PRDM5 / PR domain zinc finger protein 5 · IHC design guide

Design Immunohistochemistry for PRDM5

Plan PRDM5 paraffin IHC around the nuclear tissue pattern reported by HPA (HPA tissue IHC). This guide covers fixation consistency, staining controls and cancer-associated expression changes (UniProt).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use

Immunohistochemistry protocol sheet for PRDM5 (IHC for PRDM5): expected localisation Nuclear staining in several tissues (HPA tissue IHC), antibody A06736-1, validated IHC image, and IHC protocol steps — Printable **PRDM5** IHC protocol sheet — expected localisation Nuclear staining in several tissues (HPA tissue IHC), antibody A06736-1, controls and protocol steps. Open the full PRDM5 IHC guide →

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PRDM5 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 staining in several tissues (HPA tissue IHC)
	Staining pattern	Nuclear staining in colon glandular and marrow hematopoietic cells (HPA tissue IHC)
	Antigen retrieval	EDTA pH 8.0 HIER, heat-mediated (datasheet A06736-1)
	Positive control ⓘ	Bone marrow+4 more · see all
	Negative control ⓘ	Adipose tissue

Important caveats

Reasons your staining may differ from the expected pattern.

	Fixation	Keep fixation consistent across sections (standard IHC practice; not target-specific)
	Caveat	Cancer-associated silencing may reduce tumor staining (UniProt)
	Regulation	Silencing reported in several cancers (UniProt)
	Isoform / epitope	4 isoforms; epitope coverage needs verification (UniProt)

Section 1

Recommended PRDM5 IHC & IF Protocols

The catalog antibody’s IHC-P protocol (datasheet A06736-1) is followed by four published PRDM5 IHC protocols (PMC4318154; PMC4642625; PMC9264607; PMC5973400).

Recommended immunohistochemistry (IHC-P) protocol parameters
Sample	Paraffin-embedded human gastric cancer tissue; fixative not specified (datasheet A06736-1)
Fixation	Image fixative and duration unreported (datasheet A06736-1); verify before use.
Sectioning	4–5 µm sections on charged slides (standard)
Deparaffinisation	Xylene, graded ethanol series to water (standard)
Antigen retrieval	Heat retrieval: EDTA pH 8.0 (datasheet A06736-1); 20 min, 95–100 °C (standard)
Peroxidase block	3% H2O2, 10 min, room temperature (standard)
Blocking	10% goat serum (datasheet A06736-1)
Primary antibody	Rabbit anti-PRDM5, 0.5-1μg/ml (datasheet A06736-1)
Primary incubation	Overnight at 4 °C (datasheet A06736-1)
Detection	Streptavidin-biotin complex (SABC), DAB chromogen (datasheet A06736-1)
Counterstain	Hematoxylin, blue, dehydrate and mount (standard)
Expected result	PRDM5-positive staining in hematopoietic cells of bone marrow (HPA tissue IHC: High). HPA tissue profile: Nuclear expression in several tissues. No signal in the no-primary control.

💡Decision noteStart with EDTA pH 8.0 heat retrieval for the catalog antibody (datasheet A06736-1); use each article’s stated retrieval when reproducing its assay.

Section 2

What Is the Expected PRDM5 Staining Pattern?

PRDM5 should appear primarily in nuclei in paraffin-section IHC (UniProt Q9NQX1: nucleus; HPA: nuclear expression in several tissues). Look for staining in hematopoietic cells of bone marrow and glandular cells of colon or cervix, among other reported populations (HPA: High). PRDM5 has no transmembrane segment, so membrane staining is unexpected (UniProt Q9NQX1: topology). HPA rates its tissue IHC reliability Enhanced, with medium consistency between staining and RNA data (HPA: tissue IHC reliability).

