SOX9 - Antibodies - The Human Protein Atlas


	Antibody HPA001758	Antibody HPA070776	Antibody CAB022456	Antibody CAB068240

ANTIBODY INFORMATION
Provider	Atlas Antibodies Sigma-Aldrich	Atlas Antibodies Sigma-Aldrich	Merck (Formerly Chemicon)	Atlas Antibodies
Product name	HPA001758	HPA070776	AB5535	AMAb90795
Host species	Rabbit	Rabbit	Rabbit	Mouse
Clonalityⁱ The antibodies are designated mAB for monoclonal and pAb for polyclonal.	pAb	pAb	msAb	mAb
Concentration	0.04 mg/ml	0.012 mg/ml	Not known	Not known
Purity	Affinity purified using the PrEST-antigen as affinity ligand	Affinity purified using the PrEST-antigen as affinity ligand	Affinity	Protein A/G
Released in versionⁱ The release of the Human Protein Atlas in which the antibody was first published.	2.0	22.0	5.0	13.0
Referencesⁱ References to publications in which the antibody has been used.	17			2
Proper citation	Atlas Antibodies Cat#HPA001758, RRID:AB_1080067	n/a	n/a	Atlas Antibodies Cat#AMAb90795, RRID:AB_2665670
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 N/A IHC WB PA	ICC N/A IHC WB PA	ICC N/A 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.	Enhanced - Independent antibodiesⁱ This method is based on comparing the staining pattern using two independent antibodies with no overlapping epitopes. A similar staining pattern (main and additional locations) results in an enhanced antibody validation. Antibody staining overlaps with antibody HPA070776. Immunofluorescent staining of human cell line U-251MG shows localization to nucleoplasm. Protein location across all samples similar between independent antibodies Enhanced - Geneticⁱ Antibody validation by siRNA-mediated knock-down of the corresponding gene. Enhanced validation is given upon >25% reduction in relative fluorescence intensity in siRNA-treted cells versus negative control. Significant downregulation > 25% by both siRNA:s. Nuclear region of segmented cells in 10x-images.	Enhanced - Independent antibodiesⁱ This method is based on comparing the staining pattern using two independent antibodies with no overlapping epitopes. A similar staining pattern (main and additional locations) results in an enhanced antibody validation. Antibody staining overlaps with antibody HPA001758. Immunofluorescent staining of human cell line U2OS shows localization to nucleoplasm. Protein location across all samples similar between independent antibodies	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 U2OS shows localization to nucleoplasm.	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 siRNA assay: U2OS tested with dilution: 1:10	Human assay: Hep-G2 fixed with PFA, dilution: 1:4 Human assay: U-251MG fixed with PFA, dilution: 1:4 Human assay: U2OS fixed with PFA, dilution: 1:4	Human assay: A-431 fixed with PFA, dilution: 1:125 Human assay: U-251MG fixed with PFA, dilution: 1:125 Human assay: U2OS fixed with PFA, dilution: 1:125
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.	N/A	N/A	N/A	Enhanced - Orthogonal Antibody staining mainly consistent with RNA expression data across 44 tissues. HIGH EXPRESSION Salivary gland RNA expression: 77.8 nTPM LOW EXPRESSION Liver RNA expression: 3.4 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
Antibody dilution				1:1500
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 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.
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 - Recombinant expressionⁱ This method is based on over-expression of the target protein in a cell line preferably not expressing the target protein. The staining of the antibody is evaluated by Western blot through analyses of samples from cell lysates with and without recombinant expression of the target protein. The results show no or weak band from the unmodified cell line lysate and a strong band in the cell line with recombinant expression. Single band corresponding to the predicted size in kDa (+/-20%). Lane 1: Marker [kDa] 250, 130, 95, 72, 55, 36, 28, 17, 10 Lane 2: Negative control (vector only transfected HEK293T lysate) Lane 3: Over-expression Lysate (Co-expressed with a C-terminal myc-DDK tag (~3.1 kDa) in mammalian HEK293T cells, LY424779) Target mass (kDa): 56.1	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. No bands detected. Analysis performed using a standard panel of samples. 250 130 95 72 55 36 28 17 10	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. Weak band of predicted size but with additional bands of higher intensity also present. 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. Only bands not corresponding to the predicted size. Analysis performed using a standard panel of samples.

