Download the data.

Updated: Jan 17, 2019

If you’re interested in checking out the data that comes from a LoopSeq kit, we have two example data sets for you, one 16S data set and one transcriptome data set.

These results come right from our service lab.

To download our transcriptome data set please click here.

For the 16S data set please find additional details and links to download that data below.

Our standard analysis includes CSV files with (1) Single molecule quantification of abundance based on Unique molecular Identifiers (UMI's), eliminating amplification biases, (2) Reference based taxonomic classification based on nine variable regions (V1-V9 data in 16S and 18S) and long-reads in Metagenomic sequencing, (3) OTU tables, (4) Rarefaction analysis, (5) RAD analysis, as well as pie chart visualizations of classification and quantification.

More about the samples. The first is a mock community from Zymoresearch.

Here is a bit about their mock community sample:

Microbial composition profiling techniques powered by Next-Generation sequencing are becoming routine in microbiomics and metagenomics studies. However, these analytical techniques can suffer from significant bias from collection to analysis. The ZymoBIOMICS® Microbial Community Standard is designed to assess bias and errors in the extraction methods of a microbiomics workflow. The Microbial Community Standard mimics a mixed microbial community of well-defined composition, containing three easy-to-lyse Gram-negative bacteria, five tough-to-lyse Gram-positive bacteria and two tough-to-lyse yeasts. Acting as a defined input from the beginning, the Microbial Community Standard can guide construction and optimization of entire workflows and can also be used as a routine quality control.

Theoretical Composition Based on Genomic DNA: Listeria monocytogenes - 12%, Pseudomonas aeruginosa - 12%, Bacillus subtilis - 12%, , Escherichia coli - 12%, Salmonella enterica - 12%, Lactobacillus fermentum - 12%, Enterococcus faecalis - 12%, , Staphylococcus aureus - 12%, Saccharomyces cerevisiae - 2%, and Cryptococcus neoformans - 2%.

You can download our data from running this sample here:

ZymoBIOMICS sample data.

The second is a sample from ATCC. Here's a bit more about that sample:

We ran a sample from ATCC using their 20 strain staggered mix genomic material. This is a microbiome standard that enables the optimization of metagenomics workflows and microbiome research applications, providing reliable comparative data while improving assay consistency. Here below are examples for Loopseq sequencing data for two of the strains from the ATCC staggered Microbiome mix together with their respective genome and expected 16S sequences:

Porphyromonas gingivalis is a bacterium with a genome size of 2.35 Mb, 48.4% GC content, and 4 identical copies of 16s rRNA.

  1. Link to the complete genome sequence: Porphyromonas gingivalis genome sequence

  2. Reference 16s sequences (File: "Porphyromonas_gingivalis_16s.fa")

  3. Loop Genomics synthetic long reads (File: "contig_list_Porphyromonas.fq")

Rhodobacter sphaeroides is a bacterium with a genome size of 4.13 Mb, 68.7% GC content, and 4 identical copies of 16s rRNA.

  1. Link to the complete genome sequences: Rhodobacter sphaeroides chromosome 1, Rhodobacter sphaeroides chromosome 2

  2. Reference 16s sequences (File: "Rhodobacter_sphaeroides_16s.fa")

  3. Loop Genomics synthetic long reads (File: "contig_list_Rhodobacter.fq")