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| Status |
Public on Feb 24, 2020 |
| Title |
YC1_control |
| Sample type |
SRA |
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| Source name |
C. albicans cells
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| Organism |
Candida albicans |
| Characteristics |
strain: YC1 (SC5314)
genotype: wild type
agent: none
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| Treatment protocol |
To the expeiment group, PMT12-BF4 was added into YPD broth at a final concentration of 1 μg/mL during the 3 h incubation, while the comtrol group was untreated.
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| Growth protocol |
C. albicans cells were grown overnight at 30°C, washed twice with sterile ddH2O, diluted to 0.25 OD600/mL in 5 mL YPD broth, and then incubated at 30°C for 3 h with shaking at 200 rpm.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were centrifuged at 4°C for 10 min at 3,250 rpm, and washed with ice-cold ddH2O to discard medium. Total RNA was extracted using TRIzol reagent (Invitrogen, USA). Collected cells were freeze in liquid N2, and vortexed with beads. After adding 1 mL TRIzol, cultures were centrifuged at 4°C /12,000g for 10 min, and the supernatant was transferred to a new tube. After 5 min incubation at room temperature, 200 μL of chloroform was added and mixed thoroughly, and tubes were incubated at room temperature for 3 min, centrifuged at 4°C/12,000g for 15 min, and supernatant was transferred to a new tube. Tubes were added 500 μL of isopropanol, incubated at room temperature for 10 min, centrifuged at 4°C/12,000g for 10 min, and the supernatant was discarded. Pellet containing RNA was washed twice with 75% ethanol and resuspend with RNase free water.
The mRNA was enriched with oligo(dT) magnetic beads and shortened into approximately 200-base fragments in fragmentation buffer. The first strand of cDNA was synthesized by the use of a random hexamer, buffer, dNTPs, and RNase H, and the second by the use of DNA polymerase I. The double strand cDNAs were purified with magnetic beads. After end preparation and 3’ end single nucleotide adenine addition were performed, sequencing adaptors were ligated to the fragments, and amplified by PCR. An Aglient 2100 bioanalyzer and ABI StepOnePlus real-time PCR system were used to qualify and quantify the sample library, and the library products were sequenced via an illumina HiSeq 2000 instrument.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
RNA-seq reads were processed using "Trinity v2.3.2".
Read quality was evaluated using "MultiQC v1.2".
The alignment and the read count quantification were performed with "bowtie2 v2.3.2" and "RSEM v1.2.31" respectively, and the alignment QC report was evaluated using "Qualimap v2".
The gene expression level is calculated by using FPKM method.
Genome_build: C. albicans SC5314, ASM18296v3
Supplementary_files_format_and_content: A tab-delimited text file includes FPKM, BLASTP, BLASTX, and annotation
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| Submission date |
Apr 02, 2019 |
| Last update date |
Feb 24, 2020 |
| Contact name |
Li-Hang Hsu |
| E-mail(s) |
a50104123@gmail.com
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| Organization name |
National Taiwan University
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| Department |
Plant Pathology and Microbiology
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| Lab |
Applied Microbiology Lab.
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| Street address |
No. 1, Sec. 4, Roosevelt Rd
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| City |
Taipei city |
| State/province |
Taiwan (R.O.C) |
| ZIP/Postal code |
10671 |
| Country |
Taiwan |
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| Platform ID |
GPL19036 |
| Series (1) |
| GSE129191 |
Transcriptional network controlled by Candida albicans treated by a gemini quaternary ammonium compound, 1, 5-bis(dodecyl)-1, 1, 3, 5, 5-pentamethyl-3-aza-1, 5-pentanediammonium ditetrafluoroborate (PMT12-BF4) |
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| Relations |
| BioSample |
SAMN11316738 |
| SRA |
SRX5624228 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3702157_YC1_control.txt.gz |
102.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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