Protocol for Patient-Derived Organoids from Bile Samples and Gene Knockdown

21 patients undergoing endoscopic retrograde cholangiopancreatography (ERCP) provided bile samples for this protocol. The workflow, authored by Carla Roja and last updated in May 2026, details steps to generate and expand organoids, achieving an 81% establishment rate. It includes methods for siRNA delivery and DNA-based profiling in paired bile-organoid samples.

Use Cases

• Establishing organoid cultures from bile based on the described step-by-step protocol.
• Performing gene expression knockdown via siRNA delivery in 3D organoid cultures as demonstrated.
• Profiling organoids using DNA-based methods like targeted sequencing and copy-number analysis mentioned in the description.
• Studying morphological heterogeneity in cultures derived from malignant biliary strictures as reported.

Strengths

• Protocol was optimized and applied in a real-world cohort of 21 patients.
• Expandable organoids were established in 17 out of 21 cases (81%).
• Includes two complementary workflows for siRNA delivery in 3D cultures.
• Documented under a permissive CC-BY-4.0 license.

Limitations

• Dataset is a 165.6 KB PDF protocol document, not a structured data file.
• Row count and column-level documentation are absent.
• Description metadata is limited; actual data quality requires manual inspection after download.

Provenance

Source

figshare

Collection Method

Bile samples collected during endoscopic retrograde cholangiopancreatography (ERCP) procedures from patients with benign and malignant biliary conditions.

Freshness

Last updated 2026-05-29 06:29:09