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FAF1 / FAS-associated factor 1 · IHC design guide
Design Immunohistochemistry for FAF1
Plan chromogenic FAF1 IHC with nuclear and cytoplasmic staining as the tissue reference (HPA tissue IHC). Start the catalog antibody at 2.5 μg/mL and compare strong salivary gland or testis staining with reported unstained cell populations (datasheet: IHC; HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
FAF1 Immunohistochemistry Experimental Design Guide
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before staining
| Expected localisation | Nuclear and cytoplasmic tissue staining (HPA tissue IHC) | |
| Staining pattern | General cytoplasmic and nuclear staining (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen) | |
| Positive control | Salivary gland+4 more · see all | |
| Negative control | Caudate+2 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation consistent across sections (standard IHC practice; not target-specific); Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A03842) | |
| Caveat | Only medium consistency between staining and RNA (HPA tissue IHC) | |
| Regulation | Most abundant in testis; stimulus effects unknown (UniProt) | |
| Isoform / epitope | 2 isoforms; no transmembrane span; epitope coverage unknown (UniProt) |
Section 1
Recommended FAF1 IHC & IF Protocols
The catalog antibody’s IHC-P protocol is paired with three published FAF1 staining protocols for gastric tissue and mouse ovary (PMC3530185; PMC5352377; PMC5902905).
| Sample | Tissue sections; selected-image fixative not specified (standard IHC workflow) |
| Fixation | Image fixative and duration unreported (datasheet A03842); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat-induced epitope retrieval in Tris-EDTA buffer, pH 9.0, 20 min at 95–98 °C (standard rule: nuclear antigen) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% normal serum of the secondary host, 30 min, room temperature (standard) |
| Primary antibody | Rabbit anti-FAF1, 2.5 μg/mL (datasheet A03842) |
| Primary incubation | Overnight at 4 °C (standard) |
| Detection | HRP-polymer secondary, DAB chromogen 5–10 min (standard) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | FAF1-positive staining in glandular cells of salivary gland (HPA tissue IHC: High). HPA tissue profile: General cytoplasmic and nuclear expression. No signal in the no-primary control. |
💡Decision noteStart with Tris-EDTA pH 9.0 retrieval at 95–98 °C for 20 min for nuclear FAF1 (page antigen retrieval; UniProt Q9UNN5: nucleus).
Section 2
What Is the Expected FAF1 Staining Pattern?
FAF1 is a nuclear protein with no transmembrane segment (UniProt Q9UNN5: subcellular location and topology). In tissue IHC, expect nuclear and cytoplasmic staining, especially in salivary glandular cells and cells in testis seminiferous ducts (HPA tissue IHC: general profile; High in both cell populations). HPA rates the tissue pattern Approved, with medium consistency between antibody staining and RNA expression (HPA tissue IHC: reliability).
| Nuclear and cytoplasmic staining in salivary glandular cells or cells in testis seminiferous ducts. | This fits the reported tissue pattern, with High staining in both cell populations (HPA tissue IHC: profile and positive tissues). Assess the named cells within each section; HPA's tissue observations do not imply that every cell in that tissue stains equally. |
| Strong staining restricted to plasma membranes or extracellular material, without a convincing cellular pattern. | This differs from the reported nuclear and cytoplasmic tissue pattern and nuclear UniProt location (HPA tissue IHC: profile; UniProt Q9UNN5: subcellular location). Review morphology, the negative control and detection background before interpreting it as FAF1; UniProt reports no transmembrane segment (UniProt Q9UNN5: topology). |
| Prominent signal in cholangiocytes, chondrocytes or caudate glial cells. | Those specific cell populations were not detected in HPA tissue IHC (HPA tissue IHC: negative tissues). Unexpected staining warrants a check for cross-reactivity or endogenous detection activity; a tissue label alone cannot substitute for identifying the stained cell type. |
| Diffuse colour across cells and surrounding section, obscuring nuclei and tissue boundaries. | Treat this as possible background before scoring compartments (general IHC practice). Inspect the negative control, blocking and chromogen development; the HPA report of general cytoplasmic and nuclear expression does not establish that indiscriminate staining is a true positive (HPA tissue IHC: profile). |
| No detectable signal in salivary glandular cells or cells in testis seminiferous ducts. | These are reported High cell populations, so an absent signal calls for a run-level check (HPA tissue IHC: positive tissues). Confirm tissue identity and cellular preservation, then review antibody dilution, retrieval and detection against the catalog antibody's IHC-P instructions (general IHC practice). |
💡Expected FAF1 appearanceCall a positive result when the named salivary glandular cells or testis seminiferous-duct cells show discernible nuclear and cytoplasmic staining consistent with their reported High level (HPA tissue IHC: profile and positive tissues); indiscriminate extracellular colour is suspect background (general IHC practice).
