Applications

Cofactor can produce a large variety of libraries for multiple applications and from a wide range of sample types. Several examples are outlined in greater detail below. Additional libraries may be possible upon request.

Fragment View »



Whole genome characterization by single-pass shotgun sequencing of fragments from total DNA, PCR products, etc.

Paired-end View »



Whole genome characterization by shotgun sequencing from both ends of DNA fragments with ~200bp inserts. Specialty large inserts libraries are available upon request for an additional charge.

ChIP-Seq View »



Discovery & quantitation of protein-DNA interactions by sequencing DNA from immunoprecipitations.

MicroRNA View »



Discovery & quantitation of novel microRNAs and isoforms by sequencing cDNAs of microRNAs isolated from total RNA.

TranscriptomeView»



Quantitative whole transcriptome profiling (RNA-seq) by sequencing cDNAs constructed from messenger RNA isolated from total RNA.

Bisulfite View »



Genome methylation profiling by sequencing DNA fragments bisulfite treated to convert non-methylated C’s into U’s.



Capture View »


Single-nucleotide polymorphism and insertion/deletion detection by targeted selection and sequencing of discreet genomic regions of interest.



ChIP-Seq

Discovery & quantitation of protein-DNA interactions by sequencing DNA from immunoprecipitations

If you can recover it by immunoprecipitation, we can sequence it! Cofactor has vast experience sequencing IP products from transcription factors, histone modifications, and even RNA binding-proteins.

Companies like AbCam and Sigma produce antibodies targeting a vast array of proteins and their modifications. Using these or your own antibodies, ChIP-seq protocols call for the cross-linking of DNA/RNA with neighboring proteins,
sonicating the fragments until they are very small (~200bp), and then purifying the DNA/RNA.

In this way we can define the actual binding locations of proteins genome-wide. Alternatively, we can provide whole-epigenome profiling by sequencing the ChIP products of one or many histone modifications.

1 lane/1 SOLiD barcode is usually sufficient for a transcription factor. Histone modifications should be treated more like whole-genome re-sequencing projects.

For ChIP-seq, you can submit any total amount of DNA but it must include at least 20 nano-grams of DNA in the 150-250 bp size range for Illumina or in the 100-200 bp size range for SOLiD.