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Sample GSM4572066 Query DataSets for GSM4572066
Status Public on Nov 28, 2021
Title Ca_mac_2
Sample type SRA
 
Source name Whole cell
Organisms Candida albicans; Mus musculus
Characteristics sample type: C. albicans SC5314 + M. musculus
condition: macrophage
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.
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.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
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.
 
Submission date May 27, 2020
Last update date Nov 30, 2022
Contact name Michael Lorenz
Organization name UTHealth Houston
Street address 6431 Fannin
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL18449
Series (1)
GSE151288 Comparative transcriptomic analysis of the response of CUG-clade Candida species to phagocytosis
Relations
BioSample SAMN15033195
SRA SRX8406557

Supplementary file Size Download File type/resource
GSM4572066_Ca_mouse_2.quant.sf.txt.gz 1.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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