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- Table of Contents
Plan CYP1A1 staining in paraffin sections using the catalog antibody’s IHC range of 0.5–1 μg/mL (datasheet PB9544). Compare cytoplasmic staining with tissue controls while accounting for the uncertain HPA staining profile (HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Cytoplasm observed (HPA tissue IHC); ER and inner mitochondrial membrane annotated (UniProt) | |
| Staining pattern | General cytoplasmic staining, including glandular cells (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6 HIER, heat-mediated (datasheet PB9544) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
| Fixation | Keep fixation consistent (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 PB9544) | |
| Caveat | Very low agreement between staining and RNA data (HPA tissue IHC) | |
| Regulation | Expression varies by tissue (UniProt) | |
| Isoform / epitope | Three isoforms; antibody epitope coverage is unknown (UniProt) |
The catalog antibody has its own IHC-P protocol (datasheet PB9544). The four published protocols below provide tissue-specific methods for comparison (PMC1310924; PMC11544920; PMC4201582; PMC8082009).
| Sample | Paraffin-embedded Mouse Kidney tissue; fixative not specified (datasheet PB9544) |
| Fixation | Image fixative and duration unreported (datasheet PB9544); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: Citrate pH 6, 20 min (datasheet PB9544) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet PB9544) |
| Primary antibody | Rabbit anti-CYP1A1, 0.5-1μg/ml (datasheet PB9544) |
| Primary incubation | Overnight at 4 °C (datasheet PB9544) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet PB9544) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | CYP1A1-positive staining in glandular cells of adrenal gland (HPA tissue IHC: Medium). HPA tissue profile: General cytoplasmic expression. No signal in the no-primary control. |
CYP1A1 is annotated in the endoplasmic reticulum and microsome membranes, mitochondrial inner membrane, and cytoplasm, with no annotated transmembrane segment (UniProt P04798 topology). On paraffin sections, look for cytoplasmic staining in bronchial respiratory epithelial cells or selected glandular cells reported at medium intensity (HPA tissue IHC). Treat that pattern as provisional: tissue staining has Uncertain reliability, and the listed antibody’s IHC validation is Uncertain (HPA tissue IHC; HPA CAB018654).
| Cytoplasmic staining in bronchial respiratory epithelial cells or glandular cells. | This fits the reported general cytoplasmic profile; HPA records medium staining in bronchus and in selected glandular tissues, including colon and duodenum (HPA tissue IHC). The expected compartment also fits CYP1A1’s cytoplasmic and membrane annotations (UniProt P04798 subcellular location). Judge cell identity and distribution alongside intensity, because HPA rates its tissue pattern Uncertain (HPA tissue IHC). |
| Predominantly nuclear staining with little cytoplasmic signal. | A nuclear-only pattern does not match the supplied CYP1A1 locations or HPA’s general cytoplasmic profile (UniProt P04798 subcellular location; HPA tissue IHC). Treat it as suspect and compare the negative reagent control and another tissue section before assigning it to CYP1A1 (general IHC practice). The available records do not establish a diagnostic nuclear staining pattern. |
| Strong staining in adipocytes, skeletal myocytes, or smooth muscle cells. | Those cell types are listed as Not detected in the supplied tissue observations (HPA tissue IHC). Reproducible staining there warrants checking cell identification, cross-reactivity, and endogenous detection activity with appropriate controls (general IHC practice). A Not detected entry is an observation under HPA’s conditions, not proof that every specimen or biological state must be negative (HPA tissue IHC). |
| Diffuse chromogen across tissue and spaces between cells. | Widespread, cell-independent deposit obscures the cytoplasmic pattern used for interpretation (HPA tissue IHC; general IHC practice). Check the negative reagent control, reagent carryover, blocking, and wash quality (general IHC practice). Background alone cannot establish CYP1A1 expression, especially while the tissue pattern and the listed antibody’s IHC result remain Uncertain (HPA tissue IHC; HPA CAB018654). |
| No visible staining in a bronchus section expected to show signal. | HPA reports medium staining in bronchial respiratory epithelial cells, making bronchus a useful comparison specimen, though not a guaranteed positive control (HPA tissue IHC). Confirm that recognizable epithelium is present, then review the catalog antibody’s stated IHC-P conditions and the detection controls (general IHC practice). HPA’s Uncertain reliability prevents calling a negative section a technical failure by itself (HPA tissue IHC). |
| Compartment and topology | CYP1A1 is annotated at endoplasmic reticulum and microsome membranes, mitochondrial inner membrane, and cytoplasm, without an annotated transmembrane segment (UniProt P04798 topology). Paraffin IHC may read these closely spaced structures as cytoplasmic staining; a chromogenic pattern alone does not resolve the organelle (general IHC practice). |
| Choice of comparison tissue | HPA reports medium staining in bronchial respiratory epithelial cells and several glandular cell populations, while adipocytes and skeletal myocytes are Not detected (HPA tissue IHC). These are practical comparison patterns, with limited certainty because antibody staining and RNA expression show very low consistency pending external verification (HPA tissue IHC). |
