Paren_2
mixed sample
Protocols: Cells were grown in YPD broth at 30˚C from OD600=0.01 till OD600=1.0. Pellets of 5ml cell culture were obtained by centrifuging at maximum speed for 1min. the pellets were fast frozen in liquid nitrogen.  Total RNA was isolated using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's recommendations. RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was measured using a NanoPhotometer® spectrophotometer (IMPLEN, Westlake Village, CA, USA). The RNA concentration was measured using the Qubit® RNA Assay Kit was used in a Qubit® 2.0 Fluorometer (Life Technologies, CA, USA). RNA integrity was assessed with the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Sequencing libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA), following the manufacturer's protocol. Index codes were added to attribute sequences to each sample. mRNA was purified from the total RNA with poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under an elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). A random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-) were used to synthesize the first strand cDNA. Then, second strand cDNA synthesis was performed using DNA Polymerase I and RNase H. Exonuclease/polymerase activities were used to convert the remaining overhangs into blunt ends. After adenylation of the 3' ends of the DNA fragments, the NEBNext Adaptor with hairpin loop structures was ligated to prepare for hybridization. To select cDNA fragments of 150–200 bp in length, the AMPure XP system (Beckman Coulter, Beverly, USA) was used. 3 μl of the USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min, followed by a 5 min incubation at 95°C before PCR. PCR was then performed with the Phusion High-Fidelity DNA polymerase, Universal PCR primers and the Index (X) Primer. Finally, the PCR products were purified (AMPure XP System), and the library quality was assessed using the Agilent Bioanalyzer 2100 system. Clustering of the index-coded samples was performed using the cBot Cluster Generation System and the TruSeq PE Cluster Kit v3-cBot-HS (Illumina), according to the manufacturer's instructions.
ENA first public
2026-04-25
INSDC center name
Shanghai Tenth People's Hospital
INSDC status
public
Submitter Id
E-MTAB-16883:Paren_2
broker name
ArrayExpress
collection date
not collected
genotype
wild type genotype
geographic location (country and/or sea)
not collected
isolate
not applicable
organism part
whole organism
sample name
E-MTAB-16883:Paren_2
scientific_name
Candidozyma auris
component_organism
Candidozyma auris
component_organism
Candidozyma auris