|
| Status |
Public on Apr 14, 2021 |
| Title |
CAI-4 NA 3 |
| Sample type |
SRA |
| |
|
| Source name |
C. albicans biofilm_atmospheric CO2
|
| Organism |
Candida albicans |
| Characteristics |
strain: CAI-4
environment: Atmospheric CO2
mode of growth: Biofilm on silicone surface at 37oC
biofilm stage: Mature (48hr growth)
|
| Growth protocol |
CAI-4 cells were seeded onto a silicone surface and grown as a biofilm for 48hr in either 0.03% or 5% CO2 at 37oC in RPMI-1640 media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Biofilms were washed twice with ice-cold PBS, RNA was extracted using the E.Z.N.A Yeast RNA Kit (Omega Bio-Tek, R6870-01).
mRNA-Seq libraries were prepared from 500ng total RNA using TruSeq Stranded mRNA Sample Preparation Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
03NA3-P164A_S3
|
| Data processing |
Illumina NextSeq 500 Real-Time Analysis software v2.4.11 used for basecalling.
Low quality ends (Phred score < 20) and any adaptor sequences were trimmed using TrimGalore! v0.4.3. Reads which became shorter than 40bp after trimming were removed from further analysis.
Processed reads were aligned with the reference C. albicans genome SC5314 version A21-s02-m09-r10 using HISAT2 v2.1.0 with single-end reads and reverse strand settings.
Number of mapped reads which overlapped CDS features in the genome (using the C. albicans_SC5314_version_A21-s02-m09-r10_features.gtf annotation file from Candida Genome Database) were determined using htseq-count v0.9.1 with default settings.
Differential gene expression analysis between conditions (0.03% and 5% CO2) was performed using DESeq2 v1.18.1 with default settings.
Genome_build: C. albicans genome SC5314 version A21-s02-m09-r10
Supplementary_files_format_and_content: tab-delimited text files include CDS feature counts for each sample.
Supplementary_files_format_and_content: xslx file with mean normalised counts and differentially expressed genes across all samples.
|
| |
|
| Submission date |
Apr 13, 2021 |
| Last update date |
Apr 14, 2021 |
| Contact name |
Campbell Gourlay |
| E-mail(s) |
C.W.Gourlay@kent.ac.uk
|
| Phone |
+441227823535
|
| Organization name |
University of Kent
|
| Department |
School of Biosciences
|
| Lab |
S104 - Kent Fungal Group
|
| Street address |
School of Biosciences, University of Kent
|
| City |
Canterbury |
| State/province |
Kent |
| ZIP/Postal code |
CT2 7NJ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL22403 |
| Series (1) |
| GSE172004 |
Quantitative transcriptome analysis of C. albicans biofilms grown in high and low carbon dioxide conditions. |
|
| Relations |
| BioSample |
SAMN18735919 |
| SRA |
SRX10594510 |
