Getting Started

What we need. How we get there.

Auperon works from your RNA-seq data. The essentials fit on one page. The full sample prep, vendor coordination, and shipping protocol is downloadable as a PDF or Word doc you can hand your bench team.

The input, at a glance

Auperon is built on RNA-seq depth done right.

50-150M
Read depth
paired-end reads per sample
Ribo-zero
Library prep
preferred over poly-A selection
≥5 × 10⁶
Cells per sample
frozen pellet minimum
2-8 wks
Analysis turnaround
after we receive your data

For microbial systems
Different defaults apply. 30M PE reads · rRNA depletion · RNAlater workflow · no LN2 required. See the microbial protocol.

Three ways to get us your data

Existing. New. Or public.

Auperon works from RNA-seq data — we don't run sequencing, coordinate vendors, or handle sample logistics. You send us data in one of three ways.

Path A

Existing data

Best if: you already have RNA-seq data from a prior study, ongoing program, or vendor delivery.

  • Send FASTQs — we start analysis immediately
  • Include a short description of experimental design (conditions, replicates, timepoints)
  • We evaluate whether your data supports the analysis and flag any augmentation needs at scoping
Path B

Generate new data

Best if: you don't yet have sequencing and need to generate it for this project.

  • Follow the downloadable sample prep protocol below
  • Run sequencing with the vendor of your choice — in-house core, CDMO, Novogene, Genewiz/Azenta, or others
  • Send us the FASTQs when your vendor delivers them
  • Auperon doesn't manage sequencing vendors or handle sample logistics
Path C

Point us to public data

Best if: you want to explore a hypothesis using published or repository data.

  • Send us the dataset ID and citation (GEO, SRA, ENA, ArrayExpress)
  • We evaluate whether the data supports the analysis you want
  • Good fit for feasibility work and discovery before committing to your own sequencing
Need more than data analysis?

Van Heron Labs full-service.

If your engagement needs sequencing coordination, vendor management, sample prep guidance, custom multi-omics beyond RNA-seq, or downstream commercial work, that's Van Heron Labs full-service — the enterprise pathway that handles the pipeline end-to-end.

What we handle

Cells, data formats, special cases.

Wide flexibility on inputs. If your setup falls outside the defaults, tell us at scoping and we adjust.

Data formats

  • Bulk RNA-seq — mammalian — recommended (rRNA depletion, 50-150M PE)
  • Bulk RNA-seq — microbial — recommended (rRNA depletion, ~30M PE)
  • Oxford Nanopore / long-read — supported for isoform + operon work
  • Full-length poly-A prep — supported, analysis weighted differently
  • Single-cell RNA-seq (droplet, 3′ biased) — supported, with caveats*
  • Existing published data — supported for feasibility work
*Ambient RNA contamination affects nearly all droplet single-cell datasets — flag single-cell workflows at scoping. We do not recommend bulk 3′-biased methods (QuantSeq-style, ultra-cheap shortcuts) for Auperon analysis — see the protocol for the full reasoning. Note the format at kickoff — we adjust analysis parameters to match.

Cell types

  • Mammalian bioprocessing — CHO, HEK
  • Stem cells — iPSC, ESC, MSC, hSC
  • Immune cells — CD4, CD8, TIL, Treg, NK
  • Structured 3D systems — embryoid bodies, synthetic embryos
  • Viral vector & microbial — production cells, E. coli, yeast
Novel or exploratory cell type? Tier 1 discovery is designed for exactly that.

Special cases

Default: ship cells (frozen pellets for mammalian, RNAlater-preserved for microbial); the sequencing vendor handles RNA extraction. This reduces batch effects, standardizes with library prep, and saves on extraction kits. Exceptions:

  • HPL & biofluids — extract RNA on your side, ship purified RNA
  • Low cell yield (<5 × 10⁶) — on-site extraction, ship purified RNA
  • BSL2+ material — vendor approval required in advance
  • Regulatory / GMP / chain-of-custody — extract in-house under your quality system
  • Hard-to-lyse organisms (mycobacteria, spore-formers, biofilms) — in-house specialized lysis if you have it
All handled in the downloadable protocols — recommended kits, vendor rules, and full reasoning included.
Sample prep protocols · PDF or DOCX

The full protocol, on paper.

Hand it to your bench team. We publish two versions — pick the one that matches your system.

For mammalian systems

CHO, HEK293, T cells, iPSCs, MSCs, and other mammalian cell lines. Frozen cell pellet workflow (LN2-based). 14 pages.

For microbial systems

Bacteria (gram-positive and gram-negative) and eukaryotic microbes (yeast, fungi). RNAlater-based workflow — no LN2 required. 15 pages.

Both protocols cover
  • Sequencing input requirements & depth targets
  • Sample capture — timing by study goal
  • Cell-type-specific sample prep workflow
  • Sample labeling & naming best practices
  • Tubes, storage & safe handling
  • Shipping best practices (dry ice, courier, docs)
  • Single-cell contamination awareness
  • Quality standards & refund policy
Quality standards

Confidence in the data underneath.

Every dataset gets internal QC before we begin full analysis — read quality, alignment rate, depth against the tier target, library complexity, and comparability across the experimental design.

If sequencing fails our QC — meaning it's uninterpretable at the level required to produce mechanism-backed output — we refund the engagement in full and provide our recommendations on experimental design for a future run. See the full refund policy →

Ready when you are

Have your data? Let's go.

If you have RNA-seq data or samples ready to prep, start the engagement. If you have specific technical questions before you commit, email us — we reply within one business day.

Try It Now → Ask a technical question