What am I looking at on my slide?
Clear nuclear signal in colon glandular cells or bone marrow hematopoietic cells.	This matches reported High staining in those cell populations and the expected nuclear compartment (HPA: colon and bone marrow, High; UniProt Q9NQX1: nucleus). Compare cells within the same section: the reported level describes a population, not a requirement that every cell stain equally (HPA: tissue IHC profile; general IHC interpretation).
Predominantly membrane or cytoplasmic staining with little convincing nuclear signal.	Treat this as a compartment mismatch: PRDM5 is nuclear and has no transmembrane segment (UniProt Q9NQX1: subcellular location and topology). Check whether the pattern persists in a no-primary control and with the IHC-validated antibody before assigning it to PRDM5 (general IHC practice; HPA: HPA051406 IHC Enhanced).
Strong staining chiefly in adipocytes while expected nuclear staining is absent.	HPA reports PRDM5 as Not detected in adipocytes, so that pattern warrants scrutiny (HPA: adipose tissue, adipocytes, Not detected). Cross-reactivity or endogenous detection activity are possible explanations to test with appropriate controls; the slide alone cannot distinguish them (general IHC practice).
Broad, hazy colour across nuclei, cytoplasm and surrounding tissue.	Diffuse background makes cell and compartment calls unreliable (general IHC interpretation). Compare a no-primary control, inspect blocking and washes, and assess whether the chromogenic signal remains confined to nuclei in reported positive populations (general IHC practice; HPA: nuclear tissue profile).
No nuclear signal in a reported High tissue population.	A negative result in colon glandular cells or bone marrow hematopoietic cells conflicts with the reported pattern but does not, by itself, prove PRDM5 absence (HPA: colon and bone marrow, High; general IHC interpretation). Check section quality, detection controls and the validated IHC conditions (general IHC practice).

💡Expected PRDM5 appearanceCall a convincing positive when chromogenic signal is predominantly nuclear in a reported High population, such as colon glandular cells or bone marrow hematopoietic cells; isolated membrane colour or diffuse tissue-wide haze is suspect (HPA: tissue IHC profile and High populations; UniProt Q9NQX1: nucleus and topology; general IHC interpretation).

How each factor affects the staining
Tissue and cell selection	HPA reports High staining in several distinct populations, including bronchial respiratory epithelial cells, cerebral cortical neuronal cells and cervical glandular cells (HPA: tissue IHC, High). Choose and score the named cell population within the section; a tissue label alone does not specify which cells should be positive (general IHC interpretation).
Low and undetected comparators	Adipocytes are reported Not detected; cholangiocytes in liver and myocytes in skeletal muscle are reported Low (HPA: tissue IHC). These are contextual comparators, not absolute specificity controls: weak staining in a Low population needs compartment and control checks before interpretation (general IHC interpretation).
Antibody evidence	The listed antibody HPA051406 has Enhanced IHC validation (HPA: antibody validation). HPA also describes overall tissue IHC reliability as Enhanced but notes medium consistency with RNA expression (HPA: tissue IHC reliability). Judge an individual slide against its controls and the reported cell-specific pattern (general IHC practice).
Isoforms and processing	UniProt lists 4 PRDM5 isoforms and one 1–630 chain, with no signal peptide, propeptide or glycosylation sites reported (UniProt Q9NQX1: isoforms and processing). These annotations do not identify the antibody epitope or predict an isoform-specific IHC pattern; avoid assigning different staining intensities to particular isoforms (UniProt Q9NQX1: supplied record).
Compartment interpretation	UniProt assigns PRDM5 to the nucleus; HPA tissue IHC likewise reports nuclear expression (UniProt Q9NQX1: subcellular location; HPA: tissue IHC profile). Score nuclear staining first. The supplied evidence does not establish a target-specific fixation or antigen-retrieval effect, so do not explain a result by asserting one (UniProt Q9NQX1 and HPA: supplied records).
IF/ICC Q&A: where should signal localize?	HPA reports mainly nucleoli and nuclear bodies, with additional nucleoplasmic localization in ICC-IF (HPA: subcellular, supported locations). This informs compartment interpretation if IF images are consulted; it does not require paraffin-section chromogenic IHC to resolve those structures (HPA: tissue IHC nuclear profile; general microscopy interpretation).

