Failure Case Library

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

All Techniques (19) 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)
Western Blot Immunodetection severe

High Non-Specific Background Signal

Entire membrane shows elevated signal intensity, making it difficult to distinguish specific protein bands from background noise. Signal-to-noise ratio is poor.

💡 6 causes ✓ 6 fixes
Western Blot Immunodetection moderate

Reverse Image - White Bands on Dark Background

Film shows 'bleached' or 'burnt-out' white bands against dark background instead of expected dark bands. Bands appear as negative images where high protein concentration exists.

💡 3 causes ✓ 3 fixes
Western Blot Immunodetection moderate

Poor Detection of Small Molecular Weight Proteins

Proteins below 15-20 kDa show weak or absent signal while larger proteins are detected normally. Small protein bands appear diffuse or masked.

💡 4 causes ✓ 4 fixes
Western Blot Immunodetection severe

Large Error Bars in Quantitative Western Blotting

Replicate Western blots show high variability in band intensity measurements. Coefficient of variation exceeds acceptable limits (>15-20%) making quantitative comparisons unreliable.

💡 4 causes ✓ 4 fixes
Western Blot Immunodetection severe

Weak or Diminished Western Blot Signal

Expected protein bands appear faint or barely visible on film or imaging system, even after extended exposure times.

💡 6 causes ✓ 6 fixes
Western Blot Immunodetection critical

Complete Absence of Western Blot Signal

No protein bands are visible on the blot, even at the expected molecular weight position. Film or imaging system shows no detectable chemiluminescence or fluorescence.

💡 6 causes ✓ 6 fixes
Western Blot Immunodetection minor

Uneven or Distorted Blot Pattern

Membrane shows irregular signal distribution with visible fingerprints, fold marks, or forceps imprints. Signal intensity varies across membrane surface in non-biological pattern.

💡 4 causes ✓ 4 fixes
Western Blot Immunodetection moderate

Speckled or Punctate Background Pattern

Membrane shows scattered dark spots or speckles across the surface, distinct from specific protein bands. Background appears grainy or particulate rather than uniformly elevated.

💡 4 causes ✓ 4 fixes
Western Blot Immunodetection moderate

Additional Bands or Wrong Molecular Weight

Blot shows unexpected extra bands at different molecular weights than predicted, or expected band appears at wrong size. Multiple bands may appear where single band is anticipated.

💡 4 causes ✓ 4 fixes
Western Blot Immunodetection severe

Large Error Bars in Quantitative Western Blotting

Quantitative measurements show high variability between replicates. Large error bars or standard deviations prevent statistical significance despite apparent differences.

💡 4 causes ✓ 4 fixes
Western Blot Immunodetection minor

Uneven or Irregular Blot Appearance

Membrane shows fingerprints, fold marks, or forceps imprints creating irregular patterns. Uneven signal distribution not related to protein bands.

💡 4 causes ✓ 4 fixes
Western Blot Immunodetection moderate

Reverse Image: White Bands on Dark Background

Film shows negative or reverse image with white or 'bleached' bands on dark background instead of expected dark bands. Also called 'burnt-out' bands.

💡 3 causes ✓ 4 fixes
Western Blot Immunodetection severe

Additional or Wrong-Sized Bands Appearing

Unexpected bands appear at molecular weights different from target protein. Multiple bands present instead of single expected band, or band appears at incorrect size.

💡 5 causes ✓ 5 fixes
Western Blot Immunodetection moderate

High Background in Rapid Immunodetection Protocol

When using rapid immunodetection methods, membrane shows elevated background specific to fast protocols. Issue not present with standard overnight protocols.

💡 5 causes ✓ 5 fixes
Western Blot Immunodetection severe

High Background Signal on Western Blot

Overall high background across entire membrane reduces signal-to-noise ratio. Specific bands difficult to distinguish from background noise.

💡 6 causes ✓ 6 fixes
Western Blot Immunodetection critical

Complete Absence of Signal in Western Blot

No bands are visible on the Western blot membrane or film. Complete absence of signal despite confirmed protein loading and transfer.

💡 6 causes ✓ 6 fixes
Western Blot Immunodetection moderate

Poor Detection of Small Molecular Weight Proteins

Proteins smaller than 15-20 kDa show weak or absent signal while larger proteins detect normally. Small protein bands are masked or obscured.

💡 4 causes ✓ 4 fixes
Western Blot Immunodetection severe

Weak or Faint Bands in Western Blot

Protein bands appear faint or barely visible on the Western blot membrane or film despite proper loading. Signal intensity is insufficient for detection or quantification.

💡 6 causes ✓ 6 fixes
Western Blot Immunodetection moderate

Speckled or Spotted Background Pattern

Discrete spots or speckles appear across the membrane background rather than uniform signal. Pattern resembles aggregates or particulates.

💡 4 causes ✓ 4 fixes