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| Status |
Public on Dec 01, 2023 |
| Title |
B.xylanisolvens, corn fiber, R3 |
| Sample type |
SRA |
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| Source name |
Bacteria
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| Organism |
Bacteroides xylanisolvens |
| Characteristics |
strain: CL03T12C04
cell type: Bacteria
treatment: Corn Fiber
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| Growth protocol |
Bacteria were cultured in Hungate tubes with a containing 90 % N2, 5 % CO2, 5 % H2 atmosphere. Cultures were performed in a minimum medium adapted from YCFA medium supplemented with 0.5 % or 0.1% carbohydrate. Cultures were stopped 12 h after inoculation.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNeasy kit (Qiagen)
Directional RNA-Seq Libraries were constructed using the TruSeq Stranded Total RNA library prep kit, with bacteria Ribo-Zero reagents (Illumina), following the manufacturer’s instructions. After the Ribo-Zero step, the samples were checked on the Agilent Bioanalyzer for proper rRNA depletion. Final libraries quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit.
Libraries were pooled in equimolar proportions and sequenced on a single read 75pb run, on an Illumina NextSeq500 instrument.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
BX_M_R3
counts_BX.csv
BX_fibre_mais_vs_controle2_DESeq_results.csv
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| Data processing |
bcl2fastq2-2.18.12 (demultiplex)
Cutadapt 3.2 (adapter trimming)
FastQC v0.11.5 (quality control)
Assembly: B.xylanisolvens:NZ_JH724294,NZ_JH724295,NZ_JH724296,NZ_JH724297,NZ_JH724298,NZ_JH724299,NZ_JH724300,NZ_JH724301,NZ_JH724302,NZ_JH724303,NZ_JH724304,NZ_JH724305,NZ_JH724306/B;thetaiotaomicron:NC_004663.1/R.intestinalis:NZ_LR027880.1/S.variabile:NZ_GG704769,NZ_GG704770,NZ_GG704771,NZ_GG704772,NZ_GG704773,NZ_GG704774,NZ_GG704775,NZ_GG704776,NZ_GG704777,NZ_GG704778,NZ_GG704779
Supplementary files format and content: Table xxxx_DESeq_results.csv contains the raw, unfiltered results. There is one gene per row and in columns the metrics calculated by DEseq2 during the analysis: ID: gene name//baseMean: average of normalized counts for all samples/replicates involved in the comparison/log2FoldChange: log2 of the ratio of counts between the 2 conditions/lfcSE: standard error of this fold change/stat: the value of the statistical (Wald) test, used to calculate the pvalue. It is the ratio between log2FoldChange and lfcSE./pvalue: This value determines the significance of the statistical value or test. It indicates the probability that an observed fold change could be due to chance. The closer the p-value is to 0, the more significant the test, and the more real the differential in expression observed between the 2 conditions./- padj: adjusted (or corrected) pvalue, which takes into account multiple tests. As the statistical test is performed on each gene and each test is associated with a possible error, accumulating tests increases this error. We need to take this into account and make a correction for the number of tests performed. DEseq2 uses the Benjamini-Hochberg method./- then normalized counts for the samples involved in the comparison
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| Submission date |
Jul 12, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
paul Biscarrat |
| E-mail(s) |
paul.Biscarrat@inrae.Fr
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| Phone |
0681646634
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| Organization name |
INRAE
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| Street address |
4 AVENUE JEAN JAURES-DOMAINE VILVERT
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| City |
JOUY EN JOSAS |
| State/province |
ile de france |
| ZIP/Postal code |
78350 |
| Country |
France |
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| Platform ID |
GPL33567 |
| Series (1) |
| GSE237111 |
Effect of supplementation of a minimal culture medium with inulin, corn fiber and pectin, compared with a glucose condition, on the gene expression of a set of bacteria of the intestinal microbiota |
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| Relations |
| BioSample |
SAMN36411096 |
| SRA |
SRX20989684 |
| 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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