Cofactor can produce single-end, paired-end, and mate-pair whole-genome libraries, bisulfite-converted whole genome methylation libraries, DNA binding protein, RNA binding protein, and histone modification ChIP-seq libraries, whole-transcriptome RNA libraries, small RNA libraries, Reduced Representation Sequencing (RRS) libraries, PCR product libraries, Barcoded/ Multiplexed libraries, and FFPE genomic libraries. Other libraries may be possible upon request.
Paired-end libraries provide additional longer-range linking information that allows reads that would otherwise have to be discarded to map back to more repetitive locations. They also allow for the detection of moderately sized indels. Current PE libraries sequence the read-length off of each end of the same DNA fragment (available for RNA/cDNAs too!) and have a defined ~200bp gap in the middle with known standard deviation.
Mate-pair libraries are essentially longer-insert paired-end libraries with insert sizes from 5 to 20kb.
Bisulfite conversion converts non-methylated C’s into Uracil’s that are converted to T’s after one round of PCR. After mapping, this can be used to identify the positions of all methyl-C’s in the genome.
ChIP libraries can be produced from any DNA or RNA obtained by fragmentation, cross linking, co-immunoprecipitation with your favorite antibody of the DNA now cross-linked to the antibody’s target protein, and subsequent DNA/RNA purification. In this way, you can determine the actual binding sites of proteins in a whole-genome way.
By providing total RNA we can produce and sequence cDNA libraries that allow you to simultaneously define the entire transcribed portion of a genome as well as quantitate the level of transcription of each portion (genic or non-coding). This quantitation is as accurate as qRT- PCR and more broad than a microarray because it requires no a priori knowledge of putatively transcribed regions.
MicroRNA libraries are essentially the same as whole-transcriptome libraries but include only small fragments in a defined range (~20-40bp) that should include many types of non-coding RNAs. This allows you to both discover and quantitate the level of all small RNAs in a genome.
If you want to take measurements from a defined random subset of the genome (to reduce costs, for instance), we can construct libraries from bands of restriction digests so that you have high coverage over a smaller set of genome sites. This can be combined with most other types of libraries.
If you have PCR products or DNA isolated from Formalin-Fixed Paraffin-Embedded (FFPE) tissue, we can create sequencing libraries from these samples using specialized protocols.