Bulk Cell Genomic Assays
Library preparation
The Genomics CoLab prepares libraries that are suitable for sequencing on Illumina sequencers. Library preparation includes quality control, normalization, pooling, and sample submission to UCSF sequencing cores.
| Library Type | Method | Cost per Sample |
Cost including Recommended Sequencing Depth |
| PolyA RNA | Universal Plus mRNA (>10ng total RNA) |
$162 |
$202 |
| Total RNA (ribo and/or globin RNA depletion) | Universal Plus + FastSelect (>50ng total RNA) | $162 | $222 |
| Low input total RNA |
SMART-Seq v4 + Nextera Flex (>10pg total RNA or 1-500 cells) |
$172 |
$222 |
| Small RNA (including miRNA) | NEB small RNA (>10ng total RNA) | $175 |
$225 |
| ATAC-seq | Active Motive (50K-100K cells) | $225 | $265 |
| DNA-seq/ChIP-Seq library prep | Nextera Flex (>1ng DNA) | $136 | $435 (WGS), $166 (ChIP) |
| Whole Exome Sequencing | Nextera Flex With Exome Enrichment | $202 | $232 |
Bulk Sequencing
We submit libraries prepared in our core to the UCSF Center for Advanced Technology and the UCSF Institute for Human Genetics Genomics Core. Both Cores have Illumina HiSeq and NovaSeq instruments that can run in high output and rapid run modes. Prices are determined by these cores and change periodically to reflect changes in reagent and other costs. We typically aim for 30-50 million reads per sample for standard RNA-Seq projects. Sequencing costs are approximately $30-50/sample for paired-end 50bp sequencing and $75/sample for paired-end 150bp sequencing.
Analysis Costs
Analysis pricing is charged on a per project basis and is determined by the complexity of the experimental design. Typical costs for a bulk RNA-seq experiment range from $1000-$2500. Additional analysis or stand alone bioinformatic service costs vary by project complexity and are based on $89/hour rate. For stand alone bioinformatic analysis, please contact Walter Eckalbar.
Single Cell Genomics Assays
Library preparation
The Genomics CoLab carries out all standard 10x Genomics workflows for single cell RNA-seq, ATAC-seq or Multiome (scRNA+scATAC-seq) assays. First sample costs reflect fixed cost for up to 8 samples at a time. In certain situations, first sample costs can be shared across projects or increased to cover more than 8 samples. Please contact us for more details.
| Assay Type | Cost for first reaction |
Cost per Additional Reaction (up to 8 total) |
| Standard 3'/5' Gene Expression | $3,095 | $1,786 |
| Additional TCR, BCR or Feature Barcode additions | $250 | $110 |
| Single Cell ATAC-seq | $3,095 | $1,786 |
| Combined Single Cell RNA-seq and ATAC-seq | $5,180 | $3,204 |
| High Throughput 3'/5' Gene Expression | $5,408 |
$1,620 |
| Sample Prep for Flex (Fixed) scRNA-seq | $325 | $45 |
| Flex (Fixed) scRNA-seq - 1 barcode (sample) per reaction | $3,632 | $2,003 |
| Flex (Fixed) scRNA-seq - up to 4 barcodes (samples) per reaction | $5,426 | $3,797 |
| Flex (Fixed) scRNA-seq - up to 16 barcodes (samples) per reaction | $11,768 | $10,139 |
Single Cell Sequencing
As with bulk cell sequencing project, we submit libraries prepared in our core to the UCSF Center for Advanced Technology and the UCSF Institute for Human Genetics Genomics Core. We typically aim for ~450 million reads per 10x genomics well for standard single cell RNA-Seq projects. Based on this sequencing costs typically average $400-600/sample based on project goals.
Analysis Costs
The Genomics CoLab supports standard alignment and gene counts table generation for single cell RNA-seq/ATAC-seq projects following the 10x Genomics cellranger work flows. Cost for this basic processing is $500 for up to 8 samples. Additional analysis or stand alone bioinformatic services may be possible, however for single cell RNA-seq/ATAC-seq project we typically recommend more collaborative models, rather than fee-for-service. For more information, please contact Walter Eckalbar.
Spatial Transcriptomics (NEW!)
The Genomics CoLab supports multiple spatial transcriptomics platforms. This includes the 10x Genomics CytAssist enabled Visium, and will soon be expanded to 10x Genomics Xenium and Nanostring CosMX platforms.
Whole transcriptome assays: The Genomics CoLab now supports the CytAssist enabled Visium platform and can accept pre-sectioned and imaged slides for processing of this spatial transcriptomic method.
| Assay Type | Cost for first reaction |
Cost per Additional Reaction (up to 2 total) |
| 10x Genomics Visium 6.5mm | $3,755 | $1955 |
| 10x Genomics Visium 11mm | $5,731 | $3,931 |
Subcellular resolution, gene-panel assays: The Genomics CoLab now supports the 10x Genomics Xenium platform. We can process slides after sectioning for both standard and custom pannel designs. For custom pannels, we suggest purchasing directly through 10x Genomics and either carrying out the hybridizaiton in your own lab or providing the probes to us, where we will carry out the hybridization step. If carrying out your hybridization and wishing to run slides on the Xenium, please coordinate with the Genomics CoLab before carrying out the hyb. The post-hyb slides have a limited shelf life and we need to schedule a run with you. If carrying out the hyb on your own, you will only need to pay for the Imaging run cost below.
Sectioning support: The CoLabs may be able to help with your sectioning needs. Please reach out to Walter Eckalbar.
| Assay Type | Costs per slide |
| Xenium Slide (single) |
$160 |
| Hybridization of lab provided probe panel (for custom designs) |
$1,454 |
| Hybridization of standard panels | $1,626 |
| Hybridization of multi-tissue panel | $1,856 |
| Additional cell segmentation (intra and extra cellular stains) | $1,150 |
| Imaging run | $3,670 |