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Ebraccatus_Priority_Effects

Version 3 2023-02-03, 19:06
Version 2 2022-09-20, 13:37
Version 1 2022-03-10, 19:15
dataset
posted on 2023-02-03, 19:06 authored by Korin JonesKorin Jones, Myra HugheyMyra Hughey, Lisa BeldenLisa Belden

The EPE was a collection of short term studies in which the eggs of hourglass treefrogs were inoculated with bacteria in different orders in order to test for the presence of priority effects in tadpole bacteria community development. The first experiment was an inoculation experiment with frog embryos using two bacterial isolates. To complement our tadpole experiment, a follow-up experiment was conducted in which broth containing wells within a well-plate were similarly inoculated with bacteria under two nutrient concentrations (Full LB broth or a 1:20 dilution LB broth). We then conducted a third test in which embryos were inoculated first with a single bacterium and then with a synthetic community of bacteria.The sequences included are 16S rRNA sequences of the V4 variable region. 

Funding

Department of Biological Sciences at Virginia Tech, Vassar College, and Tom and Ana Moore. During the writing of this manuscript, KRJ was supported by a National Science Foundation Graduate Research Fellowship

History

Publisher

University Libraries, Virginia Tech

Corresponding Author Name

Korin Rex Jones

Files/Folders in Dataset and Description

[20200116_pool_LB7752_S1_R2_001.fastq.gz] – Experiment 1: Barcodes for single end 16S sequences from tadpoles. [20200116_pool_LB7752_S1_R1_001.fastq.gz] – Experiment 1: Single end 16S Illumina sequences from tadpoles. [211117_pool_LB9513_S1_R1_001.fastq.gz] – Experiment 2: Single end 16S Illumina sequences from tadpoles. [211117_pool_LB9513_S1_R2_001.fastq.gz] – Experiment 2: Barcodes for single end 16S sequences from tadpoles. [EIE_Metadata_AS.csv] – Meta data file containing treatment information. Treatments are labeled in terms of isolate order with a 24 hour time frame between inoculations. Ex. AS = A inoculated first, then S inoculation 24 hours later. • A= Acinetobacter, S= Stenotrophomonas, W= sterile water [EIE_Illumina_file.xlsx] – Meta data file sent to Illumina necessary for processing raw sequence data. This includes barcode sequences and linker primer sequences [Prio_Seq.zip] – Raw Illumina sequences for isolate experiment. [Fastq] – Contains forward and reverse reads for the isolate experiment designated by R1 and R2. The first characters prior to the underscore represent the sample names. *_R1 *_R2 [Prio_Seq_Meta.csv] – Meta data file containing treatment information. Treatment descriptions: o Per = simultaneous inoculation at a given percent that was immediately collected and frozen for sequencing  Per_50 = 50/50 isolate split  Per_A_75 = 75/25 isolate split favoring A  Per_S_75 = 75/25 isolate split favoring S o Full_50 = simultaneous inoculation for both isolates in equal proportions, full nutrient broth o Dil_50 = simultaneous inoculation for both isolates in equal proportions, diluted nutrient broth o A_75_Dil = simultaneous inoculation of 75/25 isolate split favoring A, diluted broth o A_75_Full= simultaneous inoculation of 75/25 isolate split favoring A, full broth o S_75_Dil= simultaneous inoculation of 75/25 isolate split favoring S, diluted broth o S_75_Full= simultaneous inoculation of 75/25 isolate split favoring S, full broth o A = only isolate A o S = only isolate S o A_Dil = A in dilute broth o A_Full = A in full broth o S_Dil = S in dilute broth o S_Full = S in full broth o AS_Full = A inoculation followed by inoculation with S six hours later in full broth o AS_Dil = A inoculation followed by inoculation with S six hours later in dilute broth o SA_Full = A inoculation followed by inoculation with A six hours later in full broth o SA_Dil = A inoculation followed by inoculation with A six hours later in dilute broth o Dil = Diluted broth o Comm_Std = unused community standard [CPE_Meta.csv] – Meta data file containing treatment information. This includes barcode sequences and linker primer sequences Treatments are labeled in terms of isolate order with a 24 hour time frame between inoculations. Ex. A = A inoculated first, then the community inoculation 24 hours later. • A= Acinetobacter, S= Stenotrophomonas, E= Erwinia, Control= sterile water [Exp1_Qiime2 _documentation.docx] – Documentation file of qiime2 code used to process Experiment 1 samples. Used with qiime2 version – 2019.1 [Coculture_Qiime2_documentation.docx] – Documentation file of qiime2 code used to process co-culture samples. Used with qiime2 version 2019.1 [Exp2_Qiime2 _documentation.docx] – Documentation file of qiime2 code used to process Experiment 2 samples. Used with qiime2 version – 2021.8 [Exp_1_Code.Rmd] – R notebook script used to analyze samples from Experiment 1. [Co-Culture_Script.Rmd] – R notebook script used to analyze co-culture samples. [Exp_2_Code.Rmd] – R notebook script used to analyze samples from Experiment 2.

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