UESC Immunohistochemistry data
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Mouse expression data summary

This document presents our data in a MISFISHIE-compliant manner. You can download all of the data tables in this page individually, or all together as a zip archive of TSV or CSV files. You can also download a zip archive of all the mouse IHC images ( 73 MB).

Experimental Design:

  • Experiment Description: An immunohistochemical comparison of various anti-CD antibodies in many different mouse bladder and prostate tissue sections.
  • Assay Type: Immunohistochemistry
  • Experiment Type: Comparison of multiple tissue specimens and antibodies
  • Experimental factors: antibody; specimen; organism (mouse)
  • The number of hybridizations/stains performed in the experiment: 72
  • URL of any supplemental websites or database accession numbers related to the experiment: http://scgap.systemsbiology.org/data/
  • Contact information for communicating with the experimenter(s): Eric Deutsch, Institute for Systems Biology, 1441 N 34th St, Seattle WA 98103 (edeutsch systemsbiology.org)

Specimens (BioMaterials) used, section or mount preparation (Treatment):

  • The origin of the biological specimens (e.g., name of the organism, the provider of the specimen) and their characteristics: e.g., sex, developmental stage, age, strain, genotype, phenotype, disease state, treatments, etc. All information critical for other researchers to be able to reproduce the biomaterials as closely as possible must be provided (not limited to the above examples). Referencing an established ontology for the terms you use is HIGHLY encouraged. All specimens were obtained from the University of Washington Medical Center.
  • Manipulation of specimens into sections (or preparation for mounting if whole mounts), and the protocols used: Specimen Preparation Protocol

    Specimen Designator Tissue Type Organism Gender
    mb-1 Bladder Mus musculus Unknown
    mb-2 Bladder Mus musculus Unknown
    mb-10 Bladder Mus musculus Unknown
    mp-1 Prostate Mus musculus Male
    mp-2 Prostate Mus musculus Male
    mp-3 Prostate Mus musculus Male
    mp-4 Prostate Mus musculus Male
    mp-5 Prostate Mus musculus Male
    mp-6 Prostate Mus musculus Male
    mp-10 Prostate Mus musculus Male
    View All Rows   Export as: TSV CSV

Probe or antibody information:

  • Unambiguous genomic identification of the probe or antibody:
  • At minimum, the gene identifier and the reference database containing the identifier
  • If available, the full sequence of the probe, or clone identifiers of the antibody.
  • Protocol for how the probes or antibodies were designed and produced or the source from which they were obtained. For GFP experiments, the promoter sequence should be specified as the "probe".
  • For probes or antibodies purchased from a company, the company name and catalog number must be provided, as well as the web site which details the specifications if available.
  • For a custom made antibody the putative antigen and references to studies that characterize the sensitivity and specificity of the antibody in tissue immunostains should be provided. Virtually all monoclonal antibodies purchased from BD Pharmingen

    Ab Name Ref Db Accession Origin Vendor Details
    CD1a Locus Link 909 321 CD1a
    CD1b Locus Link 910 321 CD1b
    CD1c Locus Link 911 321 CD1c
    CD1d Locus Link 912 321 CD1d
    CD1e Locus Link 913 321 CD1e
    CD2 Locus Link 914 321 CD2
    CD3delta Locus Link 915 321 CD3delta
    CDe Locus Link 916 321 CDe
    CD3gamma Locus Link 917 321 CD3gamma
    CD4 Locus Link 920 321 CD4
    View All Rows   Export as: TSV CSV

Staining protocols and parameters:

  • Number of detectable probes or antibodies on the hybridization or stain. For most hybridizations/stains this will be one. If multiple hybridizations/stains are applied to a section, i.e. for confocal microscopy, the number will exceed one.

    Slide Designator Specimen Designator Antibodies Number of Antibodies
    CD90 mb-2 mb-2 CD90mouse 1
    CD107b mb-2 mb-2 CD107bmouse 1
    CD24 mb-2 mb-2 CD24mouse 1
    CD13 mb-1 mb-1 CD13mouse 1
    CD138 mb-1 mb-1 CD138mouse 1
    CD13 mb-2 mb-2 CD13mouse 1
    CD138 mb-2 mb-2 CD138mouse 1
    CD138 mp-2 mp-2 CD138mouse 1
    CD24 mp-2 mp-2 CD24mouse 1
    CD90 mp-2 mp-2 CD90mouse 1
    View All Rows   Export as: TSV CSV

  • The protocol and conditions used to produce the hybridization or immunostain, including mounting onto the slide/substrate and subsequent treatments of the section, i.e. immunohistochemical stain protocol: Slide Preparation Protocol
  • Also provide protocols for the assay controls:

