Differential gene and transcript expression pattern of human primary monocytes from healthy young subjects were profiled under different sequencing depths (50M, 100M, and 200M reads).
Therefore, we analyzed the genome coverage of the CG, CHG, and CHH sites under different sequencing depths (Additional file 1).
Some replicate runs were generated under different sequencing conditions (SOLiD5500 technology vs wildfire technology) and this is indicated when appropriate.
In addition, the pair-end reads can be used as the single-end reads to evaluate the allele identification under different sequencing protocols.
We analyzed the genome coverage of the CG, CHG, and CHH sites under different sequencing depths, distributions of MeDIP-Seq reads in different CG density regions, and the read distribution analysis including the distribution in cattle chromosomes and in the different genome components.
We first examined the numbers of genes detected under different sequencing depths, gene numbers (ranging from 15,874 to 17,546) almost saturated when the clean tag number was up to four millions (Additional file 2: Figure S1), our sequence data therefore is capable of detecting nearly all the transcribed genes in our samples.
More excitingly, we found that there is a clear semiquantitative transition from one morphology (e.g., G20) to another (e.g., T30) when using different sequence combinations under identical experimental conditions.
As expected, different sequence classes were under different purifying selection pressures.
The different sequence logos constructed are available online within the CAARD introduced under "Results".
All 28 binders showed different sequence mutations.
