SCGN - Antibodies - The Human Protein Atlas


	Antibody HPA006641	Antibody CAB004005	Antibody CAB044060	Antibody CAB062563	Antibody CAB068232

ANTIBODY INFORMATION
Provider	Atlas Antibodies Sigma-Aldrich	Medical University of Vienna	Atlas Antibodies Sigma-Aldrich	Atlas Antibodies	Atlas Antibodies
Product name	HPA006641	scgn	SCGN 13B8	AMAB90630	AMAb90632
Host species	Rabbit	Rabbit	Mouse	Mouse	Mouse
Clonalityⁱ The antibodies are designated mAB for monoclonal and pAb for polyclonal.	pAb	pAb	mAb	mAb	mAb
Concentration	0.225 mg/ml	Not known	Not known	Not known	Not known
Purity	Affinity purified using the PrEST-antigen as affinity ligand	Not known	Protein A/G	Protein A/G	Protein A/G
Released in versionⁱ The release of the Human Protein Atlas in which the antibody was first published.	3.1	2.0	16.0	12.0	13.0
Referencesⁱ References to publications in which the antibody has been used.	13			1
Proper citation	Atlas Antibodies Cat#HPA006641, RRID:AB_1079874	n/a	n/a	Atlas Antibodies Cat#AMAb90630, RRID:AB_2665612	Atlas Antibodies Cat#AMAb90632, RRID:AB_2665613
Validation summaryⁱ All assays through which the antibody has been validated. Assays&annotation provide a detailed description of the different assays. The pie-charts indicate degree of validation.	N/A ICC IHC N/A WB PA	ICC IHC N/A WB N/A PA	N/A ICC IHC N/A WB N/A PA	N/A ICC IHC N/A WB N/A PA	N/A ICC IHC N/A WB N/A PA
IMMUNOCYTOCHEMISTRYⁱ Immunocytochemistry is used to validate the antibody staining and for assessing and validating the protein expression pattern in selected human cell lines.
Validationⁱ Results of validation by standard or enhanced validation. Standard validation is based on concordance with available experimental gene/protein characterization data in the UniProtKB/Swiss-Prot database. Standard validation results in scores Supported, Approved or Uncertain. Enhanced validation is performed using either siRNA knockdown, tagged GFP cell lines or independent antibodies. For the siRNA validation the decrease in antibody-based staining intensity upon target protein downregulation is evaluated. For the GFP validation the signal overlap between the antibody staining and the GFP-tagged protein is evaluated. For the independent antibodies validation the evaluation is based on comparison of the staining of two (or more) independent antibodies directed towards independent epitopes on the protein. For all cases except the siRNA validation, an image representative of the antibody staining pattern is shown. For the siRNA validation, a box plot of the results is shown.	N/A	Supportedⁱ Reliability scores for antibodies used in immunocytochemistry are set by comparing the staining pattern in cell lines with external experimental evidence for protein localization. The scores are termed Supported, Approved and Uncertain. The subcellular location is supported by literature. Immunofluorescent staining of human cell line A-431 shows localization to cytosol.	N/A	N/A	N/A

Antibody dilution		Human assay: A-431 fixed with PFA, dilution: 1:2000 Human assay: U-251MG fixed with PFA, dilution: 1:2000 Human assay: U2OS fixed with PFA, dilution: 1:2000
IMMUNOHISTOCHEMISTRYⁱ Immunohistochemistry is used for validating antibody reliability by assessing staining pattern in 44 normal tissues. Validation scores include Enhanced, Supported, Approved and Uncertain.
Validationⁱ Results of validation by standard or enhanced validation based on assessment of antibody performance in 44 normal tissues. Standard validation results in scores Supported, Approved or Uncertain. An image representative of the antibody staining pattern is shown. Enhanced validation results in the score Enhanced and includes two methods: Orthogonal validation and Independent antibody validation. For orthogonal validation, representative images of high and low expression are shown. For independent antibody validation, four images of each independent antibody are displayed.	Enhanced - Orthogonal Antibody staining mainly consistent with RNA expression data across 42 tissues. HIGH EXPRESSION Pancreas RNA expression: 45.6 nTPM LOW EXPRESSION Fallopian tube RNA expression: 0.1 nTPM	Enhanced - Orthogonal Antibody staining mainly consistent with RNA expression data across 43 tissues. HIGH EXPRESSION Pancreas RNA expression: 45.6 nTPM LOW EXPRESSION Fallopian tube RNA expression: 0.1 nTPM	Supported In the cortex and hippocampus, dense axonal network and occasional neuronal cell bodies exhibit moderate-intensity immunostaining. In well-defined selected regions/nuclei of the brain, strong-intensity immunostaining of abundand neuronal cell bodies, axons and dendrites is noticed. These are: glomerular-, mitral cell-, and internal plexiform layers of the olfactory bulb, dorsal part of the lateral septum, nucleus accumbens shell, multiple BNST nuclei, ventral pallidum, multiple nuclei of the anterior hypothalamus, dorsomedial-, paraventricular-, arcuate- and some lateral hypothalamus nuclei of the tuberal hypothalamus, dorsal lateral geniculate nucleus, some habenular nuclei, optical (superior) layer of the superior colliculus, dorsal motor nucleus of the vagus, cuneiform nucleus. . (Mouse brain)	Enhanced - Orthogonal Antibody staining mainly consistent with RNA expression data across 43 tissues. HIGH EXPRESSION Pancreas RNA expression: 45.6 nTPM LOW EXPRESSION Fallopian tube RNA expression: 0.1 nTPM	Enhanced - Orthogonal Antibody staining mainly consistent with RNA expression data across 44 tissues. HIGH EXPRESSION Pancreas RNA expression: 45.6 nTPM LOW EXPRESSION Fallopian tube RNA expression: 0.1 nTPM

