SOD1 - Antibodies - The Human Protein Atlas


	Antibody HPA001401	Antibody CAB008670

ANTIBODY INFORMATION
Provider	Atlas Antibodies Sigma-Aldrich	AbFrontier
Product name	HPA001401	LF-PA0013
Host species	Rabbit	Rabbit
Clonalityⁱ The antibodies are designated mAB for monoclonal and pAb for polyclonal.	pAb	pAb
Concentration	0.04 mg/ml	Not known
Purity	Affinity purified using the PrEST-antigen as affinity ligand	Ammonium Sulfate Precipitation
Released in versionⁱ The release of the Human Protein Atlas in which the antibody was first published.	2.0	3.1
Referencesⁱ References to publications in which the antibody has been used.	13
Proper citation	Atlas Antibodies Cat#HPA001401, RRID:AB_1080132	ABFrontier Cat#LF-PA0013, RRID:AB_1623312
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.	ICC IHC WB PA	N/A ICC IHC 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.	Enhanced - Recombinant expressionⁱ Antibody validation by comparing the staining pattern of the antibody targeting the endogenous protein with that of a GFP-tagged recombinant version of the protein. Enhance validation is given when antibody staining of the endogenous protein overlaps with the tagged protein, potentially also with some additional localizations. Antibody staining overlaps with GFP tagged protein Immunofluorescent staining of transgenic HeLa cells show antibody staining in nucleoplasm, plasma membrane & cytosol and GFP expression in nucleoplasm, plasma membrane & cytosol.	N/A

Antibody dilution	Human assay: A-431 fixed with PFA, dilution: 1:20 Human assay: U-251MG fixed with PFA, dilution: 1:20 Human assay: U2OS fixed with PFA, dilution: 1:20 GFP assay: Recombinant HeLa (BAC 5764) tested with dilution: 1:10
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 45 tissues. HIGH EXPRESSION Liver RNA expression: 1594.4 nTPM LOW EXPRESSION Pancreas RNA expression: 113.8 nTPM	Supportedⁱ Immunohistochemistry is used for validating antibody reliability by assessing staining pattern in 44 normal tissues. Validation scores include Enhanced, Supported, Approved and Uncertain. Immunohistochemical staining of human cerebral cortex shows strong nuclear positivity in glial cells. Cerebral cortex

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
Antibody dilution	1:500	1:600
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.
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.	Medium 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.	Enhanced - Capture MSⁱ This method is based on comparison between the molecular weight of the stained band visualized by the antibody against the protein size obtained by a capture MS method in which multiple gel slices are cut out from the electrophoretic separation of cell lysates of RT4 and U-251 and analysed separately by proteomics. The band detected by the antibody should be equivalent to the same of the intended target protein and its peptide(s). Antibody band pattern is confirmed by capture-MS. 206 113 82 49 32 26 18	Supportedⁱ 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. Single band corresponding to the predicted size in kDa (+/-20%). Analysis performed using a standard panel of samples. 220 112 84 47 32 26 17

Antibody dilution	1:250	1:500
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

Antibody dilution	1:1000
RELEVANT PUBLICATIONS
	NQO2 is a reactive oxygen species generating off-target for acetaminophen Miettinen TP et al Mol Pharm 2014;11(12):4395-404 Application: WB
	myo-Inositol Oxygenase Overexpression Accentuates Generation of Reactive Oxygen Species and Exacerbates Cellular Injury following High Glucose Ambience: A NEW MECHANISM RELEVANT TO THE PATHOGENESIS OF DIABETIC NEPHROPATHY Sun L et al J Biol Chem 2016;291(11):5688-5707 Application: WB
	Caffeine intake decreases oxidative stress and inflammatory biomarkers in experimental liver diseases induced by thioacetamide: Biochemical and histological study Amer MG et al Int J Immunopathol Pharmacol 2017;30(1):13-24 Application: IHC
	Amyotrophic lateral sclerosis patient iPSC-derived astrocytes impair autophagy via non-cell autonomous mechanisms Madill M et al Mol Brain 2017;10(1):22 Application: WB
	Reactive Astrocytes Promote ALS-like Degeneration and Intracellular Protein Aggregation in Human Motor Neurons by Disrupting Autophagy through TGF-β1 Tripathi P et al Stem Cell Reports 2017;9(2):667-680 Application: ICC-IF
	DNA repair deficiency sensitizes lung cancer cells to NAD+ biosynthesis blockade Touat M et al J Clin Invest 2018;128(4):1671-1687 Application: ELISA
	Thermal proteome profiling of breast cancer cells reveals proteasomal activation by CDK4/6 inhibitor palbociclib Miettinen TP et al EMBO J 2018;37(10): Application: WB
	Discovery of Orally Bioavailable, Quinoline-Based Aldehyde Dehydrogenase 1A1 (ALDH1A1) Inhibitors with Potent Cellular Activity Yang SM et al J Med Chem 2018;61(11):4883-4903 Application: WB
	Loss of DDHD2, whose mutation causes spastic paraplegia, promotes reactive oxygen species generation and apoptosis Maruyama T et al Cell Death Dis 2018;9(8):797 Application: WB
	Acute intermittent hypoxia induced phrenic long-term facilitation despite increased SOD1 expression in a rat model of ALS Nichols NL et al Exp Neurol 2015;273:138-50
	Chemotherapeutic agent 5-fluorouracil increases survival of SOD1 mouse model of ALS Rando A et al PLoS One 2019;14(1):e0210752 Application: WB
	Antioxidant Activity of Selected Stilbenoid Derivatives in a Cellular Model System Treml J et al Biomolecules 2019;9(9): Application: WB
	CETSA-based target engagement of taxanes as biomarkers for efficacy and resistance Langebäck A et al Sci Rep 2019;9(1):19384 Application: WB
ANTIGEN INFORMATION
Antigen	Recombinant protein fragment	Recombinant protein
Length (aa)	135
Antigen sequence	`PVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGP HFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCI IGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACG`
Matching transcripts	SOD1-201 - ENSP00000270142 [100%] SOD1-202 - ENSP00000374645 [92%]
Matching mouse transcripts	ENSMUSP00000023707 [82%] ENSMUSP00000035486 [50%] ENSMUSP00000098768 [39%]
ANTIGEN VIEWⁱ The Structure section provides predicted structures from the Alphafold protein structure database and includes structures corresponding to uniprot entries mapped to our gene set with at least one splice variant having 100% identity to the structure sequence. Displaying protein features on the AlphaFold structures Individual splice variants can be selected in the top part of the Protein Browser (see below) and both for transcripts matching the whole structure and those corresponding only to a part the full-length AlphaFold structure is shown. 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 and then also the part of the structure corresponding to the selected transcript will be shown in lightblue. Clinical and population amino acid variants can be highlighted by using the sliders to the right of the structure, which 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 protein browser displays the antigen location on the target protein(s) and the features of the target protein. The tabs at the top of the protein view section can be used to switch between the different splice variants to which an antigen has been mapped. 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). If a signal peptide is predicted by a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius (turquoise) and/or transmembrane regions (orange) are predicted by MDM, these are 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.
SOD1-201 SOD1-202

Displaying protein features on the AlphaFold structures

The Protein Browser