NOTE! This is a read-only copy of the ENCODE2 wiki.
Please go to the ENCODE3 wiki for current information.

Antibodies

From Encode2 Wiki
Jump to: navigation, search

Antibody Validation Standards

Adding antibodies to the ENCODE controlled vocabulary

Before registering your antibody with the DCC, you must complete the antibody validation form and have it approved by NHGRI. The form must comply with the antibody validation standards, as defined in the Chromatin/TF Data Standards document.

Please consult the Proposed Workflow for Registering Antibodies for additional information regarding the new antibody characterization protocol.

Before submitting data to the DCC all referenced antibodies must be registered in the ENCODE controlled vocabulary.



To register your antibody refer to the following instructions:

* New Antibodies
  * Include at least the Antibody, Description, Source, Lab and Validation Documents fields.
     * For instruction on registering Validation documents see the instructions below.
  * By convention, new antibody names follow the form <TARGET>_(<VENDOR_ID>), such as BCLAF1_(SC-101388)
  * Antibody names should avoid any non-alphanumeric characters beyond parentheses (), _ (underscore), and - (dash).
  * If you need to add lots to an already registered antibody, add a new table entry below and just fill in the antibody, lab and lot numbers.
  * If you need to only register Validation documents please see skip to the instructions below.



Please follow the below instructions to submit antibody validation documents: As of March 2010 antibody validation documents are required to register antibodies. Please include a link to your antibody document below. Documents can be uploaded into the wiki using the upload link at the bottom of the left panel.

  • Please locate your antibody by term below (Antibodies needing validation documents for human or mouse experiments ):
  * If you can't find your specific antibody, please add it to either list.
  * Please verify that the term that you will be using matches the exact antibody that you validated 
    (i.e. Antibody description and vendor Id's match your antibody found in Registered Antibodies)
  * If your antibody has not been registered please register your antibody by the above guidelines and follow the following validation documentation
    registration instructions.
  • The DCC is accepting validation documents that match the following criteria:
  * The validation document contains 2 independent validation methods, as per the ChIP-Seq Standards document. 
  * The document is in PDF format
  • When naming your document please following the below convention:
  * Antibody_Term(list of validation methods)
  * Validation methods Naming:
    a. ChIP
    b. Western_blot
    c. Immunoprecipitation
    d. siRNA
    e. Competitor_peptides
    f. Peptide_ELISA
    g. Immunoblots
    i. Dot_blot
  • When you are finished uploading documents, please email your associated wrangler so that they will appropriately register you document.

New Antibodies

Antibody Antibody Description Target Description Source Lab Lot(s) Factor ID Validation DocumentLot(s) Approved by NHGRI
(Example) BCLAF1 Mouse monoclonal IgG, raised against a synthetic peptide corresponding to a.a. 900-909 of BCLAF1 of human origin. This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins (RefSeq). Santa Cruz Biotech sc-101388 Myers BCLAF1 BCLAF1 N/A
(Example) GR (just adding lot numbers) Myers A2508, E1908 missing N/A
(Example) GR (just updating validation documents) Myers (upload document here) N/A



Antibodies needing validation documents

Some antibodies were registered before validation documents were required. Please add your validation documents as soon as you can. For a list of antibodies requiring validation documents, see http://encodewiki.ucsc.edu/EncodeDCC/index.php/2012-08-17_DCC_Progress#Missing_Antibody_Validations

Registered antibodies

Updated: 2012-01-18

The following antibodies have been registered to the ENCODE validator, and can be used in data submissions:

<embedurl>http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?type=Antibody{scrolling=auto}{height=10000}</embedurl>