Why is my staining missing, weak or wrong?
Situation	Likely cause	Next action
A reported High population has no visible nuclear stain.	The run or detection may have failed, or the section may be unsuitable; absence alone cannot distinguish these possibilities (general IHC practice; HPA: reported High population).	Review an on-run positive control and the catalog antibody's IHC-P instructions, then compare nuclear staining in colon glandular cells or bone marrow hematopoietic cells (general IHC practice; HPA: both High).
Colour appears on cell membranes instead of nuclei.	The dominant compartment conflicts with nuclear PRDM5 and its lack of a transmembrane segment (UniProt Q9NQX1: location and topology).	Check a no-primary control and reassess nuclear signal in a reported positive cell population before scoring the membrane colour as specific (general IHC practice; HPA: tissue IHC profile).
Adipocytes stain strongly.	That result conflicts with HPA's Not detected adipocyte observation; cross-reactivity or endogenous detection activity are possibilities, not proven causes (HPA: adipocytes, Not detected; general IHC practice).	Compare no-primary and positive-tissue controls, then score the adipocyte compartment separately from nearby cells (general IHC practice; HPA: adipocyte observation).
The entire section has diffuse chromogenic background.	Background can obscure nuclear localization and make intensity comparisons unreliable (general IHC interpretation).	Inspect the no-primary control and review blocking, washes and detection conditions; reassess only interpretable nuclei in the named cell population (general IHC practice; HPA: nuclear tissue profile).
A Low tissue shows weak or variable signal.	HPA reports Low staining in liver cholangiocytes and skeletal muscle myocytes, so a faint result there is hard to use as a decisive positive or negative (HPA: tissue IHC, Low; general IHC interpretation).	Use a reported High population to check the run, and describe the Low population's cell identity, nuclear localization and intensity without imposing a universal cutoff (HPA: tissue IHC; general IHC practice).
IHC shows broad nuclear staining without distinct nuclear bodies.	HPA's nucleolar and nuclear-body detail comes from ICC-IF, while its tissue IHC summary describes nuclear expression (HPA: subcellular ICC-IF; HPA: tissue IHC profile).	Score the paraffin-section result by its nuclear compartment and reported cell population; use the ICC-IF localization as context rather than requiring visible puncta (HPA: tissue IHC and subcellular; general microscopy interpretation).

Source: UniProt Q9NQX1 Human Protein Atlas tissue Human Protein Atlas subcellular

Experiment evidence

IHC & IF images showing PRDM5 staining

IHC analysis of PRDM5 using anti-PRDM5 antibody (A06736-1). PRDM5 was detected in paraffin-embedded section of human gastric cancer tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 1μg/ml rabbit anti-PRDM5 Antibody (A06736-1) overnight at 4°C. Biotinylated goat anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using Strepavidin-Biotin-Complex (SABC) (Catalog # SA1022) with DAB as the chromogen.

A06736-1 · IHCIHC analysis of PRDM5 using anti-PRDM5 antibody (A06736-1). PRDM5 was detected in paraffin-embedded section of human gastric cancer tissue.

IF analysis of PRDM5 using anti-PRDM5 antibody (A06736-1). PRDM5 was detected in immunocytochemical section of U20S cells. Enzyme antigen retrieval was performed using IHC enzyme antigen retrieval reagent (AR0022) for 15 mins. The cells were blocked with 10% goat serum. And then incubated with 2μg/mL rabbit anti-PRDM5 Antibody (A06736-1) overnight at 4°C. DyLight®488 Conjugated Goat Anti-Rabbit IgG (BA1127) was used as secondary antibody at 1:100 dilution and incubated for 30 minutes at 37°C. The section was counterstained with DAPI. Visualize using a fluorescence microscope and filter sets appropriate for the label used.