Antibody dilution	1:250	1:80	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.	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

Antibody dilution	1:2000	1:500
RELEVANT PUBLICATIONS
	Three-dimensional reconstructions of intrahepatic bile duct tubulogenesis in human liver Vestentoft PS et al BMC Dev Biol 2011;11:56			MALAT1-miR-101-SOX9 feedback loop modulates the chemo-resistance of lung cancer cell to DDP via Wnt signaling pathway Chen W et al Oncotarget 2017;8(55):94317-94329 Application: ChIP
	Cell differentiation versus cell death: extracellular glucose is a key determinant of cell fate following oxidative stress exposure Poulsen RC et al Cell Death Dis 2014;5:e1074			Generation of orthotopically functional salivary gland from embryonic stem cells Tanaka J et al Nat Commun 2018;9(1):4216 Application: IHC
	Evaluation of protein biomarkers of prostate cancer aggressiveness Rizzardi AE et al BMC Cancer 2014;14:244 Application: IHC
	Prognostic Significance of β-Catenin, E-Cadherin, and SOX9 in Colorectal Cancer: Results from a Large Population-Representative Series Bruun J et al Front Oncol 2014;4:118
	Sox9 mediates Notch1-induced mesenchymal features in lung adenocarcinoma Capaccione KM et al Oncotarget 2014;5(11):3636-50 Application: IHC, WB
	Brg1 promotes both tumor-suppressive and oncogenic activities at distinct stages of pancreatic cancer formation Roy N et al Genes Dev 2015;29(6):658-71 Application: ICC-IF, IHC
	Contribution of Mature Hepatocytes to Biliary Regeneration in Rats with Acute and Chronic Biliary Injury Chen YH et al PLoS One 2015;10(8):e0134327 Application: IHC
	Sox9 expression in canine epithelial skin tumors Fantinato E et al Eur J Histochem 2015;59(3):2514 Application: IHC
	Superficial cells are self-renewing chondrocyte progenitors, which form the articular cartilage in juvenile mice Li L et al FASEB J 2017;31(3):1067-1084 Application: IHC
	Retinoic acid signaling is dispensable for somatic development and function in the mammalian ovary Minkina A et al Dev Biol 2017;424(2):208-220 Application: IHC
	A genomic atlas of human adrenal and gonad development Del Valle I et al Wellcome Open Res 2017;2:25 Application: IHC
	Genome-wide profiling of DNA 5-hydroxymethylcytosine during rat Sertoli cell maturation Landfors M et al Cell Discov 2017;3:17013 Application: FC
	Class I histone deacetylase inhibition improves pancreatitis outcome by limiting leukocyte recruitment and acinar-to-ductal metaplasia Bombardo M et al Br J Pharmacol 2017;174(21):3865-3880 Application: IHC
	Hyperbaric oxygen protects type II collagen in interleukin-1β-induced mandibular condylar chondrocyte via inhibiting the JNK/c-Jun signaling pathway Sun Q et al Oncotarget 2017;8(36):60312-60323 Application: ICC-IF
	Cytoplasmic expression of SOX9 as a poor prognostic factor for oral squamous cell carcinoma Sumita Y et al Oncol Rep 2018;40(5):2487-2496 Application: IHC
	Evaluation of the effects of the combination of BMP-2-modified BMSCs and PRP on cartilage defects Ruan S et al Exp Ther Med 2018;16(6):4569-4577 Application: WB
	N-methyl-D-aspartate (NMDA) receptor expression and function is required for early chondrogenesis Matta C et al Cell Commun Signal 2019;17(1):166 Application: WB
ANTIGEN INFORMATION
Antigen	Recombinant protein fragment	Recombinant protein fragment	Synthetic peptide	Recombinant protein
Length (aa)	117	64
Antigen sequence	`SQRTHIKTEQLSPSHYSEQQQHSPQQIAYSPFNLPHYSPSYPPITRSQYD YTDHQNSSSYYSHAAGQGTGLYSTFTYMNPAQRPMYTPIADTSGVPSIPQ THSPQHWEQPVYTQLTR`	`PFMKMTDEQEKGLSGAPSPTMSEDSAGSPCPSGSGSDTENTRPQENTFPK GEPDLKKESEEDKF`
Matching transcripts	SOX9-201 - ENSP00000245479 [100%]	SOX9-201 - ENSP00000245479 [100%]
Matching mouse transcripts	ENSMUSP00000000579 [97%] ENSMUSP00000039466 [54%] ENSMUSP00000025003 [39%]	ENSMUSP00000000579 [100%] ENSMUSP00000125765 [34%] ENSMUSP00000101666 [31%]
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.

SOX9-201

Displaying protein features on the AlphaFold structures

The Protein Browser