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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 28, 2024 |
| Title |
Cau_only_B |
| Sample type |
SRA |
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| Source name |
Whole cell
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| Organism |
Candidozyma auris |
| Characteristics |
tissue: Whole cell
strain: AR0382
treatment: only
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| Treatment protocol |
C. auris cultures were incubated for 1 hr at 37 °C, 5% CO2 in the presence or absence of primary murine bone marrow derived macrophages (5:1 C. auris:macrophage ratio).
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| Growth protocol |
C.auris 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 |
polyA RNA |
| Extraction protocol |
C. auris-only cultures were scraped in ice cold water followed by centrifugation. For C auris-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 NovaSeq platform (Illumina) to obtain 35-45 million 2 x 151 paired-end reads. All library preparation and sequencing was performed by Psomagen.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
B-negative
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| Data processing |
Base-calling was performed by Psomagen using Illumina Real Time Analysis RTA software followed by fastq file generation with the Illumina package bcl2fastq.
To deplete reads derived from mouse macrophages, reads were first mapped to the GRCm38.p6 Mus musculus reference genome (Ensembl release 98) using Hisat2 v2.1.0, removing all reads that did align.
Reads mapping to the C. auris transcriptome were quantified using Salmon v1.10 with --gcBias and –seqBias flags enabled.
Assembly: C. auris B8441 reference transcriptome (FungiDB release 39 at fungidb.org)
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 |
Jun 28, 2023 |
| Last update date |
Jun 28, 2024 |
| 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 |
GPL28368 |
| Series (1) |
| GSE236004 |
Candida auris-macrophage cellular interactions and transcriptional response |
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| Relations |
| BioSample |
SAMN36017172 |
| SRA |
SRX20803093 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7516696_Cau_only_B.quant.sf.gz |
84.5 Kb |
(ftp)(http) |
SF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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