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Sample GSM4910703

Query DataSets for GSM4910703

Status

Public on Dec 03, 2020

Title

DMSO-1

Sample type

SRA

Source name

candida auris

Organism

[Candida] auris

Characteristics

genotype: wild type
agent: DMSO

Treatment protocol

C. auris cells of strain BJCA001 were inoculated into RPMI1640 medium and treated with DMSO and myriocin at 35 oC for 2h.

Growth protocol

C. auris cells of strain BJCA001 were inoculated into YPD and cultured at 35 oC for 24h.

Extracted molecule

total RNA

Extraction protocol

Cells were lysed by Mini-beadbeater and total RNA was harvested using GeneJET RNA Purification Kit (Thermo Scientific #K0731, #K0732)
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

Illumina OLB_1.9.4 were used for basecalling
Filter dirty raw reads by removing reads with adaptors and low quality, the obtained clean reads were mapped to reference sequences using SOAPaligner/soap2 according to Li et al., Bioinformatics, 2009. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level is calculated by using FPKM according to Mortazavi, et a., Nature Methods, 2008, and the formula is shown as follows: FPKM=106C/(NL/103). C is the number of reads that uniquely aligned to a gene, N is total number of reads that uniquely aligned to all genes, and L is the number of bases on a gene .
Genome_build: Candida auris CDC_B8441 genome (GCA_002759435.2)
Supplementary_files_format_and_content: text files containing FPKM values for each Sample

Submission date

Nov 17, 2020

Last update date

Dec 03, 2020

Contact name

Jian Bing

E-mail(s)

bingj@fudan.edu.cn

Organization name

Fudan University

Department

School of Life Sciences