|
| Status |
Public on Sep 25, 2024 |
| Title |
Aspergillus terreus strain 211, control after 1h triplicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
211
|
| Organism |
Aspergillus terreus |
| Characteristics |
strain: 211
genotype: WT211
treatment: control
|
| Treatment protocol |
Afterwards, the cultures were subjected to either DMSO (control) or 1 µg/ml AmB treatment for 1 h/4 h. Triplicates of each combination of these factors were made, resulting in a total of 24 samples.
|
| Growth protocol |
WT and ATSec strains were grown in AMM broth for 30 h at 30 °C. Triplicates of each combination of these factors were made, resulting in a total of 24 samples.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with a Promega GmbH kit (Madison, Wisconsin, USA) following the manufacturer’s instructions.
Library construction according to BGI, the company performing the RNA-sequencing: The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the DNBseq platform for the following data analysis study. For this step, the DNBseq platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
Raw reads were filtered with SOAPnuke to remove adaptors, unknown bases and low quality reads. Ribosomal RNA was removed as well, generating in the clean reads files
The clean reads were analyzed with Salmon. Salmon was run in quasi-mapping read mode, with the whole genome as a decoy and with the validateMappings option enabled
Assembly: ASM1680841v1
Supplementary files format and content: fastq files containing clean/raw RNA-seq reads
|
| |
|
| Submission date |
Sep 20, 2024 |
| Last update date |
Sep 25, 2024 |
| Contact name |
David Eisele |
| E-mail(s) |
David.Eisele@i-med.ac.at
|
| Organization name |
Medical University of Innsbruck
|
| Street address |
Schöpfstraße 41
|
| City |
Innsbruck |
| ZIP/Postal code |
6020 |
| Country |
Austria |
| |
|
| Platform ID |
GPL34927 |
| Series (1) |
| GSE277670 |
RNA-seq data of the Amphotericin (AmB)-resistant Aspergillus strain 211 and its AmB-susceptible sectorized derivative with and without AmB treatment |
|
| Relations |
| BioSample |
SAMN43845688 |
| SRA |
SRX26138223 |
