QKI / KH domain-containing RNA-binding protein QKI · IHC design guide

Design Immunohistochemistry for QKI

Plan QKI chromogenic IHC using nuclear staining in glial and trophoblastic cells as tissue benchmarks (HPA tissue IHC). Account for the cytoplasmic pattern reported in Bergmann glia when interpreting sections (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for QKI (IHC for QKI): expected localisation Nuclear tissue staining; cytoplasmic in Bergmann glia (HPA tissue IHC), antibody M01874, validated IHC image, and IHC protocol steps
Printable QKI IHC protocol sheet — expected localisation Nuclear tissue staining; cytoplasmic in Bergmann glia (HPA tissue IHC), antibody M01874, controls and protocol steps. Open the full QKI IHC guide →

QKI 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 tissue staining; cytoplasmic in Bergmann glia (HPA tissue IHC)
Staining pattern Glial and trophoblast nuclei; Bergmann glia cytoplasm (HPA tissue IHC)
Antigen retrieval EDTA pH 8.0 HIER, heat-mediated (datasheet M01874)
Positive control ⓘ Caudate+4 more · see all
Negative control ⓘ Breast+4 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)
Caveat Bergmann glia may depart from the nuclear pattern (HPA tissue IHC)
Regulation Down-regulated in schizophrenia brain (UniProt)
Isoform / epitope 6 isoforms; map the epitope before isoform-specific scoring (UniProt)
Section 1

Recommended QKI IHC & IF Protocols

The catalog antibody protocol (datasheet: M01874) accompanies published QKI IHC methods for paraffin tissue arrays (PMC6995368) and human carotid arteries (PMC4821877).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human glioma tissue; fixative not specified (datasheet M01874)
FixationImage fixative and duration unreported (datasheet M01874); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat retrieval: EDTA pH 8.0 (datasheet M01874); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet M01874)
Primary antibodyRabbit monoclonal (clone 26Q56) anti-QKI, 1:50 (datasheet M01874)
Primary incubationOvernight at 4 °C (datasheet M01874)
DetectionHRP-conjugated secondary, DAB chromogen (datasheet M01874)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultQKI-positive staining in glial cells of caudate (HPA tissue IHC: High). HPA tissue profile: Nuclear expression in several tissues, most abundant in glial cells of the CNS and placental trophoblasts. No signal in the no-primary control.
💡Decision noteStart with heat-mediated EDTA retrieval at pH 8.0 for the catalog antibody (datasheet: M01874); optimize retrieval for other antibodies using the published conditions (PMC4821877).
Section 2

What Is the Expected QKI Staining Pattern?

QKI is predominantly nuclear, with lower cytoplasmic localization; it has no transmembrane segment (UniProt Q96PU8). In paraffin sections, expect nuclear staining in glial cells of the CNS and placental trophoblasts, with High HPA staining levels in several sampled regions (HPA tissue IHC). The tissue IHC profile has Enhanced reliability, reflecting high agreement between antibody staining and RNA expression data (HPA tissue IHC).

