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| Status |
Public on May 20, 2022 |
| Title |
Time03_sample17 |
| Sample type |
SRA |
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| Source name |
Cell culture
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| Organism |
Enterococcus faecalis |
| Characteristics |
treatment: TCA
time point (minutes): 3
biological replicate: 4
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| Treatment protocol |
Fouquier D'hérouel et al., 2011; Lacoux et al., 2020.
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| Growth protocol |
E. faecalis strains were grown in standardized conditions as described in Fouquier D'hérouel, 2011. For all experiments, the strain frozen at -80°C was streaked on 1.5 % agar plate of Brain Heart Infusion (BHI), grown for 20 h at 37°C and incubated 2 h at room temperature. One single colony was used to inoculate 5 ml of liquid BHI and grown for 18 h at 37°C without agitation. The culture was then diluted 1/500-fold in a pre-warmed BHI liquid medium and grown to an OD600 ranging from 0.27 to 0.33 (OD600 ~ 0.3), as monitored manually on spectrophotometer at 600 nm weight length (Pharmacia Biotech, Novaspec II). At such a density, the bacterial population ranged from ~2 to 4 x 10^8 cfu/mL, as verified by viable cell counts on BHI plates.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Fouquier D'hérouel et al., 2011.
Innocenti et al., 2015 and Lacoux et al., 2020.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Read mapping using BWA-backtrack (version 0.7.12-r1039).
Structural reference annotation of Enterococcus faecalis V583 chromosome (AE016830.1) was enriched with sRNA annotation from Innocenti et al., 2015.
Read counts were obtained using HTSeq-count (version 0.9.1).
Differential expression analysis R library "DESeq2" and associated "median ratio method" normalization procedure.
DESeq2 p-values were converted into q-values using R library "fdrtool".
RPKM values processed using DESeq-2 with a prior-count of 33.
Genome_build: Enterococcus faecalis V583 chromosome (AE016830.1)
Supplementary_files_format_and_content: TCA_gene_expression.txt: Tab-delimited text file containing for each gene/sample raw data counts, log2rpkm with differential expression analysis results.
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| Submission date |
Jan 19, 2022 |
| Last update date |
May 20, 2022 |
| Contact name |
Cyprien Guérin |
| E-mail(s) |
cyprien.guerin@inrae.fr
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| Phone |
+33-1-3465-2896
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| Organization name |
INRAE
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| Lab |
MaIAGE
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| Street address |
INRAE - Domaine de Vilvert
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| City |
Jouy-en-Josas |
| ZIP/Postal code |
F-78350 |
| Country |
France |
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| Platform ID |
GPL23172 |
| Series (2) |
| GSE194009 |
Taurocholate acid signals a specific gene expression reprogramming affecting amino-acids and nucleotides metabolisms |
| GSE194011 |
Contrasted effects of deoxycholate and taurocholate bile acids on the gut pathobiont Enterococcus faecalis |
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| Relations |
| BioSample |
SAMN25124140 |
| SRA |
SRX13833409 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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