PTPN1 / Tyrosine-protein phosphatase non-receptor type 1 · IHC design guide

Design Immunohistochemistry for PTPN1

Plan paraffin-section PTPN1 IHC around cytoplasmic staining in immune cells (HPA tissue IHC). Use lung macrophages as a high-staining reference and adipocytes as a not detected comparison, then score staining by cell type (HPA tissue IHC).

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

Immunohistochemistry protocol sheet for PTPN1 (IHC for PTPN1): expected localisation Cytoplasmic staining (HPA tissue IHC); ER membrane location (UniProt), antibody A00613-1, validated IHC image, and IHC protocol steps — Printable **PTPN1** IHC protocol sheet — expected localisation Cytoplasmic staining (HPA tissue IHC); ER membrane location (UniProt), antibody A00613-1, controls and protocol steps. Open the full PTPN1 IHC guide →

Navigate to: Protocols Staining pattern Controls Antibodies

PTPN1 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	Cytoplasmic staining (HPA tissue IHC); ER membrane location (UniProt)
	Staining pattern	Cytoplasmic staining mainly in immune cells (HPA tissue IHC)
	Antigen retrieval	EDTA pH 8.0 HIER, heat-mediated (datasheet A00613-1)
	Positive control ⓘ	Appendix+4 more · see all
	Negative control ⓘ	Adipose tissue+4 more · see all

Important caveats

Reasons your staining may differ from the expected pattern.

	Fixation	Keep paraffin-section fixation consistent (standard IHC practice; not target-specific)
	Caveat	Staining and RNA have medium consistency (HPA tissue IHC)
	Regulation	Expression regulation not specified (UniProt)
	Isoform / epitope	No listed isoforms; one 1–435 chain (UniProt)

Section 1

Recommended PTPN1 IHC & IF Protocols

Compare the catalog antibody's IHC-P protocol (datasheet A00613-1) with 2 published PTPN1 IHC protocols (PMC6911276; PMC10626546).

Recommended immunohistochemistry (IHC-P) protocol parameters
Sample	Paraffin-embedded rat spleen tissue; fixative not specified (datasheet A00613-1)
Fixation	Image fixative and duration unreported (datasheet A00613-1); 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 A00613-1); 20 min, 95–100 °C (standard)
Peroxidase block	3% H2O2, 10 min, room temperature (standard)
Blocking	10% goat serum (datasheet A00613-1)
Primary antibody	Rabbit anti-PTPN1, 2-5μg/ml (datasheet A00613-1)
Primary incubation	Overnight at 4 °C (datasheet A00613-1)
Detection	HRP-conjugated secondary, DAB chromogen (datasheet A00613-1)
Counterstain	Hematoxylin, blue, dehydrate and mount (standard)
Expected result	PTPN1-positive staining in lymphoid tissue of appendix (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression mainly in cells of the immune system. No signal in the no-primary control.

💡Decision noteStart with heat-mediated EDTA retrieval at pH 8.0 (datasheet A00613-1); neither published excerpt specifies retrieval conditions (PMC6911276; PMC10626546).

Section 2

What Is the Expected PTPN1 Staining Pattern?

PTPN1 is associated with the endoplasmic reticulum membrane, although UniProt lists no transmembrane segment (UniProt P18031 topology). In tissue IHC, expect cytoplasmic staining, mainly in immune cells; lung macrophages and lymph node germinal center cells are high examples (HPA tissue IHC). HPA rates the tissue staining profile Approved, with medium consistency between antibody staining and RNA expression (HPA tissue IHC).

What am I looking at on my slide?
Cytoplasmic staining in lung macrophages or lymph node germinal center cells, with clear cell boundaries.	This matches the reported high staining in those cell populations (HPA tissue IHC). Compare the target cells with nearby cells on the same section; the HPA profile is Approved but has only medium staining–RNA consistency (HPA tissue IHC).
Predominantly nuclear staining, with little cytoplasmic signal in the expected cells.	This conflicts with the cytoplasmic tissue profile and endoplasmic reticulum localization (HPA tissue IHC; UniProt P18031). Treat it as suspect until controls and antibody specificity are checked; nuclear staining alone does not establish PTPN1 localization (standard IHC practice).
Strong staining restricted to adipocytes, cardiomyocytes, or gallbladder glandular cells.	HPA reports PTPN1 as not detected in these particular cell populations (HPA tissue IHC). Check cell identity and background before attributing signal to PTPN1; staining elsewhere in the same tissue may differ (standard IHC practice; HPA tissue IHC).
Uniform color over cells, extracellular spaces, and blank areas of the section.	A pattern without cell boundaries is consistent with background from detection or washing steps (standard chromogenic IHC practice). Use a no-primary control and inspect blocking, wash conditions, and chromogen development before scoring cells (standard IHC practice).
No cytoplasmic signal in the expected cells of a lung or lymph node control.	HPA reports high staining in lung macrophages and lymph node germinal center cells (HPA tissue IHC). First confirm those cells are present; then review the antibody's IHC-P instructions, retrieval, detection reagents, and control performance (standard IHC practice).

