TECHNICAL RESOURCES · 实验流程

Experiment Workflow

Q: What happens to my samples once they arrive?

Within 30 minutes technicians verify sample IDs, names and quantities against the submission form, confirm the samples are fully frozen, photograph them for records, log the storage time and move them to designated -80°C freezer locations.

Q: The dry ice was half gone on arrival — are my samples still usable?

Remaining dry ice should be ≥ 50% of the original, and samples must be fully frozen with no partially thawed state.

Q: What RIN value does an RNA sample need to pass QC?

Transcriptomics samples are measured on the Agilent Bioanalyzer and need a RIN ≥ 7.0. The same QC block also requires 28S/18S ≥ 1.5 and RNA ≥ 500 ng for WTS.

Q: What happens if my samples fail QC?

All samples must pass QC before the next stage; on failure, clients are notified immediately to agree on a solution such as reshipment or plan adjustment.

Q: How long does a project take from sample arrival to data?

WGS, DIA proteomics and LC-MS metabolomics each take roughly 15–20 working days, RNA-seq 13–17 working days, and multi-omics integration 20–30 working days depending on data complexity.

Multi-omics experiments span four core stages: sample processing, library preparation, instrument run and data QC

Methodology note · content is citable as-is

KEY POINTS

Verify sample IDs, names and quantities against the submission form
Check remaining dry ice (should be ≥ 50% of original)
Confirm samples are fully frozen (no partially thawed state)
Photograph for records and log storage time in the system
Transfer samples to designated -80°C freezer locations

01Workflow Overview

Multi-omics experiments span four core stages: sample processing, library preparation, instrument run and data QC

Sample Receipt

dry-ice sign-off, sample registration, visual inspection

Sample QC

concentration measurement, integrity assessment, QC report

Aliquoting

aliquoted by omics type, labeled and archived at -80°C

Library Prep

RNA / DNA / protein / metabolite extraction

Library QC

fragment distribution, precise concentration quantification

Sequencing / MS Run

Illumina / PacBio / Orbitrap / timsTOF

Real-Time QC

real-time data-quality monitoring during the run

Data Delivery

raw data, analysis results, report documents

After-Sales Support

data interpretation, manuscript-submission support

02Detailed Operating Procedure

Step 1 | Sample Receipt & Registration

Upon receipt, our technicians complete the following within 30 minutes:

Verify sample IDs, names and quantities against the submission form
Check remaining dry ice (should be ≥ 50% of original)
Confirm samples are fully frozen (no partially thawed state)
Photograph for records and log storage time in the system
Transfer samples to designated -80°C freezer locations

Step 2 | Sample Quality Control (QC)

Quality requirements differ by omics type; all samplesmust pass QC before proceeding to the next stage:

Genomics / epigenomics: Nanodrop A260/280 (1.8–2.0); Agilent TapeStation for DNA integrity
Transcriptomics: Agilent Bioanalyzer RIN value (≥ 7.0 required)
Proteomics: BCA protein quantification; 1D SDS-PAGE for degradation check
Metabolomics: visual inspection with hemolysis/lipemia records

Clients are notified immediately of QC failures to agree on a solution (reshipment / plan adjustment).

Step 3 | Nucleic Acid / Protein / Metabolite Extraction

Select appropriate extraction kits and protocols by omics type:

DNA extraction: Qiagen DNeasy / MagAttract magnetic-bead method (high-throughput)
RNA extraction: Qiagen RNeasy / Norgen body-fluid RNA extraction kits
Protein extraction: SDT / urea lysis buffer with sonication
Metabolite extraction: pre-chilled methanol:acetonitrile:water (2:2:1) protein precipitation

Concentration and integrity are re-measured after extraction to ensure samples entering library preparation meet quality standards.