What am I looking at on my slide?
Distinct glial nuclei stain in caudate or cerebral cortex; trophoblast nuclei stain in placenta.This matches the predominant nuclear localization (UniProt Q96PU8) and the High staining levels reported for those cell populations (HPA tissue IHC). Judge the cells and their compartments together; staining across a whole tissue section is less informative than staining in the expected cells.
Bergmann glia show cytoplasmic or membrane-associated staining in cerebellum.This is a documented exception to the predominantly nuclear tissue profile: HPA lists High staining in Bergmann glia under cytoplasm/membrane (HPA tissue IHC). Lower cytoplasmic localization is also compatible with the UniProt record (UniProt Q96PU8). Do not classify this specific appearance as artefact solely because it is extranuclear.
Staining is confined to membranes, or fills many unrelated cells without a recognizable nuclear pattern.A broadly membrane-only result conflicts with QKI's predominantly nuclear localization and lack of a transmembrane segment (UniProt Q96PU8). Check whether the apparent pattern instead comes from nonspecific deposition or tissue morphology (general IHC practice); assess Bergmann glia separately because HPA records their cytoplasm/membrane pattern (HPA tissue IHC).
Respiratory or glandular epithelium stains strongly where the reference profile reports no detection.HPA reports QKI as not detected in bronchial respiratory epithelial cells and in duodenal and pancreatic glandular cells (HPA tissue IHC). A signal there warrants a cross-reactivity or endogenous detection activity check (general IHC practice). It does not, by itself, establish that the antibody binds QKI in those cells.
Color is diffuse across nuclei, cytoplasm, and extracellular spaces, or no cells stain in a known-positive section.Diffuse color obscures the cell-specific HPA pattern; assess background and detection controls (general IHC practice; HPA tissue IHC). No signal in glia from caudate or cerebral cortex, or in placental trophoblasts, calls for a technical-control review before interpreting the section as QKI-negative (HPA tissue IHC; general IHC practice).
💡Expected QKI appearanceA convincing positive is predominantly nuclear staining in CNS glia or placental trophoblasts at HPA's High level; indiscriminate color in HPA-negative epithelial populations is suspect, while cerebellar Bergmann glia have a documented cytoplasm/membrane exception (HPA tissue IHC; UniProt Q96PU8).
How each factor affects the staining
Cell and tissue choice (HPA tissue IHC)Caudate and cerebral cortex glia and placental trophoblasts are High reference populations (HPA tissue IHC). Hippocampal glia, cardiomyocytes, endometrial stromal cells, and adipocytes are listed as Medium, so use their reported levels when interpreting a weaker pattern (HPA tissue IHC).
Subcellular context (UniProt Q96PU8; HPA tissue IHC)QKI is predominantly nuclear but also occurs at lower levels in cytoplasm (UniProt Q96PU8). Interpret the reported Bergmann glial cytoplasm/membrane staining in its cell and tissue context rather than requiring every positive cell to look exclusively nuclear (HPA tissue IHC).
Isoforms and antibody interpretation (UniProt Q96PU8)UniProt lists 6 QKI isoforms (UniProt Q96PU8). The supplied record gives no epitope or isoform coverage for a chosen IHC antibody; a staining difference therefore cannot be assigned to a particular isoform from these sources alone.
Antibody validation (HPA antibodies; HPA tissue IHC)HPA019123 and CAB022602 each have Enhanced IHC status (HPA antibodies). HPA describes the tissue profile as highly consistent with RNA expression data (HPA tissue IHC). These annotations support the reference pattern, but they do not make every unexpected signal target-specific.
What should IF/ICC show? (HPA subcellular ICC-IF)The supported main IF/ICC location is nucleoplasm (HPA subcellular ICC-IF). UniProt also records lower cytoplasmic localization (UniProt Q96PU8). Use that localization as a cross-check only; IF/ICC has its own guide, and this IHC section supplies no IF/ICC protocol option.
Fixation sensitivity (source scope)Target-specific fixation sensitivity for QKI is unreported in the supplied UniProt and HPA records. Any decisions about retrieval or other section-processing conditions should follow the chosen antibody's IHC instructions and controls (general IHC practice), without assigning an observed difference to a documented QKI fixation effect.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
Known-positive glia or trophoblasts show no signal (HPA tissue IHC).The reference cells have High reported staining, so an absent result may reflect an assay failure or sample issue; the supplied sources do not identify which (HPA tissue IHC; general IHC practice).Confirm the expected cells are present, run a known-positive section, and check the chosen antibody's IHC dilution, retrieval, detection, and counterstain instructions (general IHC practice).
Staining is weak in hippocampus, heart muscle, or endometrial stroma (HPA tissue IHC).HPA lists hippocampal glia, cardiomyocytes, and endometrial stromal cells at Medium rather than High (HPA tissue IHC). A weaker appearance in these populations alone does not establish assay failure.Compare the correct cell population with a High reference such as caudate glia or placental trophoblasts, using matched staining conditions (HPA tissue IHC; general IHC practice).
Brown signal appears in bronchial epithelium or pancreatic exocrine cells (HPA tissue IHC).Both populations are reported as not detected (HPA tissue IHC). Possible explanations include nonspecific binding or endogenous detection activity (general IHC practice); the appearance alone cannot distinguish them.Review tissue morphology and include an appropriate primary-omission and detection control; reassess blocking and detection chemistry according to the assay (general IHC practice).
Background covers much of the section or hides nuclear boundaries.Diffuse chromogen can make cell-level localization unreliable (general IHC practice). It cannot be reconciled confidently with the nuclear tissue profile while the expected cells remain indistinct (HPA tissue IHC).Check the primary-omission control, blocking, antibody dilution, wash steps, chromogen development, and counterstain balance under the chosen IHC workflow (general IHC practice).
Cerebellar staining looks cytoplasmic or membrane-associated in Bergmann glia (HPA tissue IHC).HPA specifically records this appearance at a High level in Bergmann glia (HPA tissue IHC), despite the broader predominantly nuclear localization (UniProt Q96PU8).Identify Bergmann glia in the section and compare their pattern with the HPA cell-specific description; investigate only if the signal extends indiscriminately beyond the expected cells (HPA tissue IHC; general IHC practice).
Only broad membrane staining is visible outside the documented Bergmann glial pattern.A membrane-only distribution in other cells is difficult to reconcile with predominant nuclear localization and no transmembrane segment (UniProt Q96PU8; HPA tissue IHC).Review the positive and primary-omission controls and inspect for nonspecific deposition; repeat interpretation after the expected nuclei can be assessed clearly (general IHC practice; HPA tissue IHC).

