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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 _summary.zip?organism=&export=TSV&mode=getZip>TSV or _summary.zip?organism=&export=CSV&mode=getZip>CSV files. You can also download a zip archive of all the _IHC_images.zip> IHC images ( ).

Experimental Design:

Experiment Description: An immunohistochemical comparison of various anti-CD antibodies in many different bladder and prostate tissue sections.
Assay Type: Immunohistochemistry
Experiment Type: Comparison of multiple tissue specimens and antibodies
Experimental factors: antibody; specimen; organism ()
The number of hybridizations/stains performed in the experiment:
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

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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

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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.

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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
  
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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 >
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- 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.
  
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- 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
	etc.
```
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