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The effect of reverse transcription enzymes and conditions on high throughput amplicon sequencing of the 16S rRNA

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The effect of reverse transcription enzymes and conditions on high throughput amplicon sequencing of the 16S rRNA https://t.co/8a09YPNkJu
36 days ago
The effect of reverse transcription enzymes and conditions on high throughput amplicon sequencing of the 16S rRNA https://t.co/FQ6xnMBibX https://t.co/SUW3foiDC5
RT @rnomics: The effect of reverse transcription enzymes and conditions on high throughput amplicon sequencing of the 16S rRNA https://t.co…
The effect of reverse transcription enzymes and conditions on high throughput amplicon sequencing of the 16S rRNA https://t.co/VPrNycANbk
The effect of reverse transcription enzymes and conditions on high throughput amplicon sequencing of the 16S rRNA https://t.co/1ojsnLHf9y It is assumed that the sequencing of ribosomes better reflects the active microbial community than the sequencing of the ribosomal …
77 days ago
The effect of reverse transcription enzymes and conditions on high throughput amplicon sequencing of the 16S rRNA https://t.co/3KrbP5xEl1 https://t.co/D4nN1649Ty
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Supplemental Information

Diversity, richness and evenness across experimental conditions

Diversity plot displaying species richness, Pelou evenness, and Shannon diversity for a variety of experimental conditions (X-axis). Species richness is represented as species count. Each category is an average of 4 biological replicates.

DOI: 10.7287/peerj.preprints.27780v2/supp-1

A proportional relation of most abundant classes and their respective G-C contents between the tested conditions

A comparison between the ImProm-II at 42 ◦ C and SuperScriptIV (a),the ImProm-II at 55 ◦ C and TGIRT, (b), ImProm-II at 42 ◦ C and TIGRT (c) and TGIRT and SuperScriptIV (d). Enrichment is expressed such that a class that is equally proportional in both conditions, has a value of 0. If the class shows in one condition, but its absent from another, its value would be equal to 1 or -1 respectively. Furthermore a weighted average of the GC content of each class is expressed as the bar color. Each value is an average of 4 biological replicates.

DOI: 10.7287/peerj.preprints.27780v2/supp-2

Relative abundance of phyla across the experimental conditions

Each column is an average of 4 biological replicates.

DOI: 10.7287/peerj.preprints.27780v2/supp-3

Diversity statistics code file iPython notebook

A detailed description of the procedure of generating the diversity statistical comparison between the tested conditions.

DOI: 10.7287/peerj.preprints.27780v2/supp-4

GC enrichment plot IPython notebook code

A detailed description of the code used to generate the GC enrichment figure.

DOI: 10.7287/peerj.preprints.27780v2/supp-5

Data preparation IPython notebook code

Details of the sequencing data preparation procedure, including the discarding of outlier samples and normalization of sequence counts.

DOI: 10.7287/peerj.preprints.27780v2/supp-6

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Adam Šťovíček conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Smadar Cohen-Chalamish conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Osnat Gillor conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

All sequences retrieved in this study were uploaded to European Nucleotide Archive (https://www.ebi.ac.uk/ena) submission number PRJEB32237.

The sequences are available during the review process at https://doi.org/10.6084/m9.figshare.8217794.v1.

Data Deposition

The following information was supplied regarding data availability:

The code used to generate the data is supplied in supplementary files in the IPython notebook format in the data_preparation.ipynb, diversity_statistics.ipynb and GC_enrichment_plot.ipynb files respectively.

Funding

This study was supported by the Israel Science Foundation grant number 993/11 to Osnat Gillor. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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