| Isoforms and epitope coverage | Three isoforms are listed, but the supplied record does not map the antibody epitope or establish which isoforms it detects (UniProt P04798 isoforms; HPA CAB018654). Interpret staining as antibody-reactive CYP1A1 signal rather than an isoform assignment; verify epitope coverage from antibody documentation if isoform discrimination matters (general IHC practice). |
| Detection chemistry | Endogenous activity or nonspecific reagent binding can produce chromogen independently of primary-antibody binding (general IHC practice). Use suitable negative reagent and detection controls when staining appears in unexpected cells or across tissue (general IHC practice). This is a general workflow consideration; the supplied sources report no CYP1A1-specific endogenous detection effect. |
| IF/ICC Q&A: What localisation can guide IF review? | UniProt lists cytoplasm and several membranes, while HPA’s ICC-IF summary says Membrane but supplies no main location or cell-line images (UniProt P04798 subcellular location; HPA subcellular). Review IF localisation cautiously; the supplied ICC-IF record cannot validate a detailed organelle pattern or an IF/ICC protocol (HPA subcellular). |
| Situation | Likely cause | Next action |
|---|---|---|
| Predominantly nuclear chromogen. | The compartment differs from the reported cytoplasmic profile and annotated locations (HPA tissue IHC; UniProt P04798 subcellular location). | Check the negative reagent control, section quality, and cellular landmarks; repeat interpretation against a section with recognizable cytoplasm (general IHC practice). |
| Diffuse staining hides cell boundaries. | Background from detection reagents, incomplete blocking, or inadequate washing is possible (general IHC practice). | Compare a negative reagent control, review blocking and wash steps, and score only discernible cellular staining (general IHC practice). |
| Unexpected staining in adipocytes or myocytes. | These cell types are reported Not detected, so cross-reactivity or endogenous detection activity needs consideration (HPA tissue IHC; general IHC practice). | Verify cell identity and compare primary-omission and detection controls before attributing the signal to CYP1A1 (general IHC practice). |
| Bronchial epithelium appears negative. | HPA reports medium respiratory epithelial staining, but its tissue result has Uncertain reliability (HPA tissue IHC). | Confirm epithelium is present; check the catalog antibody’s IHC-P instructions, controls, and detection sequence before changing interpretation (general IHC practice). |
| Patchy staining across a glandular section. | Differences in represented cell populations or section quality may affect the apparent pattern (general IHC practice); HPA reports selected glandular cells at medium intensity (HPA tissue IHC). | Identify glandular cells on the counterstain, compare intact areas, and document the fraction and location of positive cells (general IHC practice). |
| A sharp organelle-level claim is needed from chromogenic IHC. | The annotated membrane locations are finer than a routine chromogenic cytoplasmic pattern can reliably distinguish (UniProt P04798 subcellular location; general IHC practice). | Report cytoplasmic staining at the resolution observed; seek separately validated localisation evidence before naming a specific organelle (general IHC practice). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Uncertain — Very low consistency between antibody staining and RNA expression data. Pending external verification.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Medium | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | Medium | Protein (IHC) | HPA → |
| Cerebellum | Purkinje cells | Medium | Protein (IHC) | HPA → |
| Colon | Glandular cells | Medium | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Caudate | Glial cells | Not detected | Protein (IHC) | HPA → |
| Skeletal muscle | Myocytes | Not detected | Protein (IHC) | HPA → |
| Smooth muscle | Smooth muscle cells | Not detected | Protein (IHC) | HPA → |
Troubleshoot CYP1A1 staining in paraffin sections by checking retrieval, compartment, controls, and scoring before interpreting signal (UniProt P04798; HPA tissue IHC).
PB9544 has real IHC images from paraffin mouse and rat kidney and human mammary cancer sections, frozen human placenta, and IF images from Caco-2 cells (catalog image captions).
PB9544 is listed for IHC and IHC-F in human, mouse and rat samples, with paraffin-section images from mouse kidney, rat kidney and human mammary cancer, and a frozen-section image from human placenta (catalog applications, reactivity and IHC captions). PB9544 is also listed for IF/ICC, with an IF image from Caco-2 cells (catalog applications and IF caption).
Which to pick: Choose PB9544 for paraffin-section IHC: its mouse kidney image documents citrate retrieval at pH 6 for 20 minutes and 1 μg/ml primary antibody (PB9544 IHC caption); the fixative is unreported (PB9544 IHC caption). Choose PB9544 for IF/ICC when Caco-2 image evidence is relevant; the caption documents 2 μg/ml primary antibody (PB9544 IF caption). PB9544 is listed as reactive with human, mouse and rat and for IHC, IHC-F and IF/ICC; clonality is unreported (catalog reactivity, applications and clone field).