| Choice of positive and comparison cells | Salivary glandular cells and testis seminiferous-duct cells have High staining; adrenal glandular and bone-marrow hematopoietic cells have Medium staining (HPA tissue IHC: positive tissues). Compare the specified cell populations, since HPA's levels are cell-specific observations. |
| Low and undetected populations | HPA reports Low staining in lung macrophages and heart cardiomyocytes, and no detected staining in liver cholangiocytes (HPA tissue IHC: low and negative tissues). Low signal can be harder to distinguish from background; an undetected population is a useful comparison, not proof that an entire organ lacks FAF1. |
| Compartment evidence | UniProt lists the nucleus; HPA tissue IHC describes general nuclear and cytoplasmic expression (UniProt Q9UNN5: subcellular location; HPA tissue IHC: profile). Score both compartments in tissue sections and avoid treating cytoplasmic staining alone as proof of an artifact. |
| Antibody evidence | HPA lists CAB072814 as IHC Approved, while HPA018253 has no listed IHC status (HPA antibodies: IHC validation). The overall tissue profile is Approved with medium staining-to-RNA consistency (HPA tissue IHC: reliability); interpret a new reagent's pattern with its own controls. |
| Protein form and assay conditions | UniProt records Long and Short isoforms and a single annotated chain spanning residues 1–650, with no signal peptide or propeptide (UniProt Q9UNN5: isoforms and processing). These annotations alone do not establish an antibody's epitope, its isoform coverage or a target-specific retrieval requirement. |
| IF/ICC: where should signal localize? | Predominantly in the nucleoplasm (HPA subcellular ICC-IF: enhanced); acrosome, equatorial segment and perinuclear theca are additional reported locations (HPA subcellular ICC-IF: approved). Use this as an IF/ICC interpretation cue; the tissue IHC profile also includes cytoplasmic staining (HPA tissue IHC: profile). |
| Situation | Likely cause | Next action |
|---|---|---|
| Known-positive cells are blank. | The assay may have failed to reveal antigen; HPA reports High staining in salivary glandular cells and testis seminiferous-duct cells (HPA tissue IHC: positive tissues). | Check the positive control and tissue morphology, then verify dilution, retrieval and detection against the catalog antibody's IHC-P instructions (general IHC practice). Do not infer FAF1-specific fixation sensitivity from this result. |
| The whole section develops colour, including spaces outside cells. | Diffuse deposition may reflect blocking or detection background (general IHC practice); it is not the defined cellular profile (HPA tissue IHC: profile). | Inspect the negative control and review blocking, washes and chromogen development (general IHC practice). Score FAF1 only where a cellular compartment remains identifiable. |
| Unexpected strong signal appears in cholangiocytes, chondrocytes or caudate glial cells. | HPA reports these cells as not detected (HPA tissue IHC: negative tissues); cross-reactivity or endogenous detection activity is possible. | Confirm the cell identification, compare a negative control, and assess the detection system's endogenous activity control (general IHC practice). Treat the signal as unresolved until those checks support specificity. |
| Staining appears only on membranes or extracellular structures. | That distribution conflicts with the reported nuclear and cytoplasmic tissue profile (HPA tissue IHC: profile) and the absence of a transmembrane segment (UniProt Q9UNN5: topology). | Recheck cellular boundaries and the negative control; compare with a known-positive section processed in the same run (general IHC practice). Avoid assigning this pattern to FAF1 solely from colour intensity. |
| A low-staining population looks negative. | HPA reports Low staining in lung macrophages and heart cardiomyocytes (HPA tissue IHC: low tissues); weak true signal may be difficult to separate from background. | First verify performance in a reported High population, then compare the low-staining cells with nearby background at the same detection settings (HPA tissue IHC: positive and low tissues; general IHC practice). |
| IF/ICC shows little nucleoplasmic signal despite a coloured IHC section. | HPA reports mainly nucleoplasmic ICC-IF localization, while its tissue IHC profile includes nuclear and cytoplasmic staining (HPA subcellular ICC-IF: summary; HPA tissue IHC: profile). | Interpret each assay against its own reported pattern and controls; check cell boundaries and nuclear identification before comparing compartments (general IHC/IF practice). |
Experiment evidence
IHC & IF images showing FAF1 staining
A03842 · IHCImmunohistochemistry of FAF1 in rat spleen tissue with FAF1 antibody at 2.5 μg/mL.