💡Expected PTPN1 appearanceCall positive when identifiable lung macrophages or lymph node germinal center cells show clear, predominantly cytoplasmic staining at a readily visible level (HPA tissue IHC); isolated nuclear color or color outside cell boundaries is suspect (HPA tissue IHC; standard IHC practice).

How each factor affects the staining
Cell population and tissue context	The expected intensity is cell specific: HPA lists high staining in lung macrophages, glomerular cells, duodenal glandular cells, and lymph node germinal center cells, but low staining in cerebral cortex neuronal cells (HPA tissue IHC). Score the annotated population, not the whole tissue (standard IHC practice).
Subcellular location and topology	UniProt places PTPN1 at the endoplasmic reticulum membrane while listing no transmembrane segment (UniProt P18031 topology). Tissue IHC describes the visible signal as cytoplasmic (HPA tissue IHC); routine chromogenic staining need not resolve individual endoplasmic reticulum structures (standard IHC practice).
Antibody validation	HPA marks the IHC results for HPA012542, CAB009329, and CAB015217 Approved (HPA antibody validation). Approval supports using their reported patterns as comparators, while the tissue profile's medium staining–RNA consistency calls for controls and cell-level interpretation (HPA tissue IHC; standard IHC practice).
Protein processing and isoforms	The supplied UniProt record lists one chain spanning residues 1–435, with no signal peptide, propeptide, or listed isoforms (UniProt P18031). It gives no basis for predicting a distinct staining pattern from cleavage or an alternate isoform; avoid assigning unexpected compartments to either (UniProt P18031).
Antigen retrieval in paraffin sections	Target-specific fixation effects are not established by the supplied assay evidence. Verify with a matched IHC source before attributing a result to fixation.
IF/ICC: what pattern should be expected?	HPA reports mainly endoplasmic reticulum localization, with additional cytosolic localization marked uncertain (HPA subcellular ICC-IF). HPA012542 and CAB009329 have Supported ICC status; CAB015217 is Uncertain for ICC (HPA antibody validation). Use the separate IF/ICC guide for that application.

Why is my staining missing, weak or wrong?
Situation	Likely cause	Next action
Expected macrophages or germinal center cells appear unstained.	The target cell population may be absent from the examined field, or the IHC detection run may have failed (HPA tissue IHC; standard IHC practice).	Identify the relevant cells on the section, examine a known-positive tissue control, then check the catalog antibody's IHC-P instructions and detection controls (HPA tissue IHC; standard IHC practice).
Only nuclei are strongly colored.	The pattern conflicts with the cytoplasmic tissue profile and endoplasmic reticulum association (HPA tissue IHC; UniProt P18031).	Check a no-primary control and compare staining with annotated positive cells; reassess specificity before counting nuclear-only cells as positive (standard IHC practice; HPA tissue IHC).
Adipocytes or cardiomyocytes show strong, apparently specific color.	Those cells are listed as not detected by HPA; misleading staining or incorrect cell identification is possible (HPA tissue IHC; standard IHC practice).	Confirm morphology and inspect a no-primary control. Compare the same antibody on a tissue with an HPA high cell population before interpreting the signal (HPA tissue IHC; standard IHC practice).
The entire section has weak, diffuse brown color.	Diffuse color may reflect background from detection chemistry or insufficient washing (standard chromogenic IHC practice).	Compare a no-primary control, review blocking and washes, and adjust chromogen development using control sections (standard IHC practice). Score only identifiable cellular staining (standard IHC practice).
A negative control is stained while the positive control is clear.	Color in the negative control suggests nonspecific detection or endogenous activity; a clear positive control also requires checking the run (standard IHC practice).	Review the no-primary and reagent controls, endogenous-activity blocking, and detection steps. Repeat with appropriate controls before interpreting tissue differences (standard IHC practice).
A low-staining tissue looks negative beside a high-staining tissue.	HPA reports low staining in cerebral cortex neuronal cells but high staining in lung macrophages; visibility can differ by cell population (HPA tissue IHC).	Confirm the annotated cells and compare like cell populations under the same scoring criteria. Do not use a low-staining population alone to declare the IHC run failed (HPA tissue IHC; standard IHC practice).

