SYDE2 - Antibodies - The Human Protein Atlas


	Antibody HPA027138	Antibody HPA058378

ANTIBODY INFORMATION
Provider	Atlas Antibodies Sigma-Aldrich	Atlas Antibodies Sigma-Aldrich
Product name	HPA027138	HPA058378
Host species	Rabbit	Rabbit
Clonalityⁱ The antibodies are designated mAB for monoclonal and pAb for polyclonal.	pAb	pAb
Concentration	0.22 mg/ml	0.0415 mg/ml
Purity	Affinity purified using the PrEST-antigen as affinity ligand	Affinity purified using the PrEST-antigen as affinity ligand
Released in versionⁱ The release of the Human Protein Atlas in which the antibody was first published.	5.0	14.0
Referencesⁱ References to publications in which the antibody has been used.	1
Proper citation	Atlas Antibodies Cat#HPA027138, RRID:AB_1857686	Atlas Antibodies Cat#HPA058378, RRID:AB_2683696
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 N/A IHC WB PA
IMMUNOCYTOCHEMISTRYⁱ Immunocytochemistry is used to validate the antibody staining and for assessing and validating the protein expression pattern in selected human cell lines. Read more
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. Read more		Approvedⁱ Immunocytochemistry is used for validating antibody reliability by assessing staining pattern in cell lines. Validation scores include Enhanced, Supported, Approved and Uncertain. Read more The subcellular location is partly supported by literature or no literature is available. Immunofluorescent staining of human cell line RH-30 shows localization to nucleoli rim & the Golgi apparatus.

Antibody dilution		Human assay: RH-30 fixed with PFA, dilution: 1:21 Human assay: RT4 fixed with PFA, dilution: 1:21 Human assay: U-2 OS fixed with PFA, dilution: 1:21
IMMUNOHISTOCHEMISTRYⁱ Immunohistochemistry is used for validating antibody reliability by assessing staining pattern in 44 normal tissues. Validation scores include Enhanced, Supported, Approved and Uncertain. Read more
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. Read more	Uncertainⁱ Immunohistochemistry is used for validating antibody reliability by assessing staining pattern in 44 normal tissues. Validation scores include Enhanced, Supported, Approved and Uncertain. Read more Immunohistochemical staining of human skeletal muscle shows strong cytoplasmic positivity in subsets of muscle fibers.

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. Read more	HIER pH6
Antibody dilution	1:100
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.	No avaliable gene/protein characterization data.
RNA consistencyⁱ Consistency between immunohistochemistry data and mRNA data from HPA, GTEX and FANTOM5 is divided into five different categories: i) High consistency, ii) Medium consistency, iii) Low consistency, iv) Very low consistency, and v) Cannot be evaluated	Very low 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. Read more
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. Read more	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	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 Antibody dilution: 1:80
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. Read more	Approved Pass with quality comment low specificity (binding to 1-2 PrESTs >15% and <40%). Antibody specificity analysis with protein arrays. Predicted and matching interactions are shown in green. Antibody dilution: 1:3000	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. Antibody dilution: 1:550
RELEVANT PUBLICATIONS
	A vlincRNA participates in senescence maintenance by relieving H2AZ-mediated repression at the INK4 locus Lazorthes S et al Nat Commun 2015;6:5971 Application: ICC-IF, WB
ANTIGEN INFORMATION
Antigen	Recombinant protein fragment	Recombinant protein fragment
Length (aa)	98	73
Antigen sequence	`RSHLSISPVSLPKHQLSQSFLKSSKEYCTYVVCNATNSSLSKNCALDFNE ENDADDEGEIWYNPIPEDDDLGISSALSFGEADSAVLKLPAVNLSMLS`	`NDVDYDDVPSEDRKIGENYSKMDGPEVMIEQPIPMSKECTFQTYLTMQTI ESTVDRKNNLKDLQESIDTLIGN`
Matching transcripts	SYDE2-202 - ENSP00000340594 [100%]	SYDE2-202 - ENSP00000340594 [99%]
Matching mouse transcripts	ENSMUSP00000041897 [54%] ENSMUSP00000142954 [54%] ENSMUSP00000148542 [54%] ENSMUSP00000045160 [23%] ENSMUSP00000151057 [22%]	ENSMUSP00000041897 [67%] ENSMUSP00000142954 [67%] ENSMUSP00000148542 [67%] ENSMUSP00000081043 [28%] ENSMUSP00000073803 [25%]
ANTIGEN VIEWⁱ 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.
SYDE2-202