Comment[GEAAccession]	E-GEAD-459
MAGE-TAB Version	1.1
Investigation Title	Transcriptome dataset of C. utilis strains, WT and mutants with altered flocculation ability by TAQing2.0
Experiment Description	We investigated genome-wide gene expression profiling using RNA-seq toward Candida utilis NBRC0988 (WT) and TAQed mutants (AG4 and AG9) with altered flocculation ability by TAQing2.0. Sequencing reads were mapped to WT reference genome (accession numbers AP024664-AP024669 and DRA012057), and gene-expression levels were calculated statistically by using featureCounts (subread-2.0.1 counts).
Experimental Design	cell type comparison design	genetic modification design	genotyping design	reference design
Experimental Factor Name	treatment
Experimental Factor Type	treatment
Person Last Name	Yasukawa
Person First Name	Taishi
Person Affiliation	Mitsubishi Corporation Life Sciences Limited
Person Roles	submitter
Public Release Date	2022-02-18
Protocol Name	P-GEAD-979	P-GEAD-980	P-GEAD-981	P-GEAD-982	P-GEAD-983
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	Yeast cells were cultivated aerobically in YPD medium at 30oC. After centrifuged and harvested at logarithm phase, cells were frozen quickly by liquid nitrogen without washing procedure. Those cell-samples were conserved in -80oC until just before use.	Frozen samples were lysed in acid phenol/chloroform preheated to 65oC, and total RNA was extracted by RNeasy Mini Kit (QIAGEN) according to the standard protocol. Quality control was done in NanoDrop UV-Vis Spectrophotometer.	Libraries were generated by NEBNext Ultra II Directional RNA Library Prep Kit and NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biorabs). The libraries were eluted from AMPure beads with 0.1xTE buffer, and confirmed of the quality control: Each nucleic acid content and average size was determined in the Qubit fluorometer and MultiNA system.	Illumina platform was performed to sequence a paired-end 151-bp read. The constructed library was loaded into a flow cell, and each fragment was amplified using oligos complemental to the library adaptor sequences. After sequencing data was converted to raw data, the total number of bases, reads, GC (%), Q20 (%), and Q30 (%) were calculated.	Adaptor sequences, low-quality bases, and reads below 36-bases were removed by using Trimmomatic program (ver. 0.39). Trimmed reads were mapped into WT reference genome (accession numbers; AP024664-AP024669 and DRA012057) by using STAR-2.7.9a. Gene expression analysis was performed by featureCounts program (ver. 2.0.1).
SDRF File	E-GEAD-459.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB11630
Comment[Last Update Date]	2022-02-18