Stanf RTPCR Track Settings
 
Stanford Endogenous Transcript Levels in HCT116 Cells   (All Pilot ENCODE Transcription tracks)

Display mode:   

Show only items with score at or above:   (range: 0 to 1000)

View table schema
Source data version: ENCODE June 2005 Freeze
Data coordinates converted via liftOver from: July 2003 (NCBI34/hg16)
Data last updated at UCSC: 2007-06-14

Description

This track displays absolute transcript copy numbers for 136 genes and 12 negative control intergenic regions, determined by RTPCR in HCT116 cells.

Display Conventions and Configuration

The genomic regions are indicated by solid blocks. The shade of an item gives a rough indication of its count, ranging from light gray for zero to black for a count of 7000 or greater. To display only those items that exceed a specific unnormalized score, enter a minimum score between 0 and 1000 in the text box at the top of the track description page.

Methods

Total RNA was prepared in quadruplicate from HCT116 cells grown in culture. cDNA was prepared as described in Trinklein et al. (2004). Duplicate primer pairs were designed to each gene, and the absolute number of cDNA molecules containing each amplicon were determined by real-time PCR. The submitted data are the calculated number of molecules of each transcript containing the defined amplicon.

Verification

Four biological replicates were performed, and two primer pairs were used to measure the abundance of each transcript.

Credits

These data were generated in the Richard M. Myers lab at Stanford University (now at HudsonAlpha Institute for Biotechnology).

References

Trinklein, N.D., Chen, W.C., Kingston, R.E. and Myers, R.M. Transcriptional regulation and binding of HSF1 and HSF2 to 32 human heat shock genes during thermal stress and differentiation. Cell Stress Chaperones 9(1), 21-28 (2004).