US Based · Single Cells & Trace Inputs
Ultra-Low Input RNA Sequencing Service
High-sensitivity transcriptomic data from trace samples — rare cell populations, laser capture microdissection, and liquid biopsies. Takara SMART-Seq chemistries run end-to-end in our SF Bay Area lab.
Library prep
Takara SMART-Seq mRNA
RNA input
10 pg–10 ng, 1–1,000 cells
Sequencing
NovaSeq X+ PE150
Read depth
20M paired reads
Turnaround
Expedited available
Price
$250/sample
Volume pricing available
Service Highlights
From low input RNA to results, all in one lab
Send sorted cells, lysates, or purified RNA. Every stage is performed in-house with defined QC criteria and validated Takara SMART-Seq chemistry built for trace inputs.
Extraction & Sample QC
- >10 pg Total RNA in 15 µl
- Qubit & Fragment Analyzer QC
- Cells in lysis buffer for direct input
Library prep
- Takara SMART-Seq mRNA
- Oligo-dT full-length capture
- LNA template switching
Sequencing
- Illumina NovaSeq X+ PE150
- 20M paired reads
- UMI-corrected duplicate removal
Analysis
- 3–4 week turnaround
- >15k transcripts
- Secure FTP, S3 or BaseSpace
Sample Requirements
Check your sample compatibility
Oligo-dT capture validated for human, mouse and rat, and adaptable to any eukaryote with polyA transcripts.
| Sample type | SAMPLE REQUIREMENTS |
|---|---|
| Purified RNA | Preferred 10 ng in 15 µl, RIN >7 Lowest limit 10 pg in 15 µl, RIN >7 |
| Sorted cells | >10,000 cells for extraction 50–1,000 in lysis buffer for direct input |
| Tissue | Small flash-frozen pieces, e.g. 3 mm punch biopsies |
| Micro-dissected tissue (LCM) | Captured structures collected directly into approved lysis buffer and flash-frozen immediately. No column extraction. |
| Aspirates & biofluids | Fine needle aspirates, or plasma and serum for cfRNA. Contact us for volume guidance and plasma processing requirements. |
Alternative workflows
Have higher input, degraded or few cells? Your samples may be compatible with other services.
Need true single cell or low input immune profiling services?
Technical excellence
Built for degraded and cross-linked RNA
Automated liquid handling removes operator variance, so your samples stay comparable — whether that is eight or eight hundred.
Illumina NovaSeq X Plus with PE75 or PE150 chemistry. 10–20M reads suits expression profiling and clustering; 30–50M for deep clinical or transcription factor work; 70M+ for rare splicing and lncRNA discovery.
Service experience
Working with us
Every project is run by scientists, tracked in one portal, and processed entirely in our own lab.
PhD-Level Project Oversight
A PhD scientist owns your project from design through interpretation.
Dedicated Project Manager
One point of contact from quote through delivery.
Easy Ordering
Register samples, track status, and download results in one portal.
100% US-Based
Every stage runs in-house in Foster City, CA. No outsourcing.
Resources & insights
Technical resources
Spec Sheet
Low-Input RNA-Seq Service Overview
SMART-Seq mRNA chemistry, input thresholds, read depth options, and deliverables.
BLOG
Choosing the Right library prep for Low-Input RNA-Seq
In transcriptomics, sample quality often dictates experimental success.
BLOG
Don’t Waste Your Rare Cells: A Guide to Low-Input Sample Prep
Sorting buffers, lysis, and flash-freezing steps that protect precious samples.
Frequently asked questions
Planning your low-input project
Samples & service
What samples are compatible with ultra-low input?
Intact isolated cells, cell lysates, clinical fine needle aspirates, micro-dissected tissue, and plasma or serum biofluids. Our team will guide you to the right collection and lysis protocol for your material.
Can you handle single cells without prior extraction?
Yes. Sorting intact cells directly into our validated lysis buffer and flash-freezing immediately is our preferred method — it avoids the severe nucleic acid adsorption losses common to column extraction.
What species are supported?
Human, mouse and rat are fully validated. Any eukaryote with polyadenylated transcripts and a reference genome can be supported — contact us to discuss your organism.
Which library prep kits do you use?
Takara SMART-Seq mRNA, an oligo-dT primed full-length chemistry built for ultra-low input. If your material is degraded or you need non-coding RNA, that runs on a different workflow — see our degraded and FFPE RNA-Seq service.
Data & delivery
What sequencing depth should I choose?
10–20M reads per sample covers cost-effective profiling and standard differential expression. 30–50M expands the dynamic range for deep clinical expression and transcription factor work. 70M+ suits alternative splicing, low-abundance transcripts, and isoform discovery.
Why do my ultra-low input samples show high duplication rates?
How long is my data available for download?
Can I add analysis after I have received the FASTQ files?
Yes. Analysis can be added any time. If within the 60-day data retention window you will not need to resubmit the data. Contact your project manager and we will quote the additional analysis.
Ordering & logistics
How do I place an order?
Submit your inquiry below and our team will help create an account and walk you through submitting your samples.
How do I ship samples, and under what conditions?
What is your typical turnaround time?
Standard turnaround is 3 to 4 weeks from the day your samples pass incoming QC to final data delivery. Expedited processing is available on every order, in 10 to 14 business days — just ask your project manager.
Is there a minimum number of samples per project?
There is no order minimum. We do recommend at least three biological replicates per condition for reliable differential expression, and per-sample pricing improves with batch size.
Get started with your project
Ready to accelerate your transcriptomic research? Contact our team for a technical consultation. We will guide you through low-input sample requirements and direct sorting options aligned to your analysis goals.
- $250/sample, with volume pricing available
- Data in 3 to 4 weeks
- Unbiased full-length amplification
- 100% in-house at Foster City, CA