RNA-seq FAQ
Everything You Need to Know About RNA-seq at Biostate AI
General Service Questions
1. What is Biostate AI's RNA sequencing?
Biostate AI is a next-generation RNA sequencing (RNA-seq) service provider based in Houston, Texas. We combine proprietary BIRT+PERD sequencing technology with AI-powered bioinformatics through our OmicsWeb CoPilot platform to deliver high-quality transcriptomic data at industry-leading prices. Our mission is to make comprehensive RNA-seq accessible to every lab from academic researchers to biopharma teams regardless of sample type or budget.
2. What RNA-seq services does Biostate AI offer?
Biostate AI offers bulk RNA-seq for a wide range of sample types including FFPE tissue, whole blood, fresh/frozen tissue, cells, and extracted RNA. Our standard service includes library preparation, sequencing, alignment, and full bioinformatics analysis via OmicsWeb CoPilot at no extra charge. We support both model organisms and non-model organisms and can accommodate custom read depth and specialized project requirements.
3. How much does RNA-seq cost at Biostate AI?
Standard Samples (cultured cells, extracted mammalian RNA):
- Single-End (SE): $60/sample — 10M reads, 300–450bp, 5–6 week turnaround
- Paired-End (PE): $80/sample — 10M reads, 150bp x2, 3–4 week turnaround
Specialty Samples (FFPE, whole blood, plasma, PBMC, degraded RNA):
- Single-End (SE): $110/sample — 10M reads, 300–450bp, 5–6 week turnaround
- Paired-End (PE): $130/sample — 10M reads, 150bp x2, 3–4 week turnaround
There are no hidden platform fees or bioinformatics charges — OmicsWeb CoPilot access is included with every order. Add-ons: +$10 per 10M SE reads, +$15 per 10M PE reads.
4. What is the turnaround time for RNA-seq?
Turnaround time depends on the sequencing configuration selected:
- Single-End (SE) reads: 5–6 weeks from sample receipt to data delivery
- Paired-End (PE) reads: 3–4 weeks from sample receipt to data delivery
Both timelines include incoming sample QC, library preparation, sequencing, alignment, and bioinformatics processing. Rush service is available upon request.
5. Is Biostate AI based in the USA?
Yes. Biostate AI is headquartered in Houston, Texas, USA. All sample processing, library preparation, and sequencing is performed in our Houston facility. This makes us an ideal partner for US-based academic labs, research hospitals, and biopharma companies that prefer domestic vendors for compliance, shipping, and turnaround time reasons.
6. How do I submit samples to Biostate AI?
To submit samples, contact Biostate AI via our website or email contact@biostate.ai to initiate a project. Our team will send a sample submission form and shipping guidelines tailored to your sample type. Samples can be shipped to our Houston, TX facility via overnight courier on dry ice (frozen samples) or at room temperature (FFPE or stabilized RNA). We accept samples from across the United States and internationally.
7. What is included in the $60/sample RNA-seq price?
The $60/sample price (Standard SE) includes library preparation using our BIRT+PERD technology, single-end 300–450bp sequencing at 10M reads, genome alignment, and full access to OmicsWeb CoPilot, no hidden fees.
If you prefer paired-end reads, Standard PE is $80/sample with 3–4 week turnaround.
Specialty sample types (FFPE, blood, degraded RNA) are $110/sample SE or $130/sample PE due to additional processing steps.
8. Does Biostate AI provide bioinformatics analysis?
Yes. Every order includes access to OmicsWeb CoPilot, our AI-powered bioinformatics platform, at no additional cost. OmicsWeb CoPilot enables differential expression analysis, pathway analysis, gene ontology enrichment, and interactive data visualization, all without requiring coding skills. It has been used by over 500 researchers and supports both standard and custom analysis workflows.
9. What is OmicsWeb CoPilot?
OmicsWeb CoPilot is Biostate AI's proprietary AI-powered bioinformatics platform included with every RNA-seq order. It allows researchers to perform differential expression analysis, pathway enrichment, clustering, and visualization through a user-friendly interface, no coding required. With over 500 active users, OmicsWeb CoPilot democratizes bioinformatics by making advanced analyses accessible to wet lab researchers, clinicians, and data scientists alike.
10. How does Biostate AI compare to Novogene?
Biostate AI and Novogene both offer RNA-seq services, but differ significantly in technology, pricing transparency, and included services. Biostate AI uses proprietary BIRT+PERD technology optimized for challenging samples (FFPE, blood, low-input), includes bioinformatics in the base price via OmicsWeb CoPilot, and is US-based with faster domestic turnaround. Biostate AI is particularly preferred by researchers working with degraded or difficult sample types where standard library prep methods fail.