Sample controls for QKI IHC & IF

🧪Run caudate first and look for staining in glial cells (HPA: High in caudate glial cells). Use bronchus respiratory epithelium as the negative tissue (HPA: Not detected in bronchus respiratory epithelial cells); on the caudate slide, cells without specific staining should show only background signal, without assuming that a particular neighboring cell type is QKI-negative.
Positive control tissue: Caudate (Glial cells, HPA High)
Negative control tissue: Breast (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show QKI in A-431, U-251MG, U2OS, with annotated localisation: Nucleoplasm (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control; a nonimmune rabbit IgG control matched to the primary’s isotype and monoclonal or polyclonal format; and QKI-knockout material as a biological negative (selected caption: rabbit anti-QKI). Quench endogenous peroxidase and check for native pigment before interpreting DAB signal in caudate sections (standard chromogenic IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected M01874 paraffin-section caption does not state the fixative (selected caption: fixative unreported). That example uses heat retrieval in EDTA at pH 8.0, but does not establish that retrieval is required for every specimen (selected caption: EDTA retrieval, pH 8.0). Paraffin IHC has a supplied tissue example, while the HPA IF images support nucleoplasmic localization without establishing that IF or frozen sections are easier; brain lipofuscin may complicate fluorescence interpretation (selected caption: paraffin-section IHC; HPA: nucleoplasm supported; standard brain IF practice).

HPA tissue IHC evidence for QKI

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — High 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

TissueCell typeLevelEvidenceSource
Caudate Glial cells High Protein (IHC) HPA →
Cerebellum Bergmann glia - cytoplasm/membrane High Protein (IHC) HPA →
Cerebral cortex Glial cells High Protein (IHC) HPA →
Placenta Trophoblastic cells High Protein (IHC) HPA →
Adipose tissue Adipocytes Medium Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
Breast Adipocytes Not detected Protein (IHC) HPA →
Bronchus Respiratory epithelial cells Not detected Protein (IHC) HPA →
Cervix Glandular cells Not detected Protein (IHC) HPA →
Duodenum Glandular cells Not detected Protein (IHC) HPA →
Fallopian tube Glandular cells Not detected Protein (IHC) HPA →
Section 3

Advanced QKI IHC Tips

Use the catalog antibody’s paraffin-section result as the starting point, then judge QKI staining by cell type, compartment, and matched controls.

