Examples

Seeing is believing! To see examples of our work, head over to our results portal at https://seqresults.angstrominno.com.

Every account is preloaded with some demo orders that demonstrate sequencing results that customers can expect for each service type. These examples are not password protected and can be opened by anyone. Your actual customer data will of course be password protected to ensure your sensitive data is always secure!

Here is a little bit of background information about each of the demo orders:

Plasmid Sequencing of three common vectors

In your results portal, you will find a demo order for Whole Plasmid Sequencing of three common plasmid vectors: pUC19, pACYC-Duet, and pET-28a(+).

https://seqresults.angstrominno.com/orders/AI-3642

When you open your order page, you will first see a summary of the plasmid sizes of all the de novo assemblies. You can hover over a sample bar to get more details.

We generate multiple reports per sample such as the interactive plasmid map, fasta file, genbank file, ab1 file, etc.

This is what the interactive map looks like for the first sample (pUC19):

Here is the read length histogram with a sharp peak at the respective size for pUC19 (~2.6 kb).

Many of our customers like this interactive IGV view that aligns the raw nanopore reads with the auto-annotated de novo assembly.

We can also do reference based alignment. Here the public sequence for pUC19 was uploaded. After alignment, you can see there are no mutations and it is a 100% match.

https://seqresults.angstrominno.com/orders/AI-3642/alignment-tool

Each sample that has a successful assembly, will also have a "Quality Badge" score. This provide a quick view if the sample met important criteria regarding coverage, purity, and per base confidence.

Many more reports are available. All the files can be downloaded as zip file (with or without the raw fastq data). You can select the "Include Raw Reads" option if you want to include it in your zip. Note this file is much larger and can be several hundred megabytes or larger depending on your order size.

Amplicon Sequencing of SS3 locus

The SS3 locus is a commonly used integration locus in E. coli engineering (Bassalo 2016). Here we validated the wildtype locus (containing the gRNA target sequence) using primers

Primer Name	Sequence
SS3_forward	GGC GGT GCA CAG CAA CAC G
SS3_reverse	CCG GTG ATA CAG CTT CAA TTC CAA CC

This amplifies a short product about 250 bp long.

Result when submitted to our Linear Amplicon service: https://seqresults.angstrominno.com/orders/AI-1272

The IGV plot shows the sequencing coverage of this amplicon product. About 15-20 bp at the ends of the amplicon are cleaved when using the rapid barcoding tagmentation process. However, we can still validate that the locus has the intended engineering.

https://igv.angstrominno.com/?sessionURL=/data/AI-1272_1_SS3_locus/session.json# (make sure to log in first to SeqResults)

Here is a view of the reference aligned with the sequencing result:

https://seqresults.angstrominno.com/orders/AI-1272/alignment-tool

Bacterial Genome Sequencing of BL21(DE3)

The example below shows the Bacterial whole genome sequencing result for BL21(DE3), a host frequently used for T7 promoter expression.

For the analysis below, the updated 2024 reference sequence NZ_CP053602.1 was used.

See the result: https://seqresults.angstrominno.com/orders/AI-1179

Yeast Whole Genome Sequencing - Haploid strain with a plasmid

We purchased a commercial yeast strain containing a GFP plasmid from The-Odin.com. The online description says it is a "sample of Saccharomyces cerevisiae French Saison Yeast Strain with the extra chromosomal DNA that contains a form of the Green Fluorescent Protein"

The strain was streaked out on YPD agar media and grown at 30°C. Then the colony was inoculated into 5 mL YPD liquid media and grown for about 20 hours until saturation. The culture was separated into two conditions based on the amount of biomass. Low_yeastGFP used only 1 mL of culture while High_yeastGFP had 4 mL of culture. Each condition was pelleted and then the genomic DNA was extracted using the commercial Zymo Research Quick-DNA Fungal/Bacterial Miniprep Kit. The genomic DNA was barcoded and sequenced using Oxford Nanopore's Rapid Barcoding Kit according to manufacturer's recommendations.

Results:

All the results can be freely accessible by going to https://seqresults.angstrominno.com/orders/AI-1309 (just need to provide your email to receive a simple login code). The main result page gives you the option to download the data as a zip file. If you want the very large file containing the raw nanopore reads (4.4 Gigabytes) select the "Include Raw Reads" box.

When clicking the details for sample 1, you will see some summary statistics regarding the sequencing output such as Total Sequencing bases, longest read, number of contigs, and average coverage.

We provide a fast prediction of what the strain is by using Sourmash. A more comprehensive analysis can be done by running a BLAST search using the full genomic FASTA data.

Looking further down the page, you can see the read length histogram. From this plot, it is looks like there might be multiple plasmids around 6 kbp.

Using our "PlasmidHunter" tool, we are able to extract these plasmid sequences and provide fully annotated maps. The plasmid data can be found in the zip file. The first peak around 6,060 bp is the GFP containing plasmid (annotated as obeCFP by pLannotate).

The second plasmid appears to the native 2µ plasmid. The third plasmid peak at ~12,856 bp is the dimer of this 6,428 bp plasmid.

Yeast is known to be able to handle multiple 2µ plasmids and using our yeast WGS you can discover the full genomic sequence (and plasmids) for your strains.