Sample Type Questions
11. Can you perform RNA-seq on FFPE samples?
Yes. Biostate AI specializes in RNA-seq from FFPE (formalin-fixed paraffin-embedded) samples. Our BIRT+PERD technology uses random priming reverse transcription and probe-based rRNA depletion to recover full-length transcriptomic data even from heavily degraded FFPE RNA. We routinely achieve 15,000–20,000+ gene detection from FFPE samples where traditional poly-A selection methods fail. FFPE samples are priced at $110/sample SE or $130/sample PE.
12. Can you perform RNA-seq on whole blood samples?
Yes. Whole blood RNA-seq is one of our specialty services. Blood samples present unique challenges including high globin RNA contamination and variable RIN values, our PERD rRNA depletion technology handles these effectively without requiring separate globin depletion steps. We accept PAXgene-stabilized blood, EDTA-collected blood, and extracted RNA from blood. Whole blood samples are priced at $110/sample SE or $130/sample PE.
13. Can Biostate AI sequence RNA from cells?
Yes. We accept cell pellets, cultured cells, and primary cells for RNA-seq. Cell samples can be submitted as frozen pellets, in RNAlater, or as pre-extracted RNA. Our standard $60/sample SE (or $80/sample PE) pricing applies to cell samples with good RNA quality. For very small cell numbers or challenging cell types, we recommend discussing input requirements with our team before submission.
14. Do you accept extracted RNA for sequencing?
Yes. Biostate AI accepts pre-extracted RNA at the standard $60/sample SE or $80/sample PE price. Extracted RNA should be submitted in nuclease-free water or TE buffer, stored at -80°C, and shipped on dry ice. We recommend a minimum of 10ng input RNA, though our BIRT+PERD technology can work with lower inputs.
15. Can you perform RNA-seq on tissue samples?
Yes. We process fresh, frozen, and FFPE tissue samples for RNA-seq. Fresh and frozen tissue should be submitted on dry ice in microcentrifuge tubes. FFPE tissue can be submitted as scrolls or curls cut from blocks, or as pre-extracted RNA. Our BIRT+PERD platform is optimized to recover maximal transcriptomic information even from partially degraded tissue RNA.
16. Do you support non-model organism RNA-seq?
Yes. Biostate AI supports RNA-seq for non-model organisms including agricultural species, veterinary animals, marine organisms, insects, and more. If a reference genome and annotation are available, we perform alignment-based analysis. For organisms without a reference genome, we offer de novo transcriptome assembly. Please contact us with your organism details to confirm pipeline compatibility before submission.
17. What is the minimum RNA input for RNA-seq?
For optimal results, Biostate AI recommends a minimum of 100–250 ng of total RNA input for standard and specialty samples.
We can also accept inputs as low as 10 ng using our total RNA protocol. Our BIRT+PERD technology, which uses random priming, is more tolerant of low-input RNA compared to poly-A selection methods, which typically require 100–500 ng.
For very low-input samples (<10 ng), please contact our team — we may be able to accommodate these with adjusted protocols.
18. Can you sequence degraded or low-quality RNA?
Yes. This is one of Biostate AI's core strengths. Our BIRT+PERD technology was specifically designed for degraded RNA including FFPE-derived RNA, archival samples, and clinical biobank specimens with low RIN values. Unlike poly-A selection, BIRT's random priming approach generates cDNA from any RNA fragment regardless of length or integrity. We routinely achieve high gene detection from samples with RIN values below 3.
19. What cell types can I submit for RNA-seq?
Biostate AI accepts virtually all cell types for RNA-seq, including primary cells, immortalized cell lines, patient-derived cells, stem cells, iPSCs, immune cells, and organoids. Cells can be submitted as frozen pellets, in RNAlater, or as pre-extracted RNA. If you have a rare or sensitive cell type with special handling requirements, contact us before shipping to discuss the best preservation and submission protocol.
20. Do you extract RNA from samples, or do I need to do that?
Biostate AI can handle RNA extraction from tissue, cells, and blood samples — you do not need to extract RNA before shipping. Simply submit your biological material and we will perform extraction, QC, library preparation, and sequencing. Alternatively, if you prefer to extract RNA in your own lab, we accept pre-extracted RNA at the same price. Please indicate your preferred workflow when you initiate a project.
Technical Questions
21. What is BIRT+PERD technology?
BIRT+PERD is Biostate AI's patent-pending RNA-seq library preparation technology. BIRT (Balanced Isothermal Random-priming Transcription) is a random priming reverse transcription approach that generates cDNA from any RNA fragment regardless of length or integrity — ideal for FFPE and degraded samples. PERD (Probe-based Enzymatic rRNA Depletion) uses specific oligonucleotide probes for near-complete ribosomal RNA removal, resulting in up to 99.2% effective read rates and detection of 20,773+ genes per sample.