A03842 · IFImmunofluorescence of FAF1 in rat spleen tissue with FAF1 antibody at 2 μg/mL.
A03842-1 · IFIF analysis of FAF1 using anti-FAF1 antibody (A03842-1) and anti-Beta Tubulin antibody (M01857-3). FAF1 was detected in immunocytochemical s
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000185104-FAF1/tissue/cerebral+cortex#imid_18931273
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000185104-FAF1/tissue/colon#imid_18931199
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000185104-FAF1/tissue/liver#imid_18931192
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000185104-FAF1/tissue/kidney#imid_18931193
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA018253; green = FAF1, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA018253; green = FAF1, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for FAF1 IHC & IF
🧪Run salivary gland first and require staining in glandular cells (HPA: High in salivary-gland glandular cells). Use liver cholangiocytes as the negative tissue (HPA: Not detected in liver cholangiocytes). On the positive slide, cells without specific signal should show counterstain but no chromogen; HPA does not designate an internal negative cell population in salivary gland (HPA: salivary-gland glandular cells High).
Positive control tissue: Salivary gland (Glandular cells, HPA High)
Negative control tissue: Caudate (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show FAF1 in A-431, U-251MG, U2OS, HeLa, MCF-7, Sperm, with annotated localisation: Nucleoplasm (enhanced) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control and an isotype control matched to the primary antibody’s host species and immunoglobulin class; use FAF1-knockout material or a peptide-blocked primary as a biological specificity control where available (standard IHC practice). Quench endogenous peroxidase and check the salivary-gland section for residual background before interpreting glandular staining (standard chromogenic IHC practice).
⚠️Feasibility: A FAF1-specific fixation window or fixation effect is unreported in the supplied evidence, and the selected A03842 rat-spleen IHC caption does not state a fixative (A03842 tissue-IHC caption). Antigen-retrieval dependence is unreported, so optimize retrieval empirically for paraffin sections; the supplied evidence does not establish that frozen sections or IF are easier (A03842 tissue-IHC caption; HPA: tissue staining). In salivary gland, distinguish cellular glandular staining from signal in luminal material or other background (HPA: High in glandular cells; standard IHC interpretation).
HPA tissue IHC evidence for FAF1
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Medium consistency between antibody staining and RNA expression data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Salivary gland | Glandular cells | High | Protein (IHC) | HPA → |
| Testis | Cells in seminiferous ducts | High | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Medium | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Medium | Protein (IHC) | HPA → |
Section 3
Advanced FAF1 IHC Tips
Troubleshoot FAF1 staining in paraffin-section IHC by checking retrieval, compartment-specific signal, controls and scoring; the IF guidance addresses the separate application.
How should I retrieve FAF1 when nuclear staining is weak?
Use Tris-EDTA pH 9.0 HIER at 95–98 °C for 20 min for FAF1 paraffin-section IHC (page retrieval rule: nuclear antigen). Keep section thickness, heating vessel and cooling time consistent across the comparison so a retrieval change can be judged separately from section variation (standard IHC practice). FAF1 is reported in the nucleus, while tissue IHC also shows cytoplasmic staining, so assess both compartments after retrieval (UniProt Q9UNN5 subcellular; HPA tissue IHC). If signal remains weak, compare a shorter heating time on matched sections and record whether nuclear detail improves without increased background (standard IHC practice).
Could fixation explain weak or uneven FAF1 staining?
