Single-Cell Sequencing

To initiate a single-cell sequencing project, please contact us. Project consultation is provided free-of-charge. Consultation with the core prior to starting a single-cell sequencing experiment is highly recommended to ensure accomplishment of project goals.

Single-cell sequencing services can be requested through NUcore.

For all single-cell sequencing services, please make a sample submission appointment with us in advance.

• 10x Genomics platform: Users prepare fresh or fixed cells (or nuclei) and submit it to NUSeq Core for sample QC.
• Parse Bioscience platform: Users prepare fixed cells (or nuclei) for all samples and submit them to NUSeq Core for library construction.
• SMART-Seq platform: Users collect cell(s) in 0.2mL tube and store at -80°C until sample submission to NUSeq Core.

10x Genomics Chromium Libraries: RNA-Seq Libraries – Read 1 of 28 bp (Cell Barcode and UMI), i7 Index of 10 bp (Sample Index), i5 Index of 10 bp (Sample Index), and Read 2 of 90 bp (Transcript Insert) with a sequencing depth of >20,000 reads per cell; ATAC-Seq Libraries – Read 1 of 50 bp (Transposed DNA), i7 Index of 8 bp (Sample index), i5 Index of 16 bp (10x Barcode) and Read 2 of 49 bp (Transposed DNA) with a sequencing depth of >25,000 reads per cell

Parse Biosciences Libraries: Read 1 of 74 bp, i7 Index of 6 bp, i5 Index of 0 bp, and Read 2 of 86 bp with a sequencing depth of > 20,000 reads per cell

Manual Low-Throughput scRNA/scDNA-Seq: RNA-Seq - Single-end 50 bp reads at desired sequencing depth (e.g., 20-25 million reads per mammalian sample); DNA-Seq – Paired-end 150 bp reads often used at desired sequencing depth (e.g., 30x coverage for single-cell whole genome sequencing)

Data analysis is provided upon request.

From sample submission to library preparation it typically takes 2 weeks. It takes another 2-3 weeks for sample to be sequenced followed by up to 2 weeks for raw sequence demultiplexing and read alignment.

For cell, we recommend the cell viability of >70%. For nucleus, please consult us to ensure the sample quality is good for 10x Genomics platform.

Yes. This is achievable. Please consult the core for more specifics.

Yes. This is achievable. Please consult the core for more specifics.

Please contact NUSeq (NUSeq@northwestern.edu) and we will help you through the whole workflow from sample preparation to library construction to data analysis.

From sample submission to library preparation it typically takes 3 weeks. It takes another 2-3 weeks for sample to be sequenced followed by up to 2 weeks for raw sequence demultiplexing and read alignment.

For Parse Bioscience platform, all fixed samples should be submitted to us all at once. For 100,000 cell and 1,000,000 cell kit, users can submit up to 48 and 96 samples, respectively.

For cell, we recommend using 1 million cells with cell viability of >70% prior to fixation. For nucleus, please consult us to ensure the sample quality is good.

Yes. This is achievable. Please consult the core for more specifics.

Please contact NUSeq (NUSeq@northwestern.edu) and we will help you through the whole workflow from sample preparation to library construction to data analysis.

For sorted cell, please provide us 2-4 individual samples for protocol optimization. Please collect cell by sorter or manual pipetting in 0.2 mL tube with up to 3 µL of 1X PBS Buffer. Please store cells at -80°C until sample submission to NUSeq Core.

Please contact NUSeq (NUSeq@northwestern.edu) and we will help you through the whole workflow from sample preparation to library construction to data analysis.