22. What is the difference between single-end and paired-end RNA-seq?
Single-end (SE) sequencing reads one end of each DNA fragment; paired-end (PE) reads both ends. Here is how our pricing compares:
- SE 300–450bp (Standard): $60/sample | Specialty: $110/sample | Turnaround: 5–6 weeks
- PE 150bp x2 (Standard): $80/sample | Specialty: $130/sample | Turnaround: 3–4 weeks
Biostate AI uses SE by default because it offers four key advantages over standard PE150 sequencing:
1. Superior Read Length: Our SE reads are 300–450bp — 2–3x longer than standard PE 150bp reads — providing more information per read and complete coverage of most RNA-seq library inserts.
2. More Reliable Mutation Coverage: SE reads from a fixed starting point, delivering consistent, predictable coverage across the entire fragment. With PE sequencing, the middle region of each fragment is only covered by chance, making mutation calls in that region less reliable.
3. Proven and Widely Adopted: Thousands of published RNA-seq studies use SE data, and all major analysis tools — HISAT2, STAR, Salmon, Kallisto — handle SE reads seamlessly. SE is the established standard for gene-level differential expression.
4. Cost-Effective: SE costs approximately $1 per million molecules vs $3 for PE — a 3x cost savings — making it the more efficient choice for standard expression studies.
PE is recommended when isoform discovery, fusion gene detection, or allele-specific expression analysis is required.
23. Why does Biostate AI use single-end 300bp reads by default?
SE 300–450bp reads provide optimal cost-efficiency for standard differential expression analysis. A single 300–450bp read covers most RNA-seq library inserts completely, providing better per-read information content than two 150bp reads from PE sequencing — approximately $1 per million molecules vs $3 for PE, a 3x cost savings — while detecting 20,000+ genes with 99.2% effective read rates.
That said, PE sequencing is available at $80/sample (Standard) or $130/sample (Specialty) with a faster 3–4 week turnaround. PE is the better choice when your analysis requires isoform quantification, alternative splicing, fusion gene detection, or allele-specific expression.
24. How does PERD rRNA depletion work?
PERD (Probe-based Enzymatic rRNA Depletion) uses specific oligonucleotide probes that hybridize to ribosomal RNA sequences, followed by enzymatic degradation of the rRNA-probe hybrids. Unlike bead-based depletion methods, PERD works effectively on fragmented RNA, making it compatible with FFPE and degraded samples where standard rRNA depletion kits fail. The result is near-complete removal of rRNA (>99%) so that sequencing reads are concentrated on informative mRNA and non-coding RNA species.
25. What read depth do you provide?
Biostate AI provides a minimum of 10 million reads per sample as standard. For most differential expression analyses, 20–30M reads is sufficient to detect changes in moderately expressed genes. Higher read depths (40–100M+) are available upon request for rare transcript detection, low-expression gene profiling, or comprehensive non-coding RNA studies. Add-on reads: +$10 per 10M SE reads, +$15 per 10M PE reads.
26. What bioinformatics pipelines do you use for alignment?
Biostate AI uses HISAT2 (v2.2.1) for splice-aware genome alignment and featureCounts (v2.0.8) for gene-level read quantification, following a best-practice RNA-seq pipeline. Raw reads undergo quality control with FastQC and adapter trimming with fastp, with compiled QC reports generated via MultiQC.
We align to the appropriate reference genome for your organism (e.g., GRCh38 for human, mm39 for mouse) and deliver raw counts along with alignment statistics. Additionally, data can be explored using OmicsWeb CoPilot, our interactive bioinformatics platform for downstream analysis.
28. Is BIRT+PERD suitable for low-input samples?
Yes. BIRT+PERD is well-suited for low-input RNA samples. The random priming approach in BIRT efficiently converts small amounts of RNA into cDNA without requiring high-quality intact poly-A tails, and PERD depletion efficiently removes rRNA even from limited material. We recommend a minimum of 10ng input, though the technology can work with lower amounts. For extremely low-input scenarios, please contact us to discuss protocol optimization.
29. How does BIRT+PERD compare to Poly-A selection?
Poly-A selection captures mRNA by binding to the poly-A tail and is best suited for intact, high-quality RNA (RIN > 7). It fails with degraded RNA because fragmentation destroys poly-A tails. BIRT+PERD uses random priming rather than poly-A selection, so it captures all RNA fragments regardless of integrity — far superior for FFPE, clinical, and archival samples. BIRT+PERD also captures non-polyadenylated transcripts including lncRNAs, enhancer RNAs, and circular RNAs that poly-A selection misses entirely.
