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| Status |
Public on Nov 28, 2021 |
| Title |
Ct_only_2 |
| Sample type |
SRA |
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| Source name |
Whole cell
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| Organism |
Candida tropicalis |
| Characteristics |
sample type: C. tropicalis MYA-3404
condition: only
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| Treatment protocol |
Candida cultures were incubated for 1 hr at 37 °C, 5% CO2 in the presence or absence of primary murine bone marrow derived macrophages after which time the vast majority of fungal cells had been taken up by phagocytosis.
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| Growth protocol |
Candida cultures were grown overnight in YPD medium at 30 °C then diluted back into YPD medium at 30 °C to allow return to exponential phase. Cultures were then washed twice in phosphate buffered saline followed by dilution into Iscove's Modified Dulbecco's Medium supplemented with 10% fetal bovine serum and penicillin/streptomycin.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Candida-only cultures were scraped to detach fungal cells and pelleted by centrifugation, followed by resuspension in ice cold water and centrifugation again. For Candida-macrophage co-cultures, medium was aspirated and ice cold water was added to lyse macrophages. Wells were then scraped and samples were pelleted by centrifugation, resuspended again in ice-cold water followed by further centrifugation. Fungal cell walls were digested with zymolyase at 37 °C, followed by RNA extraction using the SV Total RNA Isolation System (Promega).
Libraries were constructed using the TruSeq Stranded RNA library preparation protocol. Sequencing was carried out using the HiSeq2000 platform (Illumina) to obtain 15-58 million 2 x 100 paired-end reads. All library preparation and sequencing was performed by Axeq Technologies.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Base-calling was performed by Axeq Technologies.
Adapters were trimmed using Trimmomatic v0.39, with additional removal of bases below a read quality of 3 at the start and end of the read and total removal of reads less than 36 bp after trimming.
Reads were mapped to a concatenated mouse-Candida transcriptome using Salmon v1.1.0 with --gcBias and --seqBias flags. Transcriptome files were generated from concatenated genome files using GffRead v0.11.6.
Genome_build: Concatenated genome files were generated from fungal genomes concatenated to the GRCm38.p6 Mus musculus reference genome (Ensembl release 98). All fungal genomes were obtained from the Candida Genome Database (http://candidagenome.org/) using current versions as of January 16, 2020, 11:57 am.
Supplementary_files_format_and_content: Salmon output files (.quant.sf). These contain gene name, length, and effective length (modeled based on factors affecting the probablility of sampling fragments from this transcript), TPM (transcripts per million, a normalized measure of abundance) and estimated number of mapped reads. For more information, see https://salmon.readthedocs.io/en/latest/file_formats.html.
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| Submission date |
May 27, 2020 |
| Last update date |
Nov 30, 2022 |
| Contact name |
Michael Lorenz |
| Organization name |
UTHealth Houston
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| Street address |
6431 Fannin
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL21876 |
| Series (1) |
| GSE151288 |
Comparative transcriptomic analysis of the response of CUG-clade Candida species to phagocytosis |
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| Relations |
| BioSample |
SAMN15033199 |
| SRA |
SRX8406575 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4572084_Ct_only_2.quant.sf.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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