A06736-1 · IFIF analysis of PRDM5 using anti-PRDM5 antibody (A06736-1). PRDM5 was detected in immunocytochemical section of U20S cells. Enzyme antigen re

HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000138738-PRDM5/tissue/cerebral+cortex#imid_14844856

HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000138738-PRDM5/tissue/colon#imid_14844774

HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000138738-PRDM5/tissue/liver#imid_14844775

HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000138738-PRDM5/tissue/kidney#imid_14844776

HPA ICC-IF BJ [Human fibroblast] — PRDM5 (HPA051406)

HPA · ICC-IF BJ [Human fibroblast]Human Protein Atlas immunofluorescence, BJ [Human fibroblast], antibody HPA051406; green = PRDM5, blue = nucleus, red = microtubules.

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Real IHC / IF data behind the staining-pattern expectations in this section.

Sample controls for PRDM5 IHC & IF

🧪Run bone marrow first; its hematopoietic cells should show PRDM5 staining (HPA: High in hematopoietic cells). Use adipose tissue as the negative tissue (HPA: Not detected in adipocytes); on the bone marrow slide, cells without convincing nuclear signal provide an internal negative comparison, but the supplied HPA row does not identify a specific negative cell type.

Positive control tissue: Bone marrow (Hematopoietic cells, HPA High)

Negative control tissue: Adipose tissue (HPA Not detected)

ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show PRDM5 in BJ [Human fibroblast], Rh30, U2OS, with annotated localisation: Nucleoli (supported), Nuclear bodies (supported) (HPA subcellular).

Technical controls: Include a no-primary (secondary-only) control, a rabbit IgG isotype control matched to the primary antibody’s clonality when known, and PRDM5 knockout material as a biological negative. For bone marrow, quench endogenous peroxidase and assess endogenous biotin because the reported IHC detection uses an avidin–biotin complex with DAB (selected-SKU caption: SABC/DAB).

⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected-SKU tissue-IHC caption does not state the fixative (selected-SKU caption: fixative not stated). The caption reports heat retrieval in EDTA at pH 8.0 for paraffin-section IHC, but does not establish whether retrieval is required for all specimens (selected-SKU caption: EDTA retrieval). The supplied evidence does not establish that frozen sections or IF/ICC are easier; marrow IHC requires attention to endogenous peroxidase and, with the reported SABC method, endogenous biotin (selected-SKU caption: SABC/DAB).

HPA tissue IHC evidence for PRDM5

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — 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
Bone marrow	Hematopoietic cells	High	Protein (IHC)	HPA →
Bronchus	Respiratory epithelial cells	High	Protein (IHC)	HPA →
Caudate	Glial cells	High	Protein (IHC)	HPA →
Cerebellum	Cells in molecular layer	High	Protein (IHC)	HPA →
Cerebral cortex	Neuronal cells	High	Protein (IHC)	HPA →

Undetected expression · recommended negative controls

Tissue	Cell type	Level	Evidence	Source
Adipose tissue	Adipocytes	Not detected	Protein (IHC)	HPA →

Section 3

Advanced PRDM5 IHC Tips

For PRDM5 chromogenic IHC, assess nuclear staining in the relevant cell population and interpret it alongside controls and tissue context (UniProt Q9NQX1; HPA tissue IHC).

Which retrieval conditions should I start with for PRDM5 in paraffin sections?

Start with heat-mediated antigen retrieval in EDTA at pH 8.0 for paraffin sections (datasheet A06736-1). The selected tissue-IHC image used this retrieval, followed by 10% goat serum blocking and 1 μg/ml primary antibody overnight at 4°C; its fixative was not reported (datasheet A06736-1). If nuclear staining is weak, check heating consistency, section adhesion and antibody incubation before changing retrieval conditions, using a positive control in the same run (standard IHC practice; HPA tissue IHC). Compare any adjusted retrieval against the starting condition and assess both nuclear signal and tissue damage, since PRDM5 is a nuclear protein (UniProt Q9NQX1; standard IHC practice).