Retrievalⁱ Antigen retrieval is a method used to restore/retrieve the epitope (antibody bidning region) of the target protein, cross-linked, and thus masked, during tissue preserving fixative treatment of the tissues.	HIER pH6	HIER pH6		HIER pH6	HIER pH6
Antibody dilution	1:500	1:12000		1:2000	1:4000
Literature conformityⁱ Conformance of the expression pattern with available gene/protein characterization data in scientific literature and data from bioinformatic predictions. UniProt is used as the main source of gene/protein characterization data and when relevant, available publications and other sources of information are researched in depth. Extensive or sufficient gene/protein data requires that there is evidence of existence on a protein level and that a substantial quantity of published experimental data is available from literature and public databases. Limited protein/gene characterization data does not require evidence of existence on a protein level and refers to genes for which only bioinformatic predictions and scarce published experimental data is available.	Consistent with extensive gene/protein characterization data.	Consistent with extensive gene/protein characterization data.		Consistent with extensive gene/protein characterization data.	Consistent with extensive gene/protein characterization data.
RNA consistencyⁱ Consistency between immunohistochemistry data and consensus RNA levels is divided into five different categories: i) High consistency, ii) Medium consistency, iii) Low consistency, iv) Very low consistency, and v) Cannot be evaluated.	Medium consistency between antibody staining and RNA expression data.	High consistency between antibody staining and RNA expression data.		High consistency between antibody staining and RNA expression data.	High consistency between antibody staining and RNA expression data.
WESTERN BLOTⁱ A Western blot analysis is performed on a panel of human tissues and cell lines to evaluate antibody specificity. For antibodies with unreliable result a revalidation using an over-expression lysate is performed.
Validationⁱ Western Blot is used for quality control of the polyclonal antibodies generated in the project. After purification, the antibodies are used to detect bands in a setup of lysate and different tissues. The result is then scored Enhanced, Supported, Approved, or Uncertain. Enhanced validation includes five different methods: Genetic validation, Recombinant expression validation, Independent antibody validation, Orthogonal validation and Capture MS validation.	Uncertainⁱ The staining of an antibody is evaluated by Western Blot through analysis of samples from different cell lysates. A supportive score is given if band(s) of predicted size in kDa (+/-20%) is detected. Current setup is not applicable due to low RNA count. Analysis performed using a standard panel of samples.	Uncertainⁱ The staining of an antibody is evaluated by Western Blot through analysis of samples from different cell lysates. A supportive score is given if band(s) of predicted size in kDa (+/-20%) is detected. Current setup is not applicable due to low RNA count. Analysis performed using a standard panel of samples.	Uncertainⁱ The staining of an antibody is evaluated by Western Blot through analysis of samples from different cell lysates. A supportive score is given if band(s) of predicted size in kDa (+/-20%) is detected. Current setup is not applicable due to low RNA count. Analysis performed using a standard panel of samples.	Uncertainⁱ The staining of an antibody is evaluated by Western Blot through analysis of samples from different cell lysates. A supportive score is given if band(s) of predicted size in kDa (+/-20%) is detected. Current setup is not applicable due to low RNA count. Analysis performed using a standard panel of samples.	Uncertainⁱ The staining of an antibody is evaluated by Western Blot through analysis of samples from different cell lysates. A supportive score is given if band(s) of predicted size in kDa (+/-20%) is detected. Current setup is not applicable due to low RNA count. Analysis performed using a standard panel of samples.

Antibody dilution	1:250	1:500	1:500	1:500	1:1000
PROTEIN ARRAY
Validationⁱ A protein array containing 384 different antigens including the antibody target is used to analyse antibody specificity. Depending on the array interaction profile the antibody is scored as Supported, Approved, or Uncertain.	Supported Pass with single peak corresponding to interaction only with its own antigen. Antibody specificity analysis with protein arrays. Predicted and matching interactions are shown in green.	N/A	N/A	N/A	N/A