    Imaging data and parameters:

    • The images. Although the MIAME specification stops short of requiring image data, the present specification requires that images be provided since the interpretation of in situ or immunohistochemistry images is subject to observer variability. Furthermore, many specimens are unique; consequently, exact reproduction can be problematic or impossible. Include both positive and negative results.
    • Image acquisition parameters:
      • Detection method by which hybridization or staining is observed (for each channel {e.g. fluorescent wavelength, etc.} if multiple probes or antibodies are used): ????
      • Image scale or total instrumental magnification: See table below
      • Image acquisition protocol: SCGAP UESC Image Acquisition Protocol
      • Imaging hardware and software used: Olympus BX41, Adobe Photoshop 5
      • Image analysis and/or editing software used (if relevant): Adobe Photoshop 5

        Image Designator Slide Designator Magnification Image
        CD107b mb-10 a- 100 CD107b mb-10 100 View
        CD107b mb-10 ba 200 CD107b mb-10 200 View
        CD138 mb-10 a- 100 CD138 mb-10 100 View
        CD138 mb-10 ba 200 CD138 mb-10 200 View
        CD13 mb-10 a- 200 CD13 mb-10 200 View
        CD24 mb-10 a- 100 CD24 mb-10 100 View
        CD24 mb-10 ba 200 CD24 mb-10 200 View
        CD44 mb-10 a- 100 CD44 mb-10 100 View
        CD44 mb-10 ba 200 CD44 mb-10 200 View
        CD47 mb-10 a- 200 CD47 mb-10 200 View
        View All Rows   Export as: TSV CSV

      Image Characterizations:

      The type of characterization that is recorded for such data can vary significantly depending on the experimental design. The following guidelines specify a minimum set of characterization features. Additional characterization of the images as required by the experimental design should also be provided. Include both positive and negative results.

      • List ontology entries (including reference to ontology, terms, accession numbers) (or provide term and definition if sufficient detail cannot be found in an existing ontology) for each structural unit used for classification. Structural units will be a type of: organ, tissue, cell, etc.

        See also: http://scgap.systemsbiology.net/ontology/Glossary.php
        Structural Unit Definition
        Luminal Epithelial Cells Epithelial cells that lines the lumens of prostate glands and ducts
        Basal Epithelial Cells Epithelial cells adjacent to the basement membrane and subjacent to the luminal/secretory epithelial cells
        Stromal Fibromuscular Cells The spindle cells that comprise the interstitium.
        Stromal Endothelial Cells The cells that line the lumen of all blood vessels
        Stromal Perineural Cells The outermost layer of stromal cells that surround peripheral nerves
        Stromal Nerve Sheath Cells Spindle cells that surround axonal processes of nerves.
        Stromal Leukocytes "White blood cells, including lymphocytes, neutrophils, eosinophils, basophils and macrophages/histiocytes"
        Cancerous Cells Cancerous cells of any type
        Normal Cells Normal cells of any type
        Atrophic glands Benign glands lined by an apparent single layer of predominantly basal cells that form a flat epithelium.
        View All Rows   Export as: TSV CSV

      • Define (or choose from an ontology) the staining intensity scale. For example, a three-point scale (of none, equivocal, or intense) is recommended for evaluating CD immunostains. Each gradation of intensity in the scale that is used should be properly defined.

        Intensity Unit Definition
        intense Immunoreaction deposit is distintly more optically dense than background and than tissue that does not express the antigen.
        equivocal "Immunoreaction deposit is either similar enough in optical density to the background and/or to tissue that does not express the antigen, or is so focal, i.e. < 5% of cells, that there is reasonable uncertain regarding whether the cells express the antigen"
        none There is either no immunoreaction deposit or reaction product is no more optically dense than background.
            Export as: TSV CSV

      • For each structural unit in each slide (or, in each image), provide quantitative measurements or estimates of:
        • Staining intensity (as defined above)
        • Fraction of the structural unit population exhibiting that intensity. If the assay does not allow the detection of non-stained members of the structural unit population, it is permissable to denote that staining at the specified level of the structural unit is visible but the fraction of the total population is unknown.
        • Other optional annotations/characterizations of the structural unit, e.g., feature density, qualitative characteristics or spatial distribution of the structural unit. Use of referenced-ontology terms is encouraged.
        Note that there may well be many or mostly negative results in the resulting data, not just positive results. Lack of staining relevant to the experiment where it could have been seen should be reported.
        For example,
        	Epithelial cell: 90% intense, 10% equivocal, 0% none
        	Basal cell: 0% intense, 20% equivocal, 80% none

        View All Rows   Export as: TSV CSV