What retrieval should I try first for weak QKI staining in paraffin sections?
Start with heat-mediated retrieval in EDTA at pH 8.0 (datasheet M01874). The catalog antibody produced a QKI signal in a paraffin-embedded human glioma section after this treatment, but the caption gives no heating time or fixative (datasheet M01874). Keep retrieval conditions constant while checking whether the 1:50 primary dilution and overnight incubation at 4°C reproduce the reported workflow (datasheet M01874). If staining remains weak, optimize heating time on adjacent sections with a matched positive control, recording tissue damage as well as signal (standard IHC practice). Reassess specificity against the expected predominantly nuclear pattern (UniProt Q96PU8; HPA tissue IHC).
How should I troubleshoot fixation-related loss of QKI staining?
Target-specific fixation sensitivity is unknown: the selected paraffin-section caption does not state a fixative (datasheet M01874). Record the specimen’s actual fixative, fixation duration, and processing history before comparing QKI results between blocks (standard IHC practice). Run adjacent sections from a consistently processed positive tissue alongside the affected section, using the reported EDTA pH 8.0 retrieval and 1:50 primary dilution (datasheet M01874). If fixation histories differ, optimize retrieval on matched material and assess nuclear detail and nonspecific staining together (standard IHC practice). Do not attribute a weak result to QKI-specific fixation sensitivity without a direct comparison (datasheet M01874: fixative unreported).
Should QKI staining be nuclear, cytoplasmic, or both?
Expect predominantly nuclear QKI, with lower cytoplasmic levels (UniProt Q96PU8); tissue IHC shows nuclear expression in several tissues (HPA tissue IHC). Supported nucleoplasmic localisation in cell imaging strengthens the nuclear expectation, although it does not establish a staining rule for every paraffin section (HPA subcellular). Cytoplasmic signal can be plausible, including a reported high signal in Bergmann glia annotated as cytoplasm or membrane (HPA tissue IHC). Score nuclei and cytoplasm separately rather than combining them into one intensity value (standard IHC practice). Investigate diffuse signal that ignores cell boundaries or appears equally strong across unrelated compartments with control sections (standard IHC practice; UniProt Q96PU8).
Can this stain distinguish QKI isoforms or modified epitopes?
QKI has 6 listed isoforms, including QKI5, QKI6, QKI7, and QKI7B (UniProt Q96PU8). Its KH domain spans residues 87–153, and listed modified residues include phosphoserine 188 and methylated arginines (UniProt Q96PU8). The supplied tissue caption does not identify the catalog antibody’s epitope or demonstrate isoform-specific recognition (datasheet M01874). Treat a positive chromogenic signal as antibody-detected QKI without assigning an isoform or modification state; use an antibody with documented epitope specificity if that distinction drives the experiment (standard IHC practice). When comparing conditions, hold retrieval and detection constant so technical variation is not mistaken for an isoform shift (standard IHC practice).
How can I adapt the QKI readout for multiplex immunofluorescence?
For the separate IF/ICC workflow, pair QKI with a validated marker for the expected cell type, such as a glial-cell marker when examining CNS glia (HPA tissue IHC; standard IF practice). Choose a fluorophore whose emission is distinguishable from tissue autofluorescence, and inspect an unstained section in each channel before setting exposure (standard IF practice). QKI lacks a transmembrane segment and is predominantly nuclear, so optimize permeabilisation for intracellular, especially nuclear, antibody access (UniProt Q96PU8; standard IF practice). Use single-stain and secondary-only controls to assess channel bleed-through and nonspecific fluorescence (standard IF practice). Do not transfer the paraffin-section antibody dilution or retrieval conditions directly to IF/ICC without testing them there (datasheet M01874; standard IF practice).
What should I check when DAB background obscures QKI-positive nuclei?
The reported paraffin-section workflow used 10% goat serum blocking, a 1:50 rabbit primary overnight at 4°C, and peroxidase-linked detection with DAB (datasheet M01874). Check a no-primary control to separate detection-system staining from antibody-dependent background (standard IHC practice). Apply an endogenous peroxidase block and compare adjacent sections with and without primary antibody, particularly where brown pigment may complicate reading (standard IHC practice). If diffuse staining persists, adjust primary concentration and washing while keeping the EDTA pH 8.0 retrieval consistent (datasheet M01874; standard IHC practice). Judge improvements by preserved nuclear contrast in expected cells, not by an overall reduction in brown signal alone (HPA tissue IHC; standard IHC practice).
How should I quantify QKI staining across tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring: QKI is predominantly nuclear, and glial cells show high tissue-IHC expression in several brain regions (UniProt Q96PU8; HPA tissue IHC). For nuclear staining, report the percentage of positive cells and an H-score based on prespecified intensity bins; record cytoplasmic staining separately (standard IHC practice). If cell abundance itself matters, report positive-cell density per mm² of evaluable tissue as well (standard IHC practice). Normalize positive counts to the number of eligible cells in the same annotated region, and exclude folds, edges, and necrotic areas using rules set before scoring (standard IHC practice). Apply identical imaging, threshold, and DAB development settings across compared sections (standard IHC practice).
How can I distinguish true QKI staining from artefact?
A credible pattern places substantial signal in nuclei of expected cells, including CNS glia or placental trophoblasts (HPA tissue IHC; UniProt Q96PU8). Some cytoplasmic staining remains plausible, so assess its cell boundaries and relationship to nuclear signal rather than rejecting it automatically (UniProt Q96PU8; HPA tissue IHC). Treat intense edge staining, necrotic deposits, or signal unrelated to intact cells as suspect, and compare them with a no-primary control (standard IHC practice). Check endogenous peroxidase activity when brown DAB signal appears in the control (standard IHC practice). Interpret negative areas against the same section’s positive cells or a matched control, because QKI expression varies by tissue and cell type (HPA tissue IHC).
Boster reagents

