|
| Status |
Public on Nov 28, 2021 |
| Title |
UV_3 |
| Sample type |
SRA |
| |
|
| Source name |
Murine bone marrow-derived macrophage
|
| Organism |
Mus musculus |
| Characteristics |
treatment: UV-killed C. albicans
mouse of origin: 3
strain: C57BL/6
|
| Treatment protocol |
Non-IFN-gamma treated macrophages were stimulated with medium only, live Candida (C. albicans, C. lusitaniae, C. parapsilosis, C. tropicalis) or UV-killed C. albicans (all in a 3:1 Candida:macrophage ratio). IFN-gamma pretreated macrophages were stimulated with 100 ng/ml LPS.
|
| Growth protocol |
Murine bone marrow-derived macrophages were obtained from female C57BL/6 mice by differentiation in vitro using 10 ng/ml M-CSF for seven days. Non-adherent cells were removed by washing, followed by scraping after incubation in PBS at 4 °C. Macrophages were incubated overnight with or without 100 U/ml IFN-gamma.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNeasy Micro kit and RNA integrity was confirmed using the Agilent Bioanalyzer.
Libraries were prepared using the TruSeq Stranded RNA library preparation kit (Illumina). Sequencing was performed using the NovaSeq 6000 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Base-calling was performed by Macrogen, Inc. using Illumina Real Time Analysis RTA software followed by fastq file generation with the Illumina package bcl2fastq.
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 aligned to a concatenated mouse-Candida reference genome using STAR v2.7.3a with the flag --quantMode TranscriptomeSAM
Transcript quantification was performed using RSEM v1.3.1
Genome_build: A concatenated reference genome was made, with Mus musculus (GRCm38, Ensembl release 98), C. albicans, C. lusitaniae, C. parapsilosis and C. tropicalis genomes (fungal genomes from http://candidagenome.org/)
Supplementary_files_format_and_content: RSEM output file (.genes.results) containing gene level expression estimates as described in http://deweylab.biostat.wisc.edu/rsem/rsem-calculate-expression.html#output.
|
| |
|
| Submission date |
Jun 17, 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 |
GPL24247 |
| Series (1) |
| GSE152700 |
Transcriptional responses of primary murine macrophages to four Candida species |
|
| Relations |
| BioSample |
SAMN15300204 |
| SRA |
SRX8567913 |
