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RNA-seq data of the Amphotericin (AmB)-resistant Aspergillus strain 211 and its AmB-susceptible sectorized derivative with and without AmB treatment

ABSTRACT: Summary taken from our paper “Aspergillus terreus Sectorization: A Morphological Phenomenon Shedding Light on Amphotericin B Resistance Mechanism”: WT and ATSec strains were grown in AMM broth for 30 h at 30 °C. 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. RNA was extracted with a Promega GmbH kit (Madison, Wisconsin, USA) following the manufacturer’s instructions. The RNA-seq experiment was conducted by BGI, generating a total of around 20 million 100bp paired-end reads with the DNBSEQ platform. BGI employed SOAPnuke (51) to remove rRNA, adaptor-containing sequences, low quality reads, and reads with high unknown nucleotide content, producing "clean reads" datasets that were used in the analysis. On average, clean read datasets contain 45.1 Mb of reads, while the raw read datasets contain 48.7 Mb. For clean reads, the mean Q20 value is 98.3%, and the mean Q30 value is 92.5%.

ORGANISM(S): Aspergillus terreus

PROVIDER: GSE277670 | GEO | 2024/09/25

REPOSITORIES: GEO

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Project description:Small RNA sequencing has been performed using eight commonly used breast cancer cell lines by Illumina as part of the Illumina iDEA Challange 2011. Total RNA of the cell lines was isolated and the sequencing library was prepared using Illuminas Small RNA v1.5 library prep protocol. This data was analyzed with Flicker, an add-on to the Illumina Genome Analyzer Pipeline software that allows for the preliminary analysis of small RNA runs on the GA. Flicker was used in this case for: * Trimming: Attempts to trim the adaptor sequence from small RNA reads Trimming is accomplished by aligning the adaptor with each read, both internally (the adaptor is fully contained within the read) and as a suffix (the adaptor overlaps the 3' end of the read). A similarity matrix is used to generate the matching score, taking into account both substitutions and indels. The alignment with the best matching score is returned, and that best alignment is trimmed from the read. A trimming threshold may be specified, and the adaptor is not trimmed unless the best score exceeds the threshold. * Aligning with Iterated ELAND: Attempts to aligns trimmed reads to targets (squashed genomes or databases such as miRBase) using the ELAND short read aligner. Each read is aligned by ELAND with specified alignment targets. ELAND was designed to align reads of a uniform length, and the trimmed reads from a small RNA run are several different lengths. We currently address this by running ELAND for reads of each length: reads are binned by length, and each bin of a given length is aligned against a specified target. Once all bins are aligned against all targets (in this case, gDNA and miRBase), the results are recombined into a single file with all the annotation information. ===== Key to Experiments HCT ID, Lane, Sample ID, Cell Line, ER +/- Status, Reads HCT20061, Lane 1, HS378, MCF7, +, 14,555,390 HCT20062, Lane 2, HS379, MDA-MB-231, -, 15,147,037 HCT20063, Lane 3, HS381, T47D, +, 14,701,254 HCT20064, Lane 4, HS377, BT-20, -, 16,529,823 HCT20065, Lane 5, HS375, BT-474, +, 16,443,361 HCT20066, Lane 6, HS380, MDA-MB-468, -, 16,746,981 HCT20067, Lane 7, HS382, ZR-75-1, +, 17,631,005 HCT20068, Lane 8, HS376, MCF10A, normal, 19,155,607

Dataset Information

RNA-seq data of the Amphotericin (AmB)-resistant Aspergillus strain 211 and its AmB-susceptible sectorized derivative with and without AmB treatment

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