Failure Case Library

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

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