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ENCODE Pilot Project: Common Consortium Resources

Common reagents and resources were identified by ENCODE pilot project members to aid in the comparison of data produced by ENCODE participants using different platforms and experimental approaches.

ENCODE Target Sequences

All ENCODE target regions have accessioned sequence entries in RefSeq (NT_*) that are updated after each human genome build is released. A list of the target regions [genome.ucsc.edu] for the different human genome builds is available at the UCSC ENCODE Browser [genome.ucsc.edu]. In addition, homologous sequences from other vertebrate genomes, identified from whole genome shotgun assemblies or obtained by direct sequencing of BAC clones, are submitted and updated continuously.

All sequences can be obtained from the NCBI Entrez search engine. They have the keyword "ENCODE" (although some alternate regions have also been accessioned and they have the word ALTERNATE in the title). The following Entrez query will retrieve all primary ENCODE target sequences:

To facilitate analysis of the comparative genomics data, the sequence data is frozen for periodic data releases. Sequence and annotation data for the ENCODE regions can be downloaded as FASTA sequence files from: Index of ENCODE Downloads.

BAC Clones for ENCODE Targets

BAC clones for the ENCODE regions for different vertebrate genomes have been identified by Eric Green's group at NHGRI/NISC [nisc.nih.gov]. The maps of identified BAC clones across the different targets for each different organism are available at the NISC Web site: Summary of BAC Maps [nisc.nih.gov]. The corresponding BAC clones can be obtained from the BACPAC Resources Center [bacpac.chori.org] at Children's Hospital Oakland Research Institute in Oakland, California or from the Arizona Genomics Institute [genome.arizona.edu].

Cell Lines

Common cell lines were identified to evaluate the performances of experiments, platforms and reagents used by investigators and to ensure that biological variation is not the cause of differences observed between experiments in different groups.

Two cell lines were chosen for their different properties:

    1. HeLa S3, a cervical adenocarcinoma, was chosen because it is can be transfected with high efficiency and large quantities of these cells can be easily synchronized in the cell cycle to facilitate studies on DNA replication.
    2. GM06990, an Epstein-Barr virus-transformed B-lymphocyte from the Utah CEPH collection was chosen as a representative lymphoblastoid cell line. These cells have a normal karyotype and can be stimulated with mitogens to activate signal transduction pathways that involve the activation of well studied genes in the ENCODE target regions.

Additional common cell lines were identified for use by Consortium members during the ENCODE pilot project. These include BJ-TERT, an immortalized foreskin fibroblast cell line; K562, an erythroblastoid cell line which expresses globin genes; and HepG2, a hepatocarcinoma cell line which expresses lipoproteins. K562 and HepG2 were selected because they express genes of interest that lie within the ENCODE regions.

Antibodies to DNA-Binding Proteins

The Consortium identified four common antibodies to use as controls in ChIP-chip cross-platform comparisons that were performed as part of the ENCODE pilot project. Antibodies that recognize RNA polymerase II and TAFII250, a component of a general transcription factor that initiates the preinitiation complex assembly for RNA polymerase II, should be bound to the promoters of all genes actively transcribed by RNA polymerase II. The RNA polymerase II antibody is available through Covance Research Products Inc. (Catalog #MMS-126R) [store.crpinc.com] and the TAFII250 antibody is available through Santa Cruz Biotechnology (Catalog #SC-735) [scbt.com].

The third common antibody recognizes STAT-1, a transcription factor induced following treatment of cells with IFN. This protein should only bind to IFN-inducible promoters following stimulation of cells and is available through Santa Cruz Biotechnology (Catalog #SC-345) [scbt.com]. An antibody against a histone modification - acetylated histone H4 - was also chosen because of its role in cell cycle progression. It is available through Upstate Cell Signaling Solutions (Catalog #06-866) [upstate.com].

Genome Tiling Microarrays

Investigators from Affymetrix and NimbleGen Systems, Inc. actively participated in the ENCODE pilot project. In addition, some ENCODE investigators collaborated with Agilent Technologies on tiling microarray experiments. Each company developed specialized microarrays that tile across the ENCODE regions and are useful for ChIP-chip and other studies.

Last Reviewed: February 11, 2014

Last updated: February 11, 2014