|
| Status |
Public on Sep 30, 2021 |
| Title |
MH_S_Lcor_2 |
| Sample type |
SRA |
| |
|
| Source name |
MH_S_Lcor
|
| Organisms |
Mus musculus; Lichtheimia corymbifera |
| Characteristics |
strain: JMRC:SF:09682
genotype/variation: WT
time point: 0hr
|
| Treatment protocol |
Macrophages were infected with spores at a MOI (Multiplicity of Infection) of 5. After 3 hr of co-incubation with MH-S, extracellular spores were removed by at least 3 washing steps with pre-warmed RPMI-1640 (PAA Laboratories) and incubated for 13 hr in prior to the RNA extraction procedure. Controls in these experiments were fungus grown for 16 hours without macrophages and macrophages without fungal spores.
|
| Growth protocol |
Spores from Lichtheimia corymbifera JMRC:SF:09682 harvested from cultures grown in KK1 medium (Kraibooj et al. 2014) at 37 °C for 7 days. Murine alveolar MH-S macrophages (ATCC: CRL-2019) were cultivated in RPMI-1640 supplemented with 10% heat inactivated fetal bovine serum at 37 °C in 5 % CO2. Macrophages were seeded in 6 well plates at 10^6 cells per well to adhere overnight.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fungal RNA was isolated using RiboPure Yeast Kit (Thermo Fisher) and macrophage RNA was isolated with the RNeasy Mini kit (Qiagen), according to the manufacturers’ instructions. The concentration and purity of RNA samples were assessed using a NanoDrop spectrophotometer and Agilent 2100 bioanalyzer. Pooling ratio: L. corymbifera : MH-S = 1 : 3.9
Random-primed cDNA library per samples, Isolation of poly(A)+ RNA mRNA-Fragmentation, Random-primed cDNA synthesis adapter-ligation and PCR amplification
Illumina HiSeq 2500, Sequence Mode: HSHOv4 SR50
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
NG-7587_MH_S_Lcor_2_lib62843_3472_4_1
|
| Data processing |
Read quality was checked using Fastqc. Trimming and Adapter clippling was applied using Trimmomatic-0.32 (parameters: windowsize=15, qualcut=25, phred="-phred33",leading=3,trailing=3,minlen=30,adapters=”adapters/TruSeq3-SE.fa”)
Trimmed reads were mapped to reference genome of Lichtheimia_corymbifera_v1.genome.fasta and of Mus_musculus.GRCm38.dna.primary_assembly using tophat2 with following parameters: -p 10 -g 1 --no-mixed --no-discordant --b2-very-sensitive --max-intron-length 100000 –no-coverage-search -o OUTDIR -G ANNOTATION INDEX FASTQFILE > OUTFILE
Mapped reads were counted using featureCounts version and DeSeq2 were used for differential expression filtering.
Genome_build: Lichtheimia corymbifera JMRC:FSU:09682 (NCBI WGS accession CBTN000000000); Mus_musculus.GRCm38.79 primaryAssembly
Supplementary_files_format_and_content: text files include counts for each gene per sample
|
| |
|
| Submission date |
May 18, 2018 |
| Last update date |
Sep 30, 2021 |
| Contact name |
Patricia Sieber |
| E-mail(s) |
patricia.sieber@uni-jena.de
|
| Organization name |
HKI
|
| Street address |
Adolf-Reichwein-Straße 23
|
| City |
Jena |
| ZIP/Postal code |
07745 |
| Country |
Germany |
| |
|
| Platform ID |
GPL25016 |
| Series (1) |
| GSE114628 |
Dual RNAseq of murine alveolar macrophage cell line MH-S confronted with resting spores of Lichtheimia corymbifera JMRC:SF:09682 |
|
| Relations |
| BioSample |
SAMN09223258 |
| SRA |
SRX4099084 |
