Alterations in gut microbiota do not play a causal role in diet-independent weight gain caused by ovariectomy

These files are associated with the following publication:https://doi.org/10.1210/jendso/bvaa173

And the sequence data are available at the European Nucleotide Archive: PRJEB40801

This link contains the metadata, sequences reads, and analysis files used in the study "Alterations in gut microbiota do not play a causal role in diet-independent weight gain caused by ovariectomy."

Alpha_diversity files:
    File: AlphaDiversity_analysis_sham_ovex
        Description: R statistical analysis file for Faith's Phylogenetic Diversity (Faith's PD) and Observed
                     Sequence Variant (SV) alpha diversity metrics
    File: faith_pd_sham_ovex
        Description: QIIME2 output file for Faith's PD alpha diversity measurements for sham/ovex samples
    File: obserevd_svs_sham_ovex
        Description: QIIME2 output file for Observed SVs alpha diversity measurements for sham/ovex samples

Beta_diversity files:
    File: BetaDiversity_analysis_sham_ovex
        Description: R statistical analysis file for beta diversiy metrics
    File: merged.sv.sham.ovex
        Description: Combined SV table and taxa table for sham/ovex samples  
    File: sv.sham.ovex
        Description: SV table for sham/ovex samples
    File: table.sham.ovex.biom
        Description: BIOM formated file for combined SV and taxa data. (For import into Phyloseq)
    File: tax.sham.ovex
        Description: Taxa table for sham/ovex samples
    File: tree.nwk
        Description: Phylogentic tree for sham/ovex data (For import into Phyloseq)

DeSeq2 Analysis files:
    File: merged.sv.sham.ovex.trimmed
        Description: Combined SV table and taxa table for sham/ovex samples. SVs found in 4 samples or less removed.  
    File: sv.table.sham.ovex.trimmed  
        Description: SV table for sham/ovex samples. SVs found in 4 samples or less removed.
    File: sham.ovex.trimmed.biom
        Description: BIOM formated file for combined SV and taxa data. SVs found in 4 samples or less removed.(For import into Phyloseq)
    File: tax.sham.ovex.trimmed
        Description: Taxa table for sham/ovex samples. SVs found in 4 samples or less removed.
    File: tree.trimmed.nwk
        Description: Phylogentic tree for sham/ovex data. SVs found in 4 samples or less removed. (For import into Phyloseq)
    File: Phyloseq.DeSeq2.Ovex.Sham
        Description: Log2 Fold change analysis (relative species abundance) done in DESeq2 for time points 1-5.
    File: Phyloseq.DeSeq2.Ovex.Sham.week3
        Description: Log2 Fold change analysis (relative species abundance) done in DESeq2 for time point 3.
    File: Phyloseq.DeSeq2.Ovex.Sham.week4
        Description: Log2 Fold change analysis (relative species abundance) done in DESeq2 for time point 4.
    File: Phyloseq.DeSeq2.Ovex.Sham.week5
        Description: Log2 Fold change analysis (relative species abundance) done in DESeq2 for time point 5.

Mapping_files including metadata (for use with sequences below):
    File: ovex_mapping  
        Description: Mapping file - maps barcodes to samples
    File: ovex_mapping_samples removed
        Description: Mapping file - maps barcodes to reads. Two samples removed for low sequence count.
                        1. Plate2    A08    806rcbc103    GCG AGC GAA GTA CCG GAC TAC HVG GGT WTC TAA T    8    870 (T2)    Ovex    F
                        2. Plate2    C02    806rcbc121    GCA ATT AGG TAC CCG GAC TAC HVG GGT WTC TAA T    26    888 (T2)    Co-Sham    O
    File: ovex_mapping_sham_ovex_samples removed
        Description: Mapping file - maps barcodes to reads. Sham/ovex samples only. One sample removed for low sequence count.
                        1. Plate2    A08    806rcbc103    GCG AGC GAA GTA CCG GAC TAC HVG GGT WTC TAA T    8    870 (T2)    Ovex    F

QIIME2 Script:

File: QIIME2_sham_ovex
    Description: This file includes the commands used in the QIIME2 pipeline.