Antibody dilution	1:3000
RELEVANT PUBLICATIONS
	Tissue profiling of the mammalian central nervous system using human antibody-based proteomics Mulder J et al Mol Cell Proteomics 2009;8(7):1612-22			Secretagogin is expressed in sensory CGRP neurons and in spinal cord of mouse and complements other calcium-binding proteins, with a note on rat and human Shi TJ et al Mol Pain 2012;8:80
	Secretagogin is a Ca2+-binding protein specifying subpopulations of telencephalic neurons Mulder J et al Proc Natl Acad Sci U S A 2009;106(52):22492-7
	Secretagogin is a Ca2+-binding protein identifying prospective extended amygdala neurons in the developing mammalian telencephalon Mulder J et al Eur J Neurosci 2010;31(12):2166-77
	The renaissance of Ca2+-binding proteins in the nervous system: secretagogin takes center stage Alpár A et al Cell Signal 2012;24(2):378-387
	Novel pancreatic beta cell-specific proteins: antibody-based proteomics for identification of new biomarker candidates Lindskog C et al J Proteomics 2012;75(9):2611-20
	Clusters of secretagogin-expressing neurons in the aged human olfactory tract lack terminal differentiation Attems J et al Proc Natl Acad Sci U S A 2012;109(16):6259-64
	Distribution of secretagogin-containing neurons in the basal forebrain of mice, with special reference to the cholinergic corticopetal system Gyengesi E et al Brain Res Bull 2013;94:1-8 Application: IHC
	Neuronal calcium-binding proteins 1/2 localize to dorsal root ganglia and excitatory spinal neurons and are regulated by nerve injury Zhang MD et al Proc Natl Acad Sci U S A 2014;111(12):E1149-58
	Calcium Binding and Disulfide Bonds Regulate the Stability of Secretagogin towards Thermal and Urea Denaturation Sanagavarapu K et al PLoS One 2016;11(11):e0165709 Application: WB
	Deafferented Adult Rod Bipolar Cells Create New Synapses with Photoreceptors to Restore Vision Beier C et al J Neurosci 2017;37(17):4635-4644 Application: IHC
	Secretagogin is increased in plasma from type 2 diabetes patients and potentially reflects stress and islet dysfunction Hansson SF et al PLoS One 2018;13(4):e0196601 Application: ICC-IF, WB
	Immature excitatory neurons develop during adolescence in the human amygdala Sorrells SF et al Nat Commun 2019;10(1):2748 Application: IHC
	Ferret brain possesses young interneuron collections equivalent to human postnatal migratory streams Ellis JK et al J Comp Neurol 2019;527(17):2843-2859 Application: ICC-IF
ANTIGEN INFORMATION
Antigen	Recombinant protein fragment	Recombinant protein	Recombinant protein	Recombinant protein	Recombinant protein
Length (aa)	139
Antigen sequence	`RDLFLHHKKAISEAKLEEYTGTMMKIFDRNKDGRLDLNDLARILALQENF LLQFKMDACSTEERKRDFEKIFAYYDVSKTGALEGPEVDGFVKDMMELVQ PSISGVDLDKFREILLRHCDVNKDGKIQKSELALCLGLK`
Matching transcripts	SCGN-201 - ENSP00000367197 [100%]
Matching mouse transcripts	ENSMUSP00000021770 [96%] ENSMUSP00000153251 [81%] ENSMUSP00000029876 [33%] ENSMUSP00000003754 [32%]
ANTIGEN VIEWⁱ The Structure section provides in-house generated structures, predicted using the Alphafold source code, for the majority of the proteins and their related isoforms. Displaying protein features on the AlphaFold structures Individual splice variants can be selected in the top part of the Protein Browser (see below) and different transcript-related features such as transmembrane regions, InterPro domains and antigen sequences for antibodies can be displayed in the structure by clicking on the respective features in the Protein Browser. Clinical and population-based amino acid variants based on data from the Ensembl variation database and AlphaMissense (AM) predictions can be highlighted using the sliders to the right of the structure. These can also be used to colour the entire structure by residue index or make the structure autorotate.The structures are displayed using the NGL Viewer and can also be zoomed-in and rotated manually. The Protein Browser The ProteinBrowser displays the antigen location on the target protein(s) and the features of the target protein. Transcript names and schematic transcript structures including exons, introns and UTRs for the different isoforms are shown on top, and can be used to switch between the structures for the different splice variants. At the top of the view, the position of the antigen (identified by the corresponding HPA identifier) is shown as a green bar. A yellow triangle on the bar indicates a <100% sequence identity to the protein target. Below the antigens, the maximum percent sequence identity of the protein to all other proteins from other human genes is displayed, using a sliding window of 10 aa residues (HsID 10) or 50 aa residues (HsID 50). The region with the lowest possible identity is always selected for antigen design, with a maximum identity of 60% allowed for designing a single-target antigen (read more). The curve in blue displays the predicted antigenicity i.e. the tendency for different regions of the protein to generate an immune response, with peak regions being predicted to be more antigenic.The curve shows average values based on a sliding window approach using an in-house propensity scale. (read more). Signal peptides (turquoise) and membrane regions (orange) based on predictions using the majority decision methods MDM and MDSEC are also displayed. Low complexity regions are shown in yellow and InterPro regions in green. Common (purple) and unique (grey) regions between different splice variants of the gene are also displayed (read more), and at the bottom of the protein view is the protein scale.

SCGN-201

Displaying protein features on the AlphaFold structures

The Protein Browser