How should fixation be handled when PRDM5 staining is weak or uneven?

Target-specific sensitivity of PRDM5 to fixation is unknown: the selected paraffin-section caption does not state a fixative (datasheet A06736-1). Record the specimen's actual fixation and processing history, then compare weak sections with a similarly processed positive control before attributing a difference to PRDM5 biology (standard IHC practice; HPA tissue IHC). Examine tissue preservation and retrieval uniformity across the section; inconsistent processing can complicate interpretation of chromogenic nuclear staining (standard IHC practice; UniProt Q9NQX1). Do not infer a preferred fixative from the reported tissue staining pattern, and report an unresolved fixation effect as a limitation when comparing specimens (HPA tissue IHC; standard IHC practice).

Where should a credible PRDM5 IHC signal appear?

Score PRDM5 primarily as a nuclear signal because UniProt places it in the nucleus and HPA reports nuclear expression across several tissues (UniProt Q9NQX1; HPA tissue IHC). HPA cell imaging further localizes PRDM5 mainly to nucleoli and nuclear bodies, with additional nucleoplasmic signal, although those details need not resolve in chromogenic tissue sections (HPA subcellular; standard IHC practice). Compare staining with nuclear morphology and the expected cell population, such as colon glandular cells, which show high HPA tissue staining (HPA tissue IHC). Predominantly diffuse cytoplasmic or extracellular DAB should prompt review of background and controls before it is assigned to PRDM5 (UniProt Q9NQX1; standard IHC practice).

Can this antibody distinguish PRDM5 isoforms or a specific nuclear epitope?

PRDM5 has 4 annotated isoforms, and the record places its SET domain at residues 8–124 (UniProt Q9NQX1). The supplied antibody caption does not identify an immunogen or mapped epitope, so staining cannot establish which isoform was detected (datasheet A06736-1; UniProt Q9NQX1). Check an antibody's documented epitope against isoform sequences before making isoform-specific claims, and keep scoring tied to the observed nuclear compartment (standard IHC practice; UniProt Q9NQX1). Because PRDM5 has no transmembrane segment or listed glycosylation sites, an apparent membrane pattern warrants scrutiny, but those annotations do not establish how fixation exposes this antibody's epitope (UniProt Q9NQX1).

How can IF help check cell identity and PRDM5 localisation?

Use IF as a complementary localisation check while keeping this page's chromogenic paraffin-section IHC conditions tied to the selected antibody caption (datasheet A06736-1). Multiplex PRDM5 with a marker for the expected cell population, such as an epithelial marker when examining HPA-positive colon glandular cells, and assess overlap within individual nuclei (HPA tissue IHC; standard IF practice). Choose spectrally separated fluorophores and a detection channel with low specimen autofluorescence, then include single-label controls to assess bleed-through (standard IF practice). Permeabilise sufficiently to access a nuclear epitope, since PRDM5 is nuclear and has no transmembrane segment; optimize that step within the separate IF workflow (UniProt Q9NQX1; standard IF practice).

What should I check when PRDM5 DAB staining is diffuse?

First compare diffuse DAB with the expected nuclear pattern and inspect a section processed without primary antibody (UniProt Q9NQX1; standard IHC practice). The selected image used a biotinylated secondary antibody, streptavidin–biotin detection and DAB, so include controls that reveal nonspecific secondary or detection-system staining (datasheet A06736-1; standard IHC practice). Peroxidase blocking and careful assessment of endogenous biotin are general safeguards for this chromogenic workflow, especially when signal persists outside nuclei (standard IHC practice). Check blocking, washing and primary-antibody concentration against the caption's 10% goat serum block and 1 μg/ml primary condition before interpreting widespread staining as PRDM5 (datasheet A06736-1; standard IHC practice).

