Failure Case Library

Real lab failures, root causes, and fixes — curated and bilingually annotated by our team.

All Techniques (8) PCR (Sigma Guide) (12) End-point PCR Primers (9) Western Blot (9) Wound Healing Assay (5) Cell Culture (Contamination) (7) Lipid Transfection (8) CCK-8 Cell Viability Assay (5) Colony Formation Assay (10) Transfection (8) Nucleic Acid Quantification (9) Transfection (Co-transfection) (1) Protein Extraction (4) Plasmid Construction (Double Digest) (1) Sanger Sequencing (2) Plasmid Construction (1) qPCR (RT-qPCR) (5) Transwell Migration / Invasion Assay (5) Immunohistochemistry (IHC) (6) PCR (Polymerase Chain Reaction) (26) Restriction Enzyme Digest (13) DNA Cleanup & Plasmid Purification (7) RNA Cleanup (4) NGS Library Preparation (NEBNext Ultra II) (7) HMW DNA Extraction (Monarch) (7) LAMP (Loop-mediated Isothermal Amplification) (7) RNA Depletion for RNA-seq (7) Bacterial rRNA Depletion (4) Cell-free DNA Extraction (8) ELISA (Competitive) (18) ELISA (Signal Problems) (11) ELISA (High Background) (8) ELISA (Inconsistent Results / High CV) (6) ELISA (Standard Curve Fit Problems) (6) Western Blot (Weak / No Signal) (6) Western Blot (Detection Problems) (7) Western Blot (Bands at Wrong MW) (5) Western Blot (Misshapen / Uneven Bands) (5) Western Blot (Unexpected Multiple Bands) (7) Western Blot (Unusual Gel Band Appearance) (3) ChIP (High Background) (1) ChIP (Low Resolution with High Background) (6) ChIP (Low Signal) (8) ChIP (PCR Amplification Problems) (4) Immunohistochemistry (High Background) (9) Immunohistochemistry (No Staining) (9) Immunoprecipitation (High Antibody Elution) (1) Immunoprecipitation (High Background) (8) Immunoprecipitation (No Protein Detected) (5) Immunoprecipitation (Protein Obstruction) (1) ELISPOT (8) Tissue Imaging (Autofluorescence) (9) Flow Cytometry (Troubleshooting) (8) ELISA Development (9) Flow Cytometry (Autofluorescence) (7) Flow Cytometry (Compensation) (7) Flow Cytometry (Fc Blocking) (7) Flow Cytometry (Fixation & Permeabilization) (9) Flow Cytometry (Isotype Controls) (7) Flow Cytometry (Fixation Buffers) (7) Western Blot (CST Guide) (8) ChIP (CST Guide) (8) Immunoprecipitation (CST Guide) (14) Immunohistochemistry (CST Guide) (14) Flow Cytometry (CST Guide) (8) ELISA (R&D Guide) (10) ELISA (Sigma Guide) (6) Western Blot Immunodetection (19) IP-Western Blot (6) Flow Cytometry (Sample Considerations) (14) Flow Cytometry (Paraformaldehyde Fixation) (14) Western Blot (Sigma Protocol) (8) PCR / RT-PCR Amplification Problems (5) Cell Culture (Cell Death) (8) Cell Culture (Precipitates) (6) PCR (Invitrogen Guide) (8) PCR / qPCR Plastics (9) Flow Cytometry (Controls) (8) Plasmid Mini-prep (1) Transfection (siRNA Knockdown) (1) Western Blot (Blue Background) (1)
Transfection moderate

Abnormal fluorescence localization (aggregates / wrong compartment)

Fluorescence forms aggregates inside cells, or localizes to a compartment different from the expected native pattern.

💡 4 causes ✓ 4 fixes
Transfection severe

Bright fluorescence but Western blot shows very low expression

GFP fluorescence is obvious under microscope, but the corresponding band on Western blot is faint or near-invisible.

💡 5 causes ✓ 5 fixes
Transfection critical

Massive cell death after transfection — reagent toxicity is too high

Cells become rounded and detached after transfection; CCK-8 shows a sharp drop in viability vs. mock-transfected control.

💡 4 causes ✓ 4 fixes
Transfection severe

Very few cells are fluorescent — transfection efficiency is extremely low

Microscopy shows scattered positive cells; flow cytometry confirms positivity rate is very low (< 5 %).

💡 5 causes ✓ 5 fixes
Transfection critical

Almost no fluorescence signal — transfection essentially failed

Under the fluorescence microscope, no GFP signal is visible; Western blot also shows essentially no target protein expression.

💡 5 causes ✓ 5 fixes
Transfection moderate

Bright at 24 h but signal rapidly decays at 48 – 72 h

Early time point shows strong fluorescence but it drops sharply within 48 – 72 h; signal varies dramatically between time points.

💡 4 causes ✓ 4 fixes
Transfection moderate

Very high replicate-well variation (poor reproducibility)

Parallel wells show very different fluorescence intensity / positive-cell rates; data fluctuates wildly between replicates.

💡 4 causes ✓ 4 fixes
Transfection severe

Empty/negative control also shows fluorescence (high false-positive background)

Untransfected or empty-vector wells show a clearly green/red signal — you can't tell if the target plasmid is really expressing.

💡 4 causes ✓ 4 fixes