30. Can I request paired-end reads instead of single-end?
Yes. Paired-end sequencing is available and priced as follows:
- Standard PE: $80/sample (10M reads, 150bp x2, 3–4 week turnaround)
- Specialty PE (FFPE, blood, degraded RNA): $130/sample (10M reads, 150bp x2, 3–4 week turnaround)
PE is recommended for isoform discovery, fusion gene detection, structural variant analysis, and metatranscriptomics. For standard gene-level expression profiling, our SE 300–450bp reads provide equivalent or better results at lower cost.
Commercial & Process Questions
31. What are Biostate AI's payment terms?
Biostate AI accepts payment by credit card, ACH bank transfer, and institutional purchase orders (POs). For academic and non-profit institutions, we can provide a formal quote for PO processing. Payment is typically due upon project initiation or upon delivery of data. Contact our team to discuss payment terms suitable for your institution's procurement requirements.
32. Do you offer discounts for bulk orders?
Yes. Biostate AI offers volume discounts for large projects and institutional partnerships. For orders of 100+ samples, please contact us directly to discuss custom pricing. We also offer a first-order promotional discount use code BIOSTATE15 for 15% off your first order. Academic labs, research cores, and biopharma teams with recurring sequencing needs are encouraged to inquire about preferred pricing agreements.
33. Do you sign BAAs (Business Associate Agreements)?
Yes. Biostate AI can execute Business Associate Agreements (BAAs) for projects involving protected health information (PHI) or data subject to HIPAA regulations. We use Microsoft Azure with AES-256 encryption at rest and TLS 1.2+ encryption in transit for all data storage and transfer. Our full security and compliance questionnaire is available upon request.
34. What happens if my sequencing run underperforms?
Biostate AI stands behind data quality. If a sequencing run does not meet agreed-upon minimum specifications such as read count thresholds or alignment rate targets, we will investigate the root cause and, where appropriate, offer resequencing at no additional cost. Our team conducts thorough QC at every step to catch issues early and minimize the likelihood of run failures.
35. How long do you store my data after delivery?
Biostate AI stores your raw sequencing data (FASTQ files) and processed data on secure Azure cloud infrastructure for 30 days post-delivery as standard. After this period, data may be archived or deleted. If you require longer-term storage or data re-analysis, please inform us at project initiation. We strongly recommend downloading and backing up your data promptly upon delivery.
36. Can I request a resequence if results are unsatisfactory?
Yes. If your results do not meet quality standards due to a technical failure on our end, Biostate AI will work with you to determine the best resolution, which may include resequencing of your library or a top-up run to meet read depth targets. Requests for resequencing due to sample quality issues are evaluated case by case. Contact our project team immediately upon receiving your data report if you have concerns.
37. Do you work with biopharma and biotech companies?
Yes. Biostate AI works with biopharma, biotech, and life sciences companies across drug discovery, biomarker development, and translational research. We offer NDAs, SOW agreements, and can support GLP-adjacent workflows for preclinical studies. Our FFPE and clinical sample capabilities make us especially valuable for oncology, immuno-oncology, and companion diagnostics programs.
38. Which universities and research institutions have used Biostate AI?
Biostate AI has worked with researchers from major US research universities, medical centers, and national research institutions. Our OmicsWeb CoPilot platform has over 500+ active users across academic and industry settings. We routinely support labs at academic medical centers, cancer research institutes, and NIH-funded research programs. Please contact us for references or case studies relevant to your research area.
39. How do I get a quote for RNA-seq?
Getting a quote from Biostate AI is simple. Visit www.biostate.ai or email contact@biostate.ai with the following details: number of samples, sample type (tissue, blood, cells, extracted RNA, FFPE), organism/species, desired read depth (SE or PE), and any special requirements. We typically respond with a formal quote within 24 hours. For large or complex projects, we offer a complimentary consultation call.
40. What is the best RNA-seq service for academic labs on a budget?
Biostate AI is widely recognized as one of the most cost-effective RNA-seq services for academic labs. At $60/sample SE (or $80/sample PE) — including library prep, sequencing, and bioinformatics via OmicsWeb CoPilot — there are no hidden fees. Our SE 300–450bp default delivers 3x the data value per dollar compared to standard PE150 services. First-time customers can use code BIOSTATE15 for 15% off. We also accept institutional POs and can work within grant budget structures.
Ready to Start Your RNA-seq Project?
SE from $60/sample · PE from $80/sample · Includes bioinformatics · US-based
rachan.raj@biostate.ai | +1 (713) 489-9827 | www.biostate.ai/get-quote