Sequencing DNA

Whole genomes

Whole genomes are best sequenced with long reads on a PacBio.  If you are resequencing something known, Pacbio will capture ewHigh quality, high molecular weight DNA from a single individual is required for best assemlby.   

 

 

DNA methylation and Motif analysis: 

DNA methylation  signatures for 6-mA a 4-mC can be directly detected during Pacbio sequencing.  Identification of methylation patterns and their underlying motifs can be obtained from pacbio genomic data if desired.   

 

 

Amplicons: 

Low throughput on single or simple amplicons for construct verification or genotyping an individual is performed by <sanger sequencing> 

High throughput and environmental amplicons less than 200bp can be sequenced on the ion proton, long amplicons, 200bp to 6kb+  (full length 16s rRNA, TrnL,  ITS, etc)  are best sequenced on a <PacBio>.  molecular barcoding amplicons during amplification allows numerous samples to be pooled 

 

 

Targeted Enrichments: 

 Hybridiszation probes and antobodies attached to matix are often used to enrich a sample for sequences of interest.  this can be genomics regions, whole chromosomes, favored gene sets,  proteins binding sites.  ChIP of genome-wide methylation patterns generates more sequencable DNA than from a transcription factor.  theoretical yields from these pulldowns can be quite low and at detection limits when the pulldown is specific and clean.  Pulldowns or large genome regions are best sequenced on a PacBio.   Our ChIP samples are sequenced on the Ion Proton.  

 

Chromatin structure:

 ATAC-seq, , Assay for Transposase-Accessible Chromatin using sequencing, is used to access informantion about the openess and this accessability of chromatin for expression.  These DNA for these libraries should be multimodal, with broad peaks rerpesenting nucleosome units.  Our ATAC seq is performed on the Ion Torrent. 

 

Amplicon panels:   

Massively multiplexed amplicon pools are routinely used to address genotypes from DNA or  expression levels from cDNA.  The Ion Proton has many cancer screening panels and even a broad transcriptome expression panel that targts 22k know features in the mouse or human transcriptome.