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| Status |
Public on Jul 26, 2019 |
| Title |
wt_15_I |
| Sample type |
SRA |
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| Source name |
fungal cells
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| Organism |
Candida albicans |
| Characteristics |
genotype: wild-type
agent: Caspofungin 10 ng/ml
time point (minutes): 15
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Trizol and glass bead lysis after which RNA was precipitated and DNase treated followed by a column purification step. 5μg DNase-treated total RNA was subjected to mRNA purification using Dynabeads mRNA purification kit (Invitrogen). Remaining rRNA contamination was checked in the bioanalyzer using Agilent RNA 6000 Pico kit (Agilent). Purified mRNA was subjected to fragmentation using the NEBNext® Magnesium RNA Fragmentation Module (New England Biolabs) and purified with RNeasy Plus Mini kit (Qiagen). Then, first-strand cDNA was synthesized with 50 ng/μl random hexamer primers using SuperScript ® III First-Strand Synthesis System for RT-PCR (Invitrogen). dNTPs were eliminated by purifying with MiniQuickSpin DNA Columns and subjected to second strand cDNA synthesis followed by clean-up with Minielute Reaction cleanup kit (Qiagen). cDNA concentration was measured using Quant-iT Picogreen dsDNA Reagents (Invitrogen) in a NanoDrop Fluorospectrophotometer ND-3300 (Thermo Fisher).
Library preparation was done using the KAPA DNA Library Preparation Kit (Kapa Biosystems) according to the manufacturer’s instructions.
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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 |
The quality of raw reads were analyzed using FastQC (Andrews, 2010).
The adapters were trimmed by using Trimmomatic with default parameters (Bolger, Lohse, & Usadel, 2014).
The reads were then mapped to C. albicans genome using tophat2 (Kim et al., 2013).
In this analysis we used C_albicans_SC5314_A22 genome and transcriptome downloaded from Candida Genome Database (Skrzypek et al., 2017).
The reads were counted using summarizeOverlaps function from the GenomicAlignments R package (Lawrence et al., 2013).
Genome_build: Differential gene expression analysis were performed using DESeq2 R package (Love, Anders, & Huber, 2014).
Supplementary_files_format_and_content: tab delimited .txt files containing the output of the HTSeq analysis (read counts)
Supplementary_files_format_and_content: raw counts of sequencing reads
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| Submission date |
Dec 06, 2018 |
| Last update date |
Jul 26, 2019 |
| Contact name |
Neeraj Chauhan |
| Organization name |
NJMS-PHRI
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| Department |
Department of Microbiology, Biochemistry & Molecular Genetics
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| Lab |
Neeraj chauhan
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| Street address |
225 Warren Street
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| City |
NEWARK |
| State/province |
New Jersey |
| ZIP/Postal code |
07103 |
| Country |
USA |
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| Platform ID |
GPL19036 |
| Series (1) |
| GSE123412 |
Gcn5 Controls Virulence of the Human Fungal Pathogen Candida albicans through Multiple Regulatory Networks |
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| Relations |
| BioSample |
SAMN10526548 |
| SRA |
SRX5099804 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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