How should PRDM5 staining be scored across specimens? ⚠ ANSWER MARKED FOR VERIFICATION

Define the relevant cell population and score nuclear DAB only, since PRDM5 is nuclear and HPA tissue expression differs by cell type (UniProt Q9NQX1; HPA tissue IHC). Report the percentage of positive nuclei and, when intensity is reproducible, an H-score using intensity grades 0–3 and a resulting range of 0–300 (standard IHC practice). Alternatively, report positive nuclei per mm² of viable tissue, with the counted area and cell-selection rules stated explicitly (standard IHC practice). Normalize comparisons to the number of eligible cells or viable area, and apply the same threshold, controls and scoring rules across batches (standard IHC practice).

How can I separate true PRDM5 staining from artefact?

A plausible positive shows nuclear staining in intact, identifiable cells, consistent with PRDM5's nuclear annotation and HPA tissue-IHC profile (UniProt Q9NQX1; HPA tissue IHC). Check whether the stained cell population fits the tissue context: HPA reports high staining in colon glandular cells but no detection in adipocytes (HPA tissue IHC). Treat staining concentrated at section edges, within necrosis, or outside nuclei cautiously, and use a no-primary control to assess endogenous enzyme and detection background (standard IHC practice; UniProt Q9NQX1). The selected gastric-cancer image demonstrates detectable staining under its stated conditions, while UniProt says PRDM5 tends to be silenced in some cancers; neither observation alone defines every specimen's status (datasheet A06736-1; UniProt Q9NQX1).

Boster reagents

Best PRDM5 / PR domain zinc finger protein 5 IHC Antibodies

The IHC-validated antibody has images of human gastric and mammary cancer paraffin sections and mouse intestine paraffin sections; IF imaging uses U20S cells (catalog image captions).

Real IHC data

Anti-PRDM5 Antibody ®

Cat # A06736-1

View product →

A06736-1 has IHC images from human gastric and mammary cancer and mouse intestine paraffin sections (catalog IHC captions). Its IF image shows U20S cells, and its listed applications include IHC, ICC and IF (catalog IF caption; catalog applications).

Which to pick: Choose A06736-1 for paraffin-section IHC: its own captions document EDTA retrieval at pH 8.0 and 1 μg/ml primary antibody (catalog IHC captions). Choose the same SKU for IF/ICC because both applications are listed and its IF caption documents 2 μg/ml in U20S cells (catalog applications; catalog IF caption). For cross-species work, the catalog lists Human, Mouse and Rat reactivity, while its IHC images document Human and Mouse tissue; the fixative is unreported (catalog reactivity; catalog IHC captions).

Each figure is that product's own IHC / IF validation image from its datasheet.

References

UniProt Consortium. UniProt entry Q9NQX1 (PRDM5_HUMAN, PR domain zinc finger protein 5).
Human Protein Atlas. PRDM5 tissue IHC expression (reliability: Enhanced).
Human Protein Atlas. PRDM5 subcellular location (ICC-IF): Mainly localized to the nucleoli and nuclear bodies. In addition localized to the nucleoplasm..
Human Protein Atlas. PRDM5 antibody validation summary (1 antibodies).
Methylation and expression of the tumour suppressor, PRDM5, in colorectal cancer and polyp subgroups. BMC cancer 2015 — PMC4318154.
Bruch's membrane abnormalities in PRDM5-related brittle cornea syndrome. Orphanet journal of rare diseases 2015 — PMC4642625.
Low expression of PRDM5 predicts poor prognosis of esophageal squamous cell carcinoma. BMC cancer 2022 — PMC9264607.
The methylation profiles of PRDM promoters in non-small cell lung cancer. OncoTargets and therapy 2018 — PMC5973400.
PubMed PMID:15077163 — UniProt-cited evidence.
PubMed PMID:14702039 — UniProt-cited evidence.
PubMed PMID:15815621 — UniProt-cited evidence.