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| Status |
Public on May 20, 2022 |
| Title |
S2_1_6 |
| Sample type |
SRA |
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| Source name |
Cell culture
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| Organism |
Enterococcus faecalis |
| Characteristics |
treatment: DCA
time point (minutes): 6
rpph: no
biological replicate: 2
technical replicate: 1
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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 |
AB 5500xl-W Genetic Analysis System |
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| Data processing |
Search of untagged reads in csfasta/qual files using Bowtie (version 1.2.2, options: -3 22 -n 0 -l 5 -C --integer-quals --col-keepends) on fasta reference containing both specific tags ("GCATAGGGGTAAA" and "GCGAGACTGAGAA") corresponding to another study.
Extraction from sam files of untagged (unmapped) reads names using Grep on the tag names.
Extract previous reads from the initial csfasta/qual using a custom Perl script.
Read mapping using Bowtie (version 1.2.2, options: -S -f -C -n 3 -l 18 -k 2 --best --chunkmbs 200 -e 3000 --nomaqround).
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: DCA_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 |
Dec 21, 2021 |
| 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 |
GPL31131 |
| Series (2) |
| GSE192438 |
Gene expression in response to deoxycholate acid constraints growth of Enterococcus faecalis |
| GSE194011 |
Contrasted effects of deoxycholate and taurocholate bile acids on the gut pathobiont Enterococcus faecalis |
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| Relations |
| BioSample |
SAMN24289145 |
| SRA |
SRX13476345 |
| 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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