Source: UniProt P18031 Human Protein Atlas tissue Human Protein Atlas subcellular

Experiment evidence

IHC & IF images showing PTPN1 staining

IHC analysis of PTP1B/PTPN1 using anti-PTP1B/PTPN1 antibody (A00613-1). PTP1B/PTPN1 was detected in a paraffin-embedded section of rat spleen tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH 8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 2 μg/ml rabbit anti-PTP1B/PTPN1 Antibody (A00613-1) overnight at 4°C. Peroxidase Conjugated Goat Anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using HRP Conjugated Rabbit IgG Super Vision Assay Kit (Catalog # SV0002) with DAB as the chromogen.

A00613-1 · IHCIHC analysis of PTP1B/PTPN1 using anti-PTP1B/PTPN1 antibody (A00613-1). PTP1B/PTPN1 was detected in a paraffin-embedded section of rat splee

HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000196396-PTPN1/tissue/cerebral+cortex#imid_4079988

HPA · CerebellumHuman Protein Atlas IHC, Cerebellum. Source: https://www.proteinatlas.org/ENSG00000196396-PTPN1/tissue/cerebellum#imid_4080007

HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000196396-PTPN1/tissue/colon#imid_4079914

HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000196396-PTPN1/tissue/liver#imid_4079923

HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA012542; green = PTPN1, blue = nucleus, red = microtubules.

← swipe / scroll for more images →

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

Sample controls for PTPN1 IHC & IF

🧪Run appendix first: lymphoid tissue should stain (HPA: High in appendix lymphoid tissue); use adipose tissue as the negative comparator, scoring adipocytes (HPA: Not detected in adipocytes). On the appendix slide, internal negative cells should lack signal above background; the supplied HPA row does not identify a specific negative cell type (HPA: appendix lymphoid tissue row).

Positive control tissue: Appendix (Lymphoid tissue, HPA High)

Negative control tissue: Adipose tissue (HPA Not detected)

ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show PTPN1 in A-431, U-251MG, U2OS, ASC52telo, RPTEC/TERT1, hTERT-RPE1 (serum starved), KOLF2.1J, with annotated localisation: Endoplasmic reticulum (supported) (HPA subcellular).

Technical controls: Include a no-primary, secondary-only slide and a concentration-matched rabbit IgG isotype control, matching the rabbit primary in the selected caption (caption: rabbit antibody A00613-1). Use PTPN1-knockout material as a biological specificity control where available, and block endogenous peroxidase before DAB detection in the lymphoid tissue section (standard IHC practice; caption: peroxidase/DAB detection).

⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected paraffin-section caption does not state a fixative (caption: fixative not stated). The reported tissue-IHC example uses heat retrieval in EDTA at pH 8.0; it does not establish whether retrieval is essential (caption: EDTA heat retrieval). The supplied evidence does not establish whether frozen sections or IF are easier; for appendix DAB staining, check for endogenous peroxidase background (standard IHC practice; HPA: High in appendix lymphoid tissue).

HPA tissue IHC evidence for PTPN1

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Medium consistency between antibody staining and RNA expression data. Antibody staining in cells/structures not annotated, view images.). 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
Appendix	Lymphoid tissue	High	Protein (IHC)	HPA →
Caudate	Glial cells	High	Protein (IHC)	HPA →
Colon	Endothelial cells	High	Protein (IHC)	HPA →
Duodenum	Glandular cells	High	Protein (IHC)	HPA →
Fallopian tube	Glandular cells	High	Protein (IHC)	HPA →

Undetected expression · recommended negative controls

Tissue	Cell type	Level	Evidence	Source
Adipose tissue	Adipocytes	Not detected	Protein (IHC)	HPA →
Cerebellum	Cells in granular layer	Not detected	Protein (IHC)	HPA →
Endometrium	Cells in endometrial stroma	Not detected	Protein (IHC)	HPA →
Gallbladder	Glandular cells	Not detected	Protein (IHC)	HPA →
Heart muscle	Cardiomyocytes	Not detected	Protein (IHC)	HPA →

Section 3

Advanced PTPN1 IHC Tips

Troubleshoot PTPN1 staining in paraffin sections by checking retrieval, cell type, compartment and controls before interpreting chromogenic signal.

