Supplementary files format and content: gff file for custom the custom annotation of Trichoderma reesei QM6a (included in submission as Treesei_QM6a.gff.bz2)
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| Submission date |
May 30, 2023 |
| Last update date |
Nov 14, 2023 |
| Contact name |
Stephane Le Crom |
| Organization name |
IBENS
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| Department |
Genomic Core Facility
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| Street address |
46 rue Ulm
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| City |
PARIS |
| ZIP/Postal code |
75230 |
| Country |
France |
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| Platform ID |
GPL33444 |
| Series (1) |
| GSE233738 |
Effect of the res-2 transcription factor gene deletion on protein secretion and stress response in the hyperproducer strain Trichoderma reesei Rut-C30 |
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| Relations |
| BioSample |
SAMN35533819 |
| SRA |
SRX20543097 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7433602_expression_output_expression_2021437.tsv.gz |
44.3 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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