|
| Status |
Public on Dec 27, 2023 |
| Title |
45_minutes_Serum_2 |
| Sample type |
SRA |
| |
|
| Source name |
whole organism total RNA
|
| Organism |
Candida albicans |
| Characteristics |
strain: NCCPF 400034
protocol: serum
time point: 120 minutes
|
| Treatment protocol |
The overnight grown Candida albicans NCCPF 400034 was then placed in complete human serum (O+ve) with 5 % CO2 and incubated at 37 °C. The cells were then harvested at different time points to extract the total mRNA. The YPD grown Candida was treated as control and the extracted RNA was sequenced using the next generation sequencing techniques.
|
| Growth protocol |
Candida albicans NCCPF 400034 was grown at 37 °C overnight in YPD medium. The cells were then washed with PBS and counted using the hemocytometer.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Ribopure Yeast Kit (Ambion). The total RNA extraction was performed as per the mannual described in the Kit protocol. Briefly, Candida albicans grown in serum for different time points were washed with the PBS and then the total RNA was extracted using the Ribopure yeast kit. RNA purity was confirmed by the nandrop and RNA integrity were confirmed by analysis on an Agilent 2100 bioanalyzer, using the RNA 6000 nano kit (Agilent) to conform RINs above 8.0. The YPD grown samples was also extracted with the above kit and the RNA purity was checked by Nanodrop.
RNA library was prepared as recommended by the IlluminaTruseq RNA sample preparation kit V2 for serum grown samples and sequencing was performed using Genome Analyzer IIX for 36 cycles. For the YPD grown sample RNA library was prepared using Ribo-zero gold kit and sequencing was performed on Illumina Hiseq for 150 cycles.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequence reads were trimmed off adaptor sequences and YPD grown sample sequence reads wer trimmed to make it 36 base pairs to maintain uniformity across the samples. Sequence reads were independently aligned using QIAGEN CLC Genomics Workbench 21.0.3 with default setting against Candida albicans genome (Assembly 22).
Differential expression, p-value and fold changes for each gene were determined using QIAGEN CLC Genomics Workbench 21.0.3 with default parameters.
Genome_build: Candida albicans SC5314 genome assembly 22
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each mRNA of respective samples.
|
| |
|
| Submission date |
Mar 10, 2021 |
| Last update date |
Dec 27, 2023 |
| Contact name |
Agam Prasad Singh |
| E-mail(s) |
singhap@nii.ac.in
|
| Organization name |
NII
|
| Department |
IDL
|
| Lab |
IDL
|
| Street address |
Aruna Asaf Ali Marg
|
| City |
New Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110067 |
| Country |
India |
| |
|
| Platform ID |
GPL15149 |
| Series (1) |
| GSE168619 |
Whole genome mRNA expression profiling during Candida albicans growth in complete human serum |
|
| Relations |
| BioSample |
SAMN18240491 |
| SRA |
SRX10303550 |