Step 4 | Library Preparation (Sequencing Samples)

Apply corresponding library-prep protocols for each sequencing type:

WGS libraries: Illumina TruSeq DNA PCR-Free or Nextera Flex
RNA-seq libraries: Illumina TruSeq Stranded mRNA / Illumina Stranded Total RNA
scRNA-seq libraries: 10x Genomics Chromium platform
ATAC-seq libraries: transposase-based tagmentation protocol

After library prep, fragment distribution is checked on Agilent TapeStation / Bioanalyzer and concentration precisely quantified by Qubit; qualified libraries proceed to pooling.

Step 5 | Sequencing / MS Acquisition

Data acquisition on platforms selected per study design:

Illumina NGS：NovaSeq X Plus / NovaSeq 6000, PE150 mode
PacBio TGS：Revio system, HiFi mode
LC-MS/MS (proteomics): Thermo Orbitrap Astral / timsTOF HT, DIA mode
LC-MS/MS (metabolomics): Thermo QE HF-X / ZenoTOF 7600, untargeted + targeted

Real-time monitoring during runs: sequencing Q30 ratios, MS1/MS2 resolution, retention-time stability and other metrics.

Step 6 | Data Analysis & Reporting

Raw data is processed through standard bioinformatics pipelines; final deliverables:

raw data files (FASTQ / RAW / WIFF)
standard analysis report (PDF + editable charts)
publication-grade vector source files (AI / SVG)
OmicsHub cloud-platform interactive analysis report

03QC Standards at Each Stage

Strict QC standards at every critical stage to ensure final data quality

Genomics QC

A260/280: 1.8–2.0

DNA integrity: no visible degradation bands; free of protein / RNA contamination; sequencing Q30 ≥ 85%.

Transcriptomics QC

RIN ≥ 7.0

28S/18S ≥ 1.5; RNA ≥ 500 ng (WTS); sequencing Q30 ≥ 90%; mapping rate ≥ 70%.

Proteomics QC

protein ≥ 0.5 μg/μL

no degradation bands on 1D gel; MS resolution ≥ 120,000 (Orbitrap); identified proteins ≥ target.

Metabolomics QC

QC-sample RSD < 15%

pooled-QC injections throughout the run; metabolite peak-area RSD < 15%；保留时间偏移 < 1 秒。

04Turnaround Reference

Standard Timelines

Genomics (WGS): approx. 15–20 working days
Transcriptomics (RNA-seq): approx. 13–17 working days
Proteomics (DIA): approx. 15–20 working days
Metabolomics (LC-MS): approx. 15–20 working days
Multi-omics integration: approx. 20–30 working days(depending on data complexity)

Expedited Services

Priority queuing: expedited fee moves your samples ahead in the queue, shortening turnaround by 30–50%
Parallel processing: multiple omics extracted and run simultaneously, greatly reducing total turnaround
Fast analysis: standard analysis completed within 3 working days (advance booking required)
Timeline budgeting: project-timeline budgeting with clear completion dates for each milestone
Contact technical support for expedited-service details

Q&AFAQ

What happens to my samples once they arrive?

Within 30 minutes technicians verify sample IDs, names and quantities against the submission form, confirm the samples are fully frozen, photograph them for records, log the storage time and move them to designated -80°C freezer locations.

The dry ice was half gone on arrival — are my samples still usable?

Remaining dry ice should be ≥ 50% of the original, and samples must be fully frozen with no partially thawed state.

What RIN value does an RNA sample need to pass QC?

Transcriptomics samples are measured on the Agilent Bioanalyzer and need a RIN ≥ 7.0. The same QC block also requires 28S/18S ≥ 1.5 and RNA ≥ 500 ng for WTS.

What happens if my samples fail QC?

All samples must pass QC before the next stage; on failure, clients are notified immediately to agree on a solution such as reshipment or plan adjustment.

How long does a project take from sample arrival to data?

WGS, DIA proteomics and LC-MS metabolomics each take roughly 15–20 working days, RNA-seq 13–17 working days, and multi-omics integration 20–30 working days depending on data complexity.