Target-specific FAF1 sensitivity to fixation is unknown from the supplied evidence; the rat spleen IHC caption does not state its fixative (A03842 caption). Record the actual fixative, time before fixation and fixation duration for each specimen, then compare sections processed together (standard IHC practice). Review nuclear detail, tissue integrity and staining in the same anatomical region before changing the antibody concentration or retrieval conditions (standard IHC practice). When comparing blocks, keep the prescribed Tris-EDTA pH 9.0, 95–98 °C, 20 min retrieval constant initially (page retrieval rule: nuclear antigen). Neither the reported phosphorylation sites nor tissue staining pattern establishes a FAF1-specific fixation effect (UniProt Q9UNN5 modified residues; HPA tissue IHC).
Should FAF1 stain nuclei, cytoplasm, or both in tissue sections?
Expect a nuclear component because FAF1 is annotated as nuclear and is mainly nucleoplasmic in subcellular imaging (UniProt Q9UNN5 subcellular; HPA subcellular). Cytoplasmic staining can also be compatible with the reported general cytoplasmic and nuclear tissue IHC profile (HPA tissue IHC). Score nuclear and cytoplasmic signal separately, using the counterstain to define nuclei and the same thresholds across specimens (standard IHC practice). Check the compartment pattern in a documented positive cell population before interpreting a predominantly cytoplasmic result; glandular cells in salivary gland and cells in seminiferous ducts are reported high (HPA tissue IHC).
How can isoforms or epitope accessibility affect FAF1 IHC?
FAF1 has Long and Short isoforms, but the supplied evidence does not map this antibody’s epitope to either isoform (UniProt Q9UNN5 isoforms; A03842 caption). Its UBA domain spans residues 1–57 and its UBX domain spans 569–646; phosphorylation is reported at residues 320, 580 and 582 (UniProt Q9UNN5 domains; UniProt Q9UNN5 modified residues). Do not assign a compartment difference to isoform loss or phosphorylation without epitope information and an independent check (standard IHC interpretation). If staining changes across processing conditions, compare adjacent sections under the same retrieval and detection settings before attributing the difference to FAF1 biology (standard IHC practice).
How should I check FAF1 localisation by multiplex IF?
For the separate IF/ICC workflow, pair FAF1 with a marker identifying the cell population under study and a nuclear counterstain, then inspect whether the FAF1 signal is mainly nucleoplasmic (HPA subcellular; standard IF practice). Choose fluorophores after measuring tissue autofluorescence in an unstained section, and place the weaker signal in a channel with less measured background (standard IF practice). FAF1 has no transmembrane segment and is reported mainly in the nucleoplasm, so include permeabilisation that permits antibody access to intracellular and nuclear epitopes (UniProt Q9UNN5 topology; HPA subcellular; standard IF practice). Confirm that the chosen fixation and permeabilisation preserve morphology using directly matched IF controls; the supplied IHC caption gives no IF fixation condition (A03842 caption; standard IF practice).
What should I change when FAF1 chromogenic staining is diffuse?
First compare the stained section with a no-primary control to assess detection-system background, then inspect whether signal follows tissue edges, folds or damaged areas (standard IHC practice). Use an appropriate endogenous peroxidase block before chromogenic detection and check the no-primary section for residual enzyme activity (standard IHC practice). The reported rat spleen image used catalog antibody A03842 at 2.5 µg/mL, but its caption does not specify the other processing conditions (A03842 caption). Optimise antibody concentration, blocking and washes one variable at a time, and retain nuclear versus cytoplasmic observations rather than treating all colour as equivalent FAF1 signal (HPA tissue IHC; standard IHC practice).
How should I quantify FAF1 across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, because tissue IHC reports both cytoplasmic and nuclear FAF1 expression (HPA tissue IHC). For a cell-based comparison, report the percentage of positive cells and an H-score calculated from intensity categories using one threshold set across all slides (standard IHC practice). For spatial questions, report positive-cell density per mm² of analysable tissue and exclude folds, necrosis and missing tissue by a prespecified rule (standard IHC practice). Normalise counts to the relevant cell population or analysable area, and process comparison sections with the same retrieval, staining and image settings (standard IHC practice).
How can I distinguish genuine FAF1 staining from artefact?
A credible result should include an anatomically plausible cell population and a nuclear component, while allowing cytoplasmic signal reported in tissue IHC (UniProt Q9UNN5 subcellular; HPA tissue IHC). Compare the pattern with reported high staining in salivary gland glandular cells or cells in seminiferous ducts and with undetected staining in liver cholangiocytes, when those cell populations are available (HPA tissue IHC). Treat isolated edge staining, necrotic regions and signal in a no-primary control as possible processing or detection artefacts (standard IHC practice). Check endogenous peroxidase activity when colour appears independent of primary antibody, and seek a second validation approach before calling an unexpected compartment or cell population FAF1-positive (standard IHC practice).
