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| Status |
Public on Jan 08, 2024 |
| Title |
3_Lcr35 + STS |
| Sample type |
SRA |
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| Source name |
Lcr35
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| Organism |
Lacticaseibacillus rhamnosus |
| Characteristics |
strain: Lcr35
environmental condition: with sodium thiosulfate (STS)
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| Growth protocol |
The C. albicans ATCC MYA-2876 strain was grown in Sabouraud dextrose broth medium, and L. rhamnosus Lcr35 in MRS medium containing or not 1 g/L STS for 48 hours. A coculture was prepared by mixing equal volumes of Lcr35 -/+ STS subculture and C. albicans ATCC MYA-2876 subculture. The controls included Lcr35 culture in MRS with and without STS and C. albicans ATCC MYA-2876 culture. The co-cultures were incubated for 6 hours at 37 ⁰C after which they were centrifuged.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by the TRIzol method. Harvested cells were immediately submerged in TRIzol reagent (Ambion) on ice (1 mL of TRIzol per 50 cm2 of culture dish surface area). The cells were disrupted using a Fastprep apparatus twice for 45 sec at speed 6. The samples were subsequently centrifuged for 10 min at 14,000 rpm and purified in TRIzol/chloroform (5:1) and chloroform. For RNA precipitation, the samples were incubated in isopropanol at −20°C overnight and centrifuged for 30 min at 10,000 g. RNA samples were washed in ethanol and resuspended in 30 μL of DEPC water (Ambion). Residual DNA in the RNA samples was removed by DNase I treatment (Ambion). The concentration of the RNA samples was determined by Invitrogen Qubit Fluorometer (Thermo Fisher Scientific), and RNA qualities were determined by Agilent RNA pico chip (Agilent Technologies, Santa Clara, California, USA).
Sequencing and analysis of the RNA data were performed by the MGX Genomics platform (Montpellier France). Ribosomal RNA was removed from each total RNA sample and libraries were produced using the Stranded mRNA Prep Ligation Kit, and sequenced using NovaSeq flow cell SP in single-read 100 pb (Illumina, San Diego, California, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
3_A2
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| Data processing |
Base-calling bcl2fastq v2.20
Quality check - FastQC (v.0.11.9)/MultiQC (v.1.11)
Short reads were mapped against the genome of L. rhamnosus Lcr35 (using BWA software (v0.7.15-r1140). Counting was performed with the software feature Counts (v2.0.3) using a gff file from Nexbiome Therapeutics. DESeq2 (v1.32.0) in R (v4.1.1) has been used to perform normalization of the read counts.
Assembly: Lcr35 (Nexbiome Therapeutics)
Supplementary files format and content: tab-delimited text file include raw gene counts for every gene (gene id|gene symbol) and every sample
Supplementary files format and content: tab-delimited text file include normalized gene counts for every gene (gene id|gene symbol) and every sample
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| Submission date |
Sep 12, 2023 |
| Last update date |
Jan 08, 2024 |
| Contact name |
sylvie miquel |
| E-mail(s) |
sylvie.miquel@uca.fr
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| Organization name |
UCA
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| Lab |
LMGE
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| Street address |
28 place henri Dunant
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| City |
Clermont-ferrand |
| ZIP/Postal code |
63000 |
| Country |
France |
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| Platform ID |
GPL33752 |
| Series (1) |
| GSE242938 |
Elemental sulfur enhances the anti-fungal effect of Lacticaseibacillus rhamnosus Lcr35 |
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| Relations |
| BioSample |
SAMN37359018 |
| SRA |
SRX21755799 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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