FAQ Which Core To Use

There are a few Cores at Penn that do DNA sequencing.  Here is what we offer

NGSC

The NGSC has 3 Illumina hiSeq2000s and a miSeq. Here is what these machines are good for:

hiSeq2000

The hiSeq2000 is good for these techniques (and their many variations) RNA-Seq, ChIP-Seq, miR-Seq, HITS-CLIP, exome capture, BIS-Seq, and whole genome sequencing in mammals.

There are two aspects of ultra-high throughput sequencing that are important counts and coverage.  Counts are important for RNA-Seq, ChIP-Seq, miR-Seq, and HITS-CLIP.  Coverage is important for exome capture, BIS-Seq, and whole genome sequencing.   The hiSeq2000 generates sequence for about 200 million fragments per lane.  For each fragment the hiSeq can produce single or paired-end 50bp or 100bp sequences.  Using 100bp pair-end sequencing, you can get up to 40Gb per lane.

In many cases a single lane can generate more counts or coverage than a sample needs.  In that case, it is important to use multiplexed adapters so we can sequence multiple samples per lane.  Multiplexed adapters are generally a good idea is they allow samples to be test sequenced for quality, then sequenced deeper as needed.

Technique	Typical Volume	Samples per Lane
RNA-Seq	30 to 200 million reads	1 to 6
ChIP-Seq	30 to 100 million reads	2 to 6
miR-Seq	10 million reads	20
HITS-CLIP	30 million reads	6
Exome capture	20-30x coverage	5 to 20
BIS-Seq	20-30x coverage	1/3
Genome Sequencing	20-30x coverage	1/3

miSeq

The miSeq uses the same libraries as the hiSeq2000. It generates only about 15 million fragments per lane, but runs very quickly, and can generate reads as long as 150bp (or longer).

It is good for sample testing, miR-Seq, amplicon sequencing, or the techniques above applied to small, e.g., bacterial genomes.