Single Cell Sequencing

BCL’s single cell sequencing service offerings deliver the reproducibility and quality needed for small or large scale single cell projects. Automated processes yield a level of data consistency and quality difficult to achieve in lower-throughput laboratories with manual sample preparation methods.

Single Cell Sequencing with
Broad Clinical Labs

Single cell sequencing services available from BCL include 10x Gene Expression (3′ or 5′), 10x Genomics Multiome (ATAC-Seq + gene expression), and SmartSeq2.

10x Single Cell
Gene Expression
(3' or 5')

The 10x Single Cell Gene Expression (3′ or 5′) (GEX) assay enables transcriptional profiling at the single cell level across thousands of cells, providing insight into how cellular heterogeneity contributes to a biological system.

Customers can target regions at the 3′ and/or 5′ end of transcripts. Both 3′ and 5′ assay versions can be supplemented with feature barcoding to enable selective targeting of cell surface proteins. The 5′ assay can also be paired with a T or B cell enrichment to further investigate immune cells.

Samples are sequenced using a workflow that enables customization of the depth of sequencing targeted for each sample, based on customers’ unique cell types and quantities.

10x Genomics Single Cell
Multiome (ATAC-Seq +
Gene Expression)

10x Genomics Single Cell Multiome (ATAC-Seq + Gene Expression) services at BCL utilize a kit developed by 10x Genomics that combines ATAC-Seq (assay for transposase accessible chromatin) and gene expression, simultaneously generating transcriptomic and epigenetic information from a single source sample. This service enables customers to access cell states and regulatory mechanisms more deeply than with single cell expression data alone.

To date, BCL has successfully generated Multiome data for nuclei derived from blood, tumor tissue, and fresh frozen brain tissue.

SmartSeq2
Single Cell
Sequencing

SmartSeq2 Single Cell Sequencing accurately profiles gene expression in single cells and is ideal for applications such as profiling gene expression in stem cell differentiation, organ development, tumor progression, and characterization of cell population responses to environmental signals and conditions.

Unlike most single cell methods, SmartSeq2 is compatible with frozen/archival sample types, and the sample preparation method results in full-length transcript capture, as opposed to 3′ tags.

Compare Single Cell Sequencing Services

Services	Inputs	Outputs
10x Single Cell Gene Expression (3' or 5')	Dissociated and filtered cells or nuclei, derived from fresh frozen tissue or PBMCs, suspended in 5–40µl of compatible buffers Optimal and strongly recommended: 10,000–15,000 cells/nuclei in 15µL of 1X PBS (calcium and magnesium-free) containing 0.04% BSA Hand delivery of samples to 27 Blue Sky Drive, Burlington, MA, 01803, with coordination of sample delivery times with BCL Project Manager	Raw BCL files
10x Single Cell Multiome (ATAC-Seq + Gene Expression)	3,000–10,000 cells or nuclei, suspended in 5 µL of cell/nuclei suspension 10x “Diluted Nuclei Buffer” (available to purchase from 10x Genomics); ~60% recovery during encapsulation	Raw BCL files; analysis available on request Sequencing coverage achieved per cell will depend on the number of nuclei submitted and the flowcell type (flowcell Gb output / total number of nuclei = estimated reads/nuclei). The minimum recommended sequencing coverage for gene expression libraries is 20,000 reads/nuclei, and 25,000 reads/nuclei for ATAC-Seq
SmartSeq2 Single Cell Sequencing	Very low concentration RNA (can be purified), 1–2ng/µl in 5–10µl buffer (water, TE, etc.); or Cell lysate in 5µl TCL or RLT Buffer + 1% beta-mercaptoethanol (BME) Single cells should be 1–100 cells per well, and cell populations should be 100–1000 cells per well Samples must be in 96 well Eppendorf twin.tec^® PCR LoBind or 96 well Eppendorf twin.tec^® PCR plates, sealed with Bio-Rad Microseal "F" foil; please ensure a tight seal seal around the edges as well as in between rows and columns Volume should be 5–10 µL per well, and all wells should have the same volume	FASTQ files

Services	10x Single Cell Gene Expression (3' or 5')
Inputs	Dissociated and filtered cells or nuclei, derived from fresh frozen tissue or PBMCs, suspended in 5–40µl of compatible buffers Optimal and strongly recommended: 10,000–15,000 cells/nuclei in 15µL of 1X PBS (calcium and magnesium-free) containing 0.04% BSA Hand delivery of samples to 27 Blue Sky Drive, Burlington, MA, 01803, with coordination of sample delivery times with BCL Project Manager
Outputs	Raw BCL files

Services	10x Single Cell Multiome (ATAC-Seq + Gene Expression)
Inputs	3,000–10,000 cells or nuclei, suspended in 5 µL of cell/nuclei suspension 10x “Diluted Nuclei Buffer” (available to purchase from 10x Genomics); ~60% recovery during encapsulation
Outputs	Raw BCL files; analysis available on request Sequencing coverage achieved per cell will depend on the number of nuclei submitted and the flowcell type (flowcell Gb output / total number of nuclei = estimated reads/nuclei). The minimum recommended sequencing coverage for gene expression libraries is 20,000 reads/nuclei, and 25,000 reads/nuclei for ATAC-Seq

Services	SmartSeq2 Single Cell Sequencing
Inputs	Very low concentration RNA (can be purified), 1–2ng/µl in 5–10µl buffer (water, TE, etc.); or Cell lysate in 5µl TCL or RLT Buffer + 1% beta-mercaptoethanol (BME) Single cells should be 1–100 cells per well, and cell populations should be 100–1000 cells per well Samples must be in 96 well Eppendorf twin.tec^® PCR LoBind or 96 well Eppendorf twin.tec^® PCR plates, sealed with Bio-Rad Microseal "F" foil; please ensure a tight seal seal around the edges as well as in between rows and columns Volume should be 5–10 µL per well, and all wells should have the same volume
Outputs	FASTQ files

Project Workflow- Single Cell Sequencing Services

Project onboarding
(contracting if required)

Regulatory Review
Quoting
Sample Kits

Sample intake and QC
(extraction optional)

Sample Receipt Incoming visual QC

Library construction

10x Single Cell Gene Expression (3′ or 5′)

10x Genomics Single Cell Multiome (ATAC-Seq + Gene Expression)

SmartSeq2 Single Cell Sequencing

Sequencing

Illumina^® sequencing technology

(system and flowcell type varies depending upon target sequencing coverage)

Data and report delivery
(bioinformatic analysis optional)

Data delivery to customer-owned cloud location in Google Cloud or Amazon Web Services; or Terra Workspace

To get started with your Single Cell project, please complete the form below, and a project manager will reach out to you.

Related Products

See our list of sequencing services to find the right one for your project

Single Cell Sequencing