TRANSLACORE_WG2_SOP_001- ProcessingFresh-FrozenTissuesforOmicsMethods_Final.pdf

TRANSLACORE_WG2_SOP_004- ProcessingPDOforOmicsMethods_Final.pdf

TRANSLACORE_WG2_SOP_003- ProcessingBLFforOmicsMethods_Final.pdf

TRANSLACORE_WG2_SOP_002- ProcessingBloodDerivativesforOmicsMethods_Final.pdf

**Standard operating procedures for omics sample preparation**

TRANSLACORE Working Group 2 (WG2) has harmonised four standard operating procedures (SOPs) for preparing biological samples for transcriptomics, translatomics and proteomics. These resources guide community members through specimen handling, stabilisation and storage, with the aim of preserving molecular integrity and improving reproducibility across participating laboratories. They connect sample preparation with the downstream analytical workflows described in WG1 SOPs.


**Fresh-frozen tissues (SOP_001)**. Covers sample receipt, frozen storage, pulverisation in liquid nitrogen and aliquoting for molecular extraction. Emphasis is placed on preventing thawing and degradation while preserving RNA, ribosomes and proteins. The SOP provides guidance for bulk RNA sequencing, ribosome profiling (RiboSeq), RNA fragmentomics, nano-tRNAseq, epitranscriptomics and proteomics.

**Blood and blood-derived specimens (SOP_002).** Addresses whole blood, plasma, serum, buffy coat, peripheral blood mononuclear cells (PBMCs) and platelet fractions. It outlines specimen-specific collection, separation, stabilisation and storage requirements, including optional monocyte enrichment. Particular attention is given to anticoagulant selection, processing delays, haemolysis and matching the blood fraction to the intended analysis. Ribosome and RNA-protein complex analyses require prompt processing of suitable cellular material; single-cell RNA sequencing requires viable cells.

**Bronchial lavage fluid (SOP_003).** Describes collection, chilled transport, sample verification, centrifugation, aliquoting and freezing. It addresses the challenges of limited biomass and variable cellular composition, with extraction guidance for bulk RNA sequencing of the cellular fraction, small RNA analyses, RNA fragmentomics, nano-tRNAseq and proteomics. RiboSeq, single-cell RNA sequencing and epitranscriptomics require dedicated validation and are outside this SOP’s scope.

**Patient-derived organoids (SOP_004).** Provides harvesting and processing procedures for organoids grown in suspension or extracellular matrices. It emphasises recording culture conditions and passage number, controlled matrix removal, and minimising handling-induced stress and translational changes. Specific guidance covers preparation for RiboSeq and other RNA- and protein-based analyses. Organoid derivation and long-term culture establishment are outside its scope.

Across all four SOPs, shared priorities include sample identification and traceability, documentation of pre-analytical variables, RNase-free handling, appropriate temperature control, quality assessment and institutional biosafety procedures. Community members should consult the complete specimen-specific SOP and the relevant WG1 protocol when planning experiments, selecting extraction methods and determining sample requirements.

The protocols were contributed by **Massimiliano Clamer** and **Paola Bernabò** (IMMAGINA BioTECHNOLOGY), **Yasemin Saygideger** (Çukurova University) and **Ahmet Acar** (METU), and harmonised for TRANSLACORE by **Arnaud Jabouille** (INSERM UMR1312, BRIC).


TRANSLACORE Working Group 2 has harmonized four standard operating procedures for preparing fresh-frozen tissues, blood and blood-derived specimens, bronchial lavage fluid, and patient-derived organoids for omics analyses. The protocols address sample handling, stabilization, processing, storage and quality assessment, with specimen-specific guidance for downstream applications. By promoting molecular integrity, traceability and consistent documentation of pre-analytical variables, these resources support reproducible research across laboratories and connect sample preparation with the analytical workflows described in Working Group 1 protocols. 

Standard operating procedures for omics sample preparation

 COST (European Cooperation in Science and Technology) is a funding agency for research and innovation networks. Our Actions help connect research initiatives across Europe and enable scientists to grow their ideas by sharing them with their peers. This boosts their research, career and innovation. (www.cost.eu) | The TRANSLACORE Cost Action is bridging disciplines and expertise across Europe in order to advance an emerging field in cancer biology: translational control in cancer. It is providing a unique opportunity to understand this biological process leading to reconsider our view of gene expression control in this disease and deliver novel therapeutic opportunities.

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Standard operating procedures for omics sample preparation

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