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Measurements for the ENCODE common cell types

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The ENCODE Consortium has designated common cell types that will be used by all investigators to aid in the integration and comparison of data produced using different technologies and platforms. To ensure consistency in cell cultures prepared in different laboratories, investigators should take the measurements below for each cell harvest.

Required Measurements

  • Growth time/passage number. The growth time of cell lines should be determined by recording the date when cells were put into culture and when they were harvested. Investigators should go back to the original stock after growing a culture for one month. Passage number should be assessed for primary cells. The passage number for primary cells should not exceed 3-4 passages.
  • Cell density. Cell density should be assessed for each cell culture.
    • The density of GM12878 cells should be maintained between 2.0 x 10^5 cells/ml and 1.0 x 10^6 cells/ml.
    • K562 cells should be grown to a maximal density of 7.5 x 10^5 cells/ml.
    • HepG2 cells should be grown to a maximum of 75% confluence.
    • HeLa-S3 should be grown to a maximal density of 5 x 10^5 cells/ml.
  • Cell cycle state. Cell cycle state should be measured by FACS analysis within 2 weeks of the time of harvest. Samples can be prepared at the time of harvest for later analysis. Staining should be done immediately before FACS analysis. A protocol for performing FACS analysis is available here. Sample FACS profiles for K562 are available here. Sample FACS profiles for HeLa-S3 are available here.

Other Issues to Consider

Presence of mycoplasma. Cell cultures should be tested at monthly for the presence of mycoplasma. The mycoplasma testing protocol used by Bionique, which does mycoplasma testing for ATCC, is available here.

Freezing Cell Aliquots

As Tier 1, 2, or 3 cells are grown, each ENCODE group should freeze an aliquot of cells for potential future phenotyping.