How should I adjust retrieval when PTPN1 staining is weak?

Start with heat-mediated retrieval in EDTA at pH 8.0 for this catalog antibody (datasheet A00613-1). The supplied paraffin-section example used that retrieval before 2 μg/ml primary antibody overnight at 4°C (caption A00613-1). If signal is weak, first check that the section was fully heated, cooled and kept hydrated during processing (standard IHC practice). Compare a retrieval-time series on adjacent sections while keeping antibody concentration, detection and imaging conditions constant (standard IHC practice). Only if that fails, test another retrieval buffer as a documented fallback alongside the EDTA reference; excessive retrieval can damage morphology (standard IHC practice).

Could fixation explain absent or patchy PTPN1 staining?

Target-specific fixation sensitivity is unknown: the selected paraffin-section caption does not report its fixative (caption A00613-1). Record each specimen’s fixative and fixation duration, then compare similarly processed sections before attributing a weak result to PTPN1 biology (standard IHC practice). The supplied staining example instead specifies EDTA at pH 8.0, 10% goat-serum block and 2 μg/ml primary antibody overnight at 4°C (caption A00613-1). Use that reported staining sequence as a comparison while documenting fixation separately (caption A00613-1; standard IHC practice). Do not infer fixation tolerance from tissue staining patterns or protein topology; neither tests fixation sensitivity (HPA tissue IHC; UniProt P18031 topology).

What compartment should I expect to stain in tissue sections?

Expect predominantly cytoplasmic staining, potentially with a perinuclear or reticular pattern consistent with endoplasmic-reticulum localisation (HPA tissue IHC; HPA subcellular; UniProt P18031). HPA supports the endoplasmic reticulum as the main subcellular location and labels additional cytosolic localisation uncertain (HPA subcellular). Judge compartment in intact cells against morphology and a matched negative control, since diffuse DAB can obscure fine reticular detail (standard IHC practice). PTPN1 interacts with EPHA3 at the cell membrane, but that interaction alone does not establish dominant membrane staining in paraffin sections (UniProt P18031). Treat predominantly nuclear or extracellular staining as a specificity question and repeat with controlled retrieval and detection (UniProt P18031; standard IHC practice).

How do epitope location and modification affect my IHC result?

The supplied record lists 0 isoforms and a phosphatase domain spanning residues 3–277, but gives no antibody epitope (UniProt P18031). It also lists modified residues including phosphotyrosines at 20 and 66, and phosphoserine at 50 (UniProt P18031). Without an epitope map, do not claim that any one modification explains lost or gained staining (UniProt P18031; standard IHC interpretation). Compare adjacent sections under matched retrieval and antibody conditions, and seek epitope documentation if results depend on a treatment (standard IHC practice). Record the exact antibody and detection conditions before comparing studies, because signal strength alone cannot identify an isoform or modification state (standard IHC interpretation).

How can I check PTPN1 localisation by multiplex IF?

For a secondary IF experiment, pair PTPN1 with a macrophage marker such as CD68 in lung, where macrophages show high tissue staining (HPA tissue IHC; standard IF practice). Choose a fluorophore channel with low measured tissue autofluorescence, and include single-label controls to assess bleed-through (standard IF practice). PTPN1 is associated with the endoplasmic reticulum, but the antibody epitope and its membrane-facing side are unreported (HPA subcellular; UniProt P18031; caption A00613-1). Compare gentle detergent permeabilisation with an otherwise matched condition when testing epitope access, rather than assuming which membrane side contains it (standard IF practice). Score cellular overlap and reticular distribution separately; the HPA cytosolic location has uncertain support (HPA subcellular; standard IF practice).

How do I reduce diffuse brown staining around PTPN1-positive cells?

Start by comparing the stained section with a no-primary control to separate antibody-associated signal from detection background (standard IHC practice). The catalog example used a 10% goat-serum block, 2 μg/ml rabbit primary overnight at 4°C, and a peroxidase-linked secondary for 30 minutes at 37°C (caption A00613-1). Include a peroxidase-blocking step before DAB development where appropriate; this is a general chromogenic IHC precaution, not PTPN1-specific evidence (standard IHC practice). If the no-primary control is clean, titrate exposure and wash conditions while preserving an adjacent reference section (standard IHC practice). Interpret fine cytoplasmic signal cautiously when heavy DAB deposition masks cell boundaries (HPA tissue IHC; standard IHC practice).

