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ivt-rna-synthesis-qpcr.md

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1# IVT mRNA/circRNA Synthesis, SPRI Purification & qPCR Quantification
2
3**URL:** https://cloud.ginkgo.bio/protocols/ivt-rna-synthesis-qpcr
4**Service terms:** https://cloud.ginkgo.bio/terms/ivt-rna-synthesis-qpcr
5**Reviewed:** 2026-09-30; prices and turnaround below are catalog estimates.
6**Status:** Ginkgo Certified
7**Price:** $99/sample
8**Turnaround:** up to 12 business days (extended: up to 17 business days for longer or clonal DNA constructs)
9**Throughput:** 384-well format throughout

IVT mRNA/circRNA Synthesis, SPRI Purification & qPCR Quantification

URL: https://cloud.ginkgo.bio/protocols/ivt-rna-synthesis-qpcr Service terms: https://cloud.ginkgo.bio/terms/ivt-rna-synthesis-qpcr Reviewed: 2026-09-30; prices and turnaround below are catalog estimates. Status: Ginkgo Certified Price: $99/sample Turnaround: up to 12 business days (extended: up to 17 business days for longer or clonal DNA constructs) Throughput: 384-well format throughout

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11## Overview
13End-to-end automated RNA production and quantification pipeline ("data in / data out"). Submit DNA sequences via CSV; Ginkgo sources DNA synthesis from commercial providers (e.g., Twist), then runs PCR template prep, in vitro transcription (linear mRNA or circRNA), SPRI bead purification, and qPCR quantification.
15**Note:** The circRNA pipeline is limited to Permuted Intron-Exon (PIE) with group I introns.
16Other RNA classes such as guide RNA, siRNA, and tRNA are outside this service scope.

Overview

End-to-end automated RNA production and quantification pipeline ("data in / data out"). Submit DNA sequences via CSV; Ginkgo sources DNA synthesis from commercial providers (e.g., Twist), then runs PCR template prep, in vitro transcription (linear mRNA or circRNA), SPRI bead purification, and qPCR quantification.

Note: The circRNA pipeline is limited to Permuted Intron-Exon (PIE) with group I introns. Other RNA classes such as guide RNA, siRNA, and tRNA are outside this service scope.

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18## Input
20- **DNA Input:** Sequences submitted via the CSV template (select linear mRNA or circRNA mode)

Input

  • DNA Input: Sequences submitted via the CSV template (select linear mRNA or circRNA mode)
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22## Output
24- Purified RNA samples in 384-well format with qPCR quantification readout
25- Spectrophotometric concentration and purity ratios (A260/A280, A260/A230) are available without a customer calibration standard
26- RT-qPCR is relative by default; absolute **qPCR** quantification requires a customer-supplied standard with identity and concentration
27- RNA integrity/fragmentation (including RIN-type assessment) is not measured
29The turnaround clock begins at order acceptance after usable input is received;
30commercial DNA synthesis lead time and shipping are excluded by the service terms.

Output

  • Purified RNA samples in 384-well format with qPCR quantification readout
  • Spectrophotometric concentration and purity ratios (A260/A280, A260/A230) are available without a customer calibration standard
  • RT-qPCR is relative by default; absolute qPCR quantification requires a customer-supplied standard with identity and concentration
  • RNA integrity/fragmentation (including RIN-type assessment) is not measured

The turnaround clock begins at order acceptance after usable input is received; commercial DNA synthesis lead time and shipping are excluded by the service terms.

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32## Automated Workflow

Automated Workflow

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34### Phase 1 - PCR Template Preparation
361. Transfer primers (Labcyte Echo)
372. Transfer templates (Labcyte Echo)
383. Stamp mastermix (Bravo 384)
394. PCR thermocycle (ATC384)

Phase 1 - PCR Template Preparation

  1. Transfer primers (Labcyte Echo)
  2. Transfer templates (Labcyte Echo)
  3. Stamp mastermix (Bravo 384)
  4. PCR thermocycle (ATC384)
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41### Phase 2 - In Vitro Transcription
431. Stamp mastermix (Bravo 384)
442. IVT incubation (ATC384)
453. Stamp DNase mix (Bravo 384)
464. Circularization for circRNA (ATC384)

Phase 2 - In Vitro Transcription

  1. Stamp mastermix (Bravo 384)
  2. IVT incubation (ATC384)
  3. Stamp DNase mix (Bravo 384)
  4. Circularization for circRNA (ATC384)
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48### Phase 3 - SPRI RNA Purification
501. Load decks with reagents (Bravo 384)
512. Magnetic bead purification (Bravo 384)
523. Unload decks (Bravo 384)

Phase 3 - SPRI RNA Purification

  1. Load decks with reagents (Bravo 384)
  2. Magnetic bead purification (Bravo 384)
  3. Unload decks (Bravo 384)
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54### Phase 4 - Quantify RNAs
561. Stamp RNAs (Bravo 384)
572. RNA yield / purity quantification (Lunatic)

Phase 4 - Quantify RNAs

  1. Stamp RNAs (Bravo 384)
  2. RNA yield / purity quantification (Lunatic)
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59### Phase 5 - Circularization Quantification
611. Echo qPCR setup (Labcyte Echo)
622. Stamp mastermix (Bravo 384)
633. Run RT-qPCR (CFX Opus)

Phase 5 - Circularization Quantification

  1. Echo qPCR setup (Labcyte Echo)
  2. Stamp mastermix (Bravo 384)
  3. Run RT-qPCR (CFX Opus)
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65## Ordering
67- **Samples:** configurable
68- **File Upload:** CSV, Excel, FASTA, TXT, PDF, ZIP (DNA sequences via CSV template)
69- **Additional Details:** free-text field for special requirements

Ordering

  • Samples: configurable
  • File Upload: CSV, Excel, FASTA, TXT, PDF, ZIP (DNA sequences via CSV template)
  • Additional Details: free-text field for special requirements
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71## Use Cases
73- mRNA production for screening and assay development
74- circRNA synthesis (PIE / group I intron designs)
75- High-throughput RNA generation with purity/yield readouts

Use Cases

  • mRNA production for screening and assay development
  • circRNA synthesis (PIE / group I intron designs)
  • High-throughput RNA generation with purity/yield readouts
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