data-raw/README.md

In tapj/AlimIntest: AlimIntest project source code

AlimIntest raw dataset

Metadata

* idx:  INDEX
* Sample_ID; Sample_ID2:    Sample identifications
* Time point:   Time point corresponding to study design illustrated on Fig. S1
* Subject_Id:   Subject idenfication
* 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 % of DNA in the tail

otu

* OTUs table from LOTUS pipeline (clustered at 97% similarity), column names correspond to Sample_ID, row names correpond to OTU id

tax

* Taxonomic identification for each OTU, taxonomy uncertainties are illustrated by "?"

sequences_files_location

* 454 Sequences files location for 16S rRNA gene amplicon and metatranscriptomic assays with corresponding Sample_ID and accession number

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