Failure Case Library

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

All Techniques (14) 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)
Immunohistochemistry (CST Guide) moderate

Suboptimal Primary Antibody Incubation

Inconsistent or weak staining results despite following protocol. Staining intensity varies between experiments using same antibody lot and tissue type.

💡 3 causes ✓ 3 fixes
Immunohistochemistry (CST Guide) moderate

High Background Staining in IHC

Excessive background signal obscuring specific staining. Non-specific binding observed throughout tissue sections, making interpretation difficult.

💡 5 causes ✓ 5 fixes
Immunohistochemistry (CST Guide) critical

Complete Absence of IHC Staining

Complete lack of staining observed in immunohistochemistry experiment despite using validated antibody. Tissue sections appear negative even when positive control should show signal.

💡 6 causes ✓ 6 fixes
Immunohistochemistry (CST Guide) severe

Incorrect Antibody Diluent Selection

Suboptimal signal intensity or background issues despite correct antibody concentration. Different antibodies show dramatically different performance in TBST/5% NGS versus SignalStain Antibody Diluent.

💡 3 causes ✓ 3 fixes
Immunohistochemistry (CST Guide) severe

Mouse-on-Mouse (MOM) Background

High background staining when using mouse primary antibody on mouse tissue. Secondary antibody binds endogenous mouse IgG throughout the tissue, creating non-specific signal.

💡 3 causes ✓ 4 fixes
Immunohistochemistry (CST Guide) moderate

Endogenous Biotin Interference

High background staining specifically in kidney, liver, or other biotin-rich tissues when using biotin-based detection. Background not resolved by standard blocking procedures.

💡 3 causes ✓ 3 fixes
Immunohistochemistry (CST Guide) severe

Inadequate Detection System Sensitivity

Weak signal or no staining despite proper primary antibody performance. Standard HRP-conjugated secondary antibodies fail to provide sufficient signal amplification.

💡 4 causes ✓ 4 fixes
Immunohistochemistry (CST Guide) severe

Suboptimal Antigen Retrieval Method Selection

Weak or absent staining despite proper antibody concentration and incubation. Clear performance differences observed when comparing different antigen retrieval heating methods.

💡 4 causes ✓ 4 fixes
Immunohistochemistry (CST Guide) moderate

Incorrect Antibody Diluent Selection

Staining quality is significantly reduced or inconsistent when using generic diluent instead of product-specific recommended diluent, as different antibodies perform optimally in different buffer compositions.

💡 3 causes ✓ 4 fixes
Immunohistochemistry (CST Guide) moderate

Insufficient Detection System Sensitivity

Signal is weak or undetectable despite correct antibody and protocol, particularly for low-abundance targets, indicating that the detection system lacks sufficient signal amplification.

💡 3 causes ✓ 4 fixes
Immunohistochemistry (CST Guide) moderate

Inadequate Washing Steps Causing Poor Contrast

High background persists with poor contrast between positive signal and background despite other optimization steps, making interpretation difficult.

💡 4 causes ✓ 4 fixes
Immunohistochemistry (CST Guide) moderate

Spotty or Uneven Background Staining Pattern

Staining pattern shows irregular, patchy, or spotty background with uneven distribution across tissue sections, indicating technical artifacts rather than biological variation.

💡 3 causes ✓ 3 fixes
Immunohistochemistry (CST Guide) severe

Weak or Suboptimal IHC Staining Intensity

Staining signal is present but significantly weaker than expected, with poor contrast between positive cells and background, making interpretation difficult.

💡 5 causes ✓ 5 fixes
Immunohistochemistry (CST Guide) severe

Antigen Retrieval Method Not Optimized for Target

Staining results are inconsistent or suboptimal despite correct antibody and detection system, with signal strength varying significantly based on retrieval method used.

💡 4 causes ✓ 4 fixes