How should I score PTPN1 across unevenly stained sections? ⚠ ANSWER MARKED FOR VERIFICATION

Define the cell population and compartment before scoring; HPA reports mainly cytoplasmic expression in immune-system cells (HPA tissue IHC). For a mixed tissue, report both the percentage of positive cells and staining intensity, or calculate an H-score from prespecified intensity categories (standard IHC practice). If counting discrete positive cells, express density per mm² of viable tissue and normalise to the area actually evaluated (standard IHC practice). Keep retrieval, chromogen development, counterstain and image thresholds consistent across sections, and exclude folds or necrotic areas by a stated rule (standard IHC practice). Report cell-type-specific results separately so differences in immune-cell abundance do not masquerade as per-cell PTPN1 changes (HPA tissue IHC; standard IHC interpretation).

When is a PTPN1-positive IHC result convincing?

A convincing result follows intact cell outlines and shows cytoplasmic staining compatible with endoplasmic-reticulum localisation (HPA tissue IHC; HPA subcellular). Cell identity matters: HPA reports high staining in lung macrophages and lymph-node germinal-center cells, with no detection in adipocytes (HPA tissue IHC). Check those expectations against the sampled region rather than treating every brown pixel as PTPN1 (HPA tissue IHC; standard IHC interpretation). Discount staining concentrated at section edges, folds or necrotic areas, and investigate signal retained in a no-primary control as possible endogenous-enzyme or detection artefact (standard IHC practice). HPA rates tissue staining approved with medium RNA consistency, so corroborate unexpected compartments or cell types before drawing a biological conclusion (HPA tissue IHC).

Boster reagents

Best PTPN1 / Tyrosine-protein phosphatase non-receptor type 1 IHC Antibodies

The IHC-validated antibody has a rat spleen paraffin-section image (A00613-1 caption). The catalog lists human, mouse and rat reactivity for A00613-1 and human reactivity for M00613 (catalog applications/reactivity).

Real IHC data

Anti-PTP1B/PTPN1 Antibody ®

Cat # A00613-1

View product →

A00613-1 has an IHC image from a paraffin-embedded rat spleen section (A00613-1 caption). M00613 lists human reactivity and IHC and ICC/IF applications, but provides no IHC or IF image (M00613 catalog applications/reactivity; image alts).

Which to pick: Choose A00613-1 for tissue IHC supported by a paraffin-section image; its caption reports heat retrieval in EDTA pH 8.0, and its catalog lists human, mouse and rat reactivity (A00613-1 caption; catalog reactivity). Choose M00613 for human IF/ICC based on its application listing and rabbit monoclonal clone IHG-16, while treating that use as unillustrated here (M00613 catalog applications/clone; image alts). The A00613-1 caption identifies a paraffin-embedded section but does not report the fixative (A00613-1 caption).

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

References

UniProt Consortium. UniProt entry P18031 (PTN1_HUMAN, Tyrosine-protein phosphatase non-receptor type 1).
Human Protein Atlas. PTPN1 tissue IHC expression (reliability: Approved).
Human Protein Atlas. PTPN1 subcellular location (ICC-IF): Mainly localized to the endoplasmic reticulum. In addition localized to the cytosol..
Human Protein Atlas. PTPN1 antibody validation summary (3 antibodies).
Curcumin inhibits proliferation of hepatocellular carcinoma cells by blocking PTPN1 and PTPN11 expression. Oncology letters 2023 — PMC10272960.
Protein tyrosine phosphatase PTPN1 modulates cell growth and associates with poor outcome in human neuroblastoma. Diagnostic pathology 2019 — PMC6911276.
CAPN1 promotes malignant behavior and erlotinib resistance mediated by phosphorylation of c-Met and PIK3R2 via degrading PTPN1 in lung adenocarcinoma. Thoracic cancer 2020 — PMC7327690.
PTPN1 is a prognostic biomarker related to cancer immunity and drug sensitivity: from pan-cancer analysis to validation in breast cancer. Frontiers in immunology 2023 — PMC10626546.
PubMed PMID:2157211 — UniProt-cited evidence.
PubMed PMID:2164224 — UniProt-cited evidence.
PubMed PMID:11780052 — UniProt-cited evidence.