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| Status |
Public on May 16, 2022 |
| Title |
CBS_25_1 [AC-1_S1] |
| Sample type |
SRA |
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| Source name |
CBS_25_mycelium
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| Organism |
Lasiodiplodia hormozganensis |
| Characteristics |
strain: CBS 339.90
temperature: 25 ºC
age: 4 days
tissue: Mycelium
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
The mycelium of each replicate (three replicates per condition) was ground in liquid nitrogen and total RNA was extracted using the Spectrum Plant Total RNA kit (Sigma), according to the manufacturer’s instructions. Samples were incubated for 15 min with the DNase I digestion set (RNase-Free DNase Set, Qiagen). Integrity and quality analysis were carried on a 2100 Bioanalyzer RNA (Agilent Technologies).
Illumina mRNA sequencing libraries were made from 500 ng total RNA of each sample using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, Vienna, Austria) according to manufacturer's protocol. Fourteen PCR cycles were used during the enrichment PCR. The size distribution, purity (absence of free adaptors) and quantity of the resulting libraries were measured using a High Sensitivity DNA chip (Agilent Technologies, Santa Clara, CA, US). The libraries were equimolarly pooled and sequenced in an Illumina Nextseq 500 high throughput flow cell, generating single-end 75bp reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
AC-1_S1
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| Data processing |
Adequate sequencing quality was confirmed using FastQC version 0.11.5 (Andrews, 2010).
First, these reads were trimmed using cutadapt version 1.11 to remove the “QuantSEQ FWD” adaptor sequence.
The trimmed reads were mapped to the genome of CBS339.90 using the STAR aligning software version 2.5.3a
The RSEM software, version v1.2.31, was used to generate count tables. Only genes with a ccounts per million (cpm) above 1 in at least 3 samples were retained.
Genome_build: L. Hormozganensis (SUB5546006,PRJNA470903)
Supplementary_files_format_and_content: tab-delimited text files include gene_id, transcirpt_id(s), gene length, effective_length, expected_counts, TPM an FPKM for each sample
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| Submission date |
May 16, 2019 |
| Last update date |
May 17, 2022 |
| Contact name |
Laurentijn Tilleman |
| Organization name |
Ghent University
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| Street address |
Ottergemsesteenweg 460
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| City |
Gent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
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| Platform ID |
GPL26676 |
| Series (1) |
| GSE131342 |
Multi-omics analyses reveal the molecular pathogenesis toolkit of Lasiodiplodia hormozganensis, a cross-kingdom pathogen |
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| Relations |
| BioSample |
SAMN11660444 |
| SRA |
SRX5847837 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3770685_1.genes.results.txt.gz |
189.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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