Best QKI / KH domain-containing RNA-binding protein QKI IHC Antibodies

QKI IHC images show human paraffin-embedded cancer sections (catalog IHC captions); IF images show human cancer sections and A549 cells (catalog IF captions). Listed reactivity spans human, mouse, rat, and monkey (catalog reactivity).

Real IHC data IHC analysis of QK1 using anti-QK1 antibody (M01874). QK1 was detected in a paraffin-embedded section of human glioma 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 1:50 rabbit anti-QK1 Antibody (M01874) 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.
Anti-QK1 Rabbit Monoclonal Antibody
Cat # M01874
Real IHC data IHC analysis of QKI using anti-QKI antibody (A01874-3). QKI was detected in a paraffin-embedded section of human glioma 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-QKI Antibody (A01874-3) 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.
Anti-QKI Antibody ®
Cat # A01874-3

M01874 has IHC images from human glioma and testis cancer paraffin sections, plus IF images from human cancer paraffin sections (catalog M01874 image captions). A01874-3 has IHC images from human glioma, bladder, renal, and breast cancer paraffin sections, plus an IF/ICC image from A549 cells (catalog A01874-3 image captions).

Which to pick: Choose M01874 for tissue IHC when a rabbit monoclonal is preferred; its human glioma paraffin-section image used EDTA pH 8 retrieval and 1:50 antibody dilution, with fixation unreported (catalog M01874 clone and IHC caption). Choose A01874-3 for IF/ICC based on its A549 cell image at 5 μg/mL; its own paraffin-section IHC image used EDTA pH 8 retrieval and 2 μg/mL, with fixation unreported (catalog A01874-3 IF and IHC captions). For cross-species selection, A01874-3 lists monkey alongside human, mouse, and rat, while M01874 lists human, mouse, and rat; the supplied IHC/IF images show human samples (catalog reactivity and image captions).

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

References

  1. UniProt Consortium. UniProt entry Q96PU8 (QKI_HUMAN, KH domain-containing RNA-binding protein QKI).
  2. Human Protein Atlas. QKI tissue IHC expression (reliability: Enhanced).
  3. Human Protein Atlas. QKI subcellular location (ICC-IF): Localized to the nucleoplasm..
  4. Human Protein Atlas. QKI antibody validation summary (2 antibodies).
  5. The RNA-binding protein QKI suppresses tumorigenesis of clear cell renal cell carcinoma by regulating the expression of HIF-1α. Journal of Cancer 2020 — PMC6995368.
  6. QKI-6 Suppresses Cell Proliferation, Migration, and EMT in Non-Small Cell Lung Cancer. Frontiers in oncology 2022 — PMC9117621.
  7. Quaking I-5 protein inhibits invasion and migration of kidney renal clear cell carcinoma via inhibiting epithelial-mesenchymal transition suppression through the regulation of microRNA 200c. Translational andrology and urology 2021 — PMC8575590.
  8. Quaking promotes monocyte differentiation into pro-atherogenic macrophages by controlling pre-mRNA splicing and gene expression. Nature communications 2016 — PMC4821877.
  9. PubMed PMID:11856480 — UniProt-cited evidence.
  10. PubMed PMID:14574404 — UniProt-cited evidence.
  11. PubMed PMID:15489334 — UniProt-cited evidence.