alimintestData: AlimIntest data

In tapj/AlimIntest: AlimIntest project source code

Description

This dataset contains all metadata and microbial data from the AlimIntest project.

Usage

alimintestData

Format

A list of 4 data frames

Variables

• metadata: study design with SCFA, qPCR and comet assays

  • idx: INDEX

  • Sample_ID; Sample_ID2: Sample identifications

  • Time point: Time point corresponding to study design illustrated on Fig. S1

  • Subject_Id: Subject identification

  • Diet_run: Diet run "r10_40" correspond to 10g fiber per day between time point n°2 and time point n°3 and 40g fiber per day between time point n°4 and time point n°5; "r40_10" correspond to the cross over to "r10_40". See Fig. S1

  • Seq_filtered: Sequence after quality checking from LOTUS pipeline

  • acetate; propionate; isobutyrate; butyrate; isovalerate; valerate; isocaproate; caproate: Short Chain Fatty Acid measurement (mM) by gas-liquid chromatography

  • log_all_Bacteria; log_Cleptum_group; log_Bcoccoides_group; log_Bacteroides_Prevotella; log_Bifidobacteria; log_Ecoli; log_Lactobacillus: Quantitative PCR assays expressed in Log10 of number of equivalent bacterial cells

  • fecal_water_pH: Fecal water pH measurement

  • Comet_assay: Single Cell Gel Electrophoresis assay expressed in

• otu: Microbial OTU table

• tax: OTU Greengenes taxonomy

• basalqpcr: extra qpcr data which correspond to time point 1 and time point 6 (see Fig. S1)

Examples

head(alimintestData$metadata)

tapj/AlimIntest documentation built on May 31, 2019, 3:48 a.m.