Boster reagents
Best FAF1 / FAS-associated factor 1 IHC Antibodies
A03842 has IHC data in rat spleen tissue (A03842 image caption); A03842-1 has IF/ICC data in A549 cells (A03842-1 image caption). Both list Human, Mouse, and Rat reactivity (catalog).
Real IHC data
Anti-FAS-associated factor 1 FAF1 Antibody
Cat # A03842
Real IF data
Anti-FAF1 Antibody ®
Cat # A03842-1
A03842 lists IHC-P and shows FAF1 staining in rat spleen tissue at 2.5 μg/mL (A03842 applications; A03842 IHC image caption). A03842-1 lists IF and ICC and shows FAF1 staining in A549 cells at 5 μg/mL (A03842-1 applications; A03842-1 IF image caption).
Which to pick: Choose A03842 for paraffin-section IHC: it lists IHC-P and its IHC image shows rat spleen tissue, although the caption does not report the fixative (A03842 applications; A03842 IHC image caption). Choose A03842-1 for IF/ICC in cells because its image shows staining in A549 cells; it does not list IHC-P (A03842-1 IF image caption; A03842-1 applications). For cross-species planning, both list Human, Mouse, and Rat reactivity, while the supplied IHC image documents rat tissue only (catalog reactivity; A03842 IHC image caption).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q9UNN5 (FAF1_HUMAN, FAS-associated factor 1).
- Human Protein Atlas. FAF1 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. FAF1 subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to the acrosome, equatorial segment and perinuclear theca..
- Human Protein Atlas. FAF1 antibody validation summary (2 antibodies).
- Reduced FAF1 Expression and Helicobacter Infection: Correlations with Clinicopathological Features in Gastric Cancer. Gastroenterology research and practice 2012 — PMC3530185.
- Fas-associated factor 1 inhibits tumor growth by suppressing Helicobacter pylori-induced activation of NF-κB signaling in human gastric carcinoma. Oncotarget 2017 — PMC5352377.
- Fas-associated protein factor 1 is involved in meiotic resumption in mouse oocytes. The Journal of reproduction and development 2018 — PMC5902905.
- Expression and Localization of Fas-Associated Factor 1 in Testicular Tissues of Different Ages and Ovaries at Different Reproductive Cycle Phases of Bos grunniens. Animals : an open access journal from MDPI 2023 — PMC9913830.
- PubMed PMID:10462485 — UniProt-cited evidence.
- PubMed PMID:10810093 — UniProt-cited evidence.
- PubMed PMID:16710414 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for FAF1 (FAS-associated factor 1). Expected localisation Nuclear and cytoplasmic tissue staining (HPA tissue IHC). Antigen retrieval: Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen). Validated IHC antibody: A03842 at 2.5 μg/mL (the product's own IHC validation image is shown). Controls (HPA): positive Salivary gland (Glandular cells); negative Caudate. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Tissue sections; selected-image fixative not specified (standard IHC workflow); 2. Fixation: Image fixative and duration unreported (datasheet A03842); verify before use.; 3. Sectioning: 4–5 µm sections on charged slides (standard); 4. Deparaffinisation: Xylene, graded ethanol series to water (standard); 5. Antigen retrieval: Heat-induced epitope retrieval in Tris-EDTA buffer, pH 9.0 , 20 min at 95–98 °C…; 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% normal serum of the secondary host, 30 min , room temperature (standard); 8. Primary antibody: Rabbit anti-FAF1, 2.5 μg/mL (datasheet A03842); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across sections (standard IHC practice; not target-specific); Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A03842); Caveat: Only medium consistency between staining and RNA (HPA tissue IHC); Isoform / epitope: 2 isoforms; no transmembrane span; epitope coverage unknown (UniProt); Regulation: Most abundant in testis; stimulus effects unknown (UniProt). Evidence: UniProt Q9UNN5, HPA tissue IHC · Approved, HPA ICC-IF · Mainly localized to the nucleoplasm. In addition localized to the…, Datasheet A03842, PMC3530185, PMC5352377. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/FAF1/immunohistochemistry-ihc-guide.