What is SCGC?

Bigelow Laboratory Single Cell Genomics Center (SCGC) is a non-profit research and service center and an integral part of Bigelow Laboratory for Ocean Sciences. The primary focus of SCGC is single cell genomics of microorganisms, but we also work with cells of humans and other multicellular organisms. Our mission is to make single cell genomics accessible to the broad research community and to serve as an engine for discoveries in microbial ecology, evolution, bioprospecting and human health.

What services does SCGC provide?

SCGC offers a one-stop solution for high-throughput single cell genomics, including flow-cytometric cell separation, genomic DNA amplification, DNA sequencing and bioinformatics. A detailed description of SCGC services is provided here.

Why should I use SCGC services?

Single cell DNA sequencing, pioneered by SCGC scientists, reads the genomic blueprints of the most fundamental units of life without the need for cultivation. This is a powerful approach to analyze biochemical properties and evolutionary histories of uncultured microorganisms, thought to constitute over 99% of biological diversity on Earth. Single cell genomics also provides unique insights into the microdiversity and evolutionary processes within microbial populations and within multicellular organisms.

SCGC is the first shared user facility of its kind. Since its establishment in 2009, SCGC has developed partnerships and supported research projects at over 100 universities, research institutes, and companies in six continents. Over 1,000,000 individual cells have been processed through our high-throughput pipeline. Sources of these cells range from diverse marine environments, to soils, the deep subsurface, gut contents, and others. This has been providing unique genomic data from many major evolutionary branches of bacteria, archaea, and eukarya that resist cultivation, making a significant impact on our understanding of life on our planet.

For a recent review of microbial single cell genomics, please see here.

Why should I sequence my SAGs at SCGC?
Specialized laboratory and computational procedures are essential in order to obtain high quality genomic sequences from SAGs. A major challenge to consider is the cross-talk of multiplexed Illumina libraries (also known as “sample bleeding” and “index switching”):

De novo assemblies of single amplified genomes (SAGs) are especially sensitive to this issue. This is due to the fact that single cell whole genome amplification is highly uneven across the genome, and deep sequencing is typically employed to facilitate the recovery of the under-amplified genome regions. As a result, even a relatively small overall fraction of mis-assigned reads may form sizeable contigs that represent over-amplified regions of co-sequenced SAGs. In 2014, SCGC established in-house infrastructure and procedures for the preparation of dual-barcoded libraries and their sequencing with NextSeq 500, followed by optimized data processing. These measures eliminated library cross-talk. To verify the efficacy of these solutions, SCGC benchmarks its entire workflow using SAGs of previously sequenced strains.

Please see the following links for additional information:

Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using illumina platform
Index switching causing “spreading-of-signal” among multiplexed samples in illumina HiSeq 4000 DNA sequencing
The go-to gene sequencing machine with very strange results
Mixing sample types in a flowcell lane generated cross contamination artefacts
Index mis-assignment between samples on HiSeq 4000 and X-ten


Will data produced by SCGC be secure and confidential?

All information about materials provided by SCGC customers is kept confidential. All data analyzed by the SCGC is owned by the SCGC customer and is not shared unless the customer provides specific written direction. For more details, please see SCGC Terms and Conditions.

How long does it take to complete SCGC services?

In most cases, it takes less than two months from the sample sort date to service completion, see upcoming sort dates on the Home Page. More time may be required for large projects and during periods of unusually high service demand.

What type of samples does SCGC process?

In general, we can process samples that are compatible with fluorescence-activated cell sorting, i.e. cells that are suspended in an aquatic solution and are smaller than 70 um in diameter. We have extensive experience working with challenging samples, such as sediments, soils, biofilms and tissues. We do not process radioactive or biosafety level III and higher samples. Please contact the SCGC manager for additional details.

Do I have to pay for SCGC services, and what are the fees?

Yes, customer fees are the only source of funds available to cover SCGC operational expenses. Fees for SCGC services are listed here.

How do I request SCGC services?

Please follow these directions.

How should I prepare and preserve samples for single cell genomics analyses at SCGCÂź?

Please follow these directions.

How should I ship samples to SCGC?

Please follow these directions.

Can FISH-labeled cells be analyzed at SCGC?

Yes, but specific FISH techniques must be applied. CARD-FISH and aldehyde fixation are NOT compatible with single cell genomics. Please apply regular (no signal amplification) FISH on either live or ethanol-fixed cells and then cryopreserve them using SCGC’s standard protocol. References for compatible FISH protocols:

Haroon MF, Skennerton CT, Steen JA, Lachner N, Hugenholtz P, Tyson GW (2013) In-solution fluorescence in situ hybridization and fluorescence-activated cell sorting for single cell and population genome recovery. Methods in Enzymology 531:3-19.

Yilmaz S, Haroon MF, Rabkin BA, Tyson GW, Hugenholtz P (2010) Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations. The ISME Journal 4:1352-1356.

What methods does SCGC use?

A detailed description of SCGC services is provided here. For further details, please see:

Stepanauskas R, Fergusson EA, Brown J, Poulton NJ, Tupper B, Labonté JM, Becraft ED, Brown JM, Pachiadaki MG, Povilaitis T, Thompson BP, Mascena CJ, Bellows WK, Lubys A. 2017. Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles. Nat Commun 8.



Can I collaborate with SCGC scientists beyond the scope of per-fee services?

Yes. General academic practices apply when collaborating with SCGC scientists beyond the scope per-fee services, such as reliance on mutual interests and the availability of time and funding. Please contact SCGC director to express your interest and to establish initial communication.

How do I name single amplified genomes (SAGs) generated by SCGC?

Please use the following convention:

Escherichia coli SCGC ZZ-999-A01

Pseudomonas sp. SCGC ZZ-999-A02

Actinobacteria bacterium SCGC ZZ-999-A03

Euryarchaeon SCGC ZZ-999-A04

The use of this convention will enable effective SAG tracking at SCGC and in public databases.

How do I acknowledge SCGC services in my scientific publications and presentations?

Please make sure to indicate Bigelow Laboratory Single Cell Genomics Center in Materials and Methods in all publications resulting from data generated at the SCGC. You can refer to the following publication that describe our methods:

Stepanauskas R, Fergusson EA, Brown J, Poulton NJ, Tupper B, Labonté JM, Becraft ED, Brown JM, Pachiadaki MG, Povilaitis T, Thompson BP, Mascena CJ, Bellows WK, Lubys A. 2017. Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles. Nat Commun 8.