Experimental Design

The recommendations below are a good starting point for standard experiments, though individual experimental goals may require modifications. If you are in doubt, please ask us for a consultation. Our decision tree can help you pick the right run type based on your desired output, read type, and priorities. The output per lane/flow cell varies by instrument and run mode. These details are outlined in our list of Instruments.

Experiment type Application Organism Output Read Type

RNAseq (polyA)

gene abundance

mammalian

10M reads

1 x 50

RNAseq (polyA)

transcript abundance, variant detection

mammalian

25M reads

2 x 75

RNAseq (polyA)

transcriptome assembly

 

50M reads

2 x 125+

RNAseq (ribozero)

transcript abundance, variant detection, non-coding RNA

mammalian

50M reads

2 x 75

RNAseq (ribozero)

gene abundance

bacterial

10M reads

1 x 50

small RNA

expression profiling

 

1-2M reads

1 x 50

small RNA

discovery

 

2-5M reads

1 x 50

RIPseq

 

mammalian

20M reads

1 x 50

RIPseq

 

drosophila

10M reads

1 x 50

Ribosomal Profiling

 

mammalian

40M reads

1 x 50

ChIPSeq

point source

mammalian

10M reads

1 x 50

ChIPSeq

point source

drosophila/c. elegans

2M reads

1 x 50

ChIPSeq

broad source

mammalian

20M reads

1 x 50

ChIPSeq

broad source

drosophila

5M reads

1 x 50

ATACseq

differences in open chromatin

 

50M reads 2 x 50

ATACseq

TF footprinting

 

200M reads

2 x 50

WGS

SNV detection

 

33X Coverage

2 x 100

WES

SNV detection

 

80X Coverage

2 x 100

WGBS

Note: low diversity

mammalian

120GB

2 x 75

RRBS

Note: low diversity

mammalian

3-5GB

2 x 75

16S amplicon

Note: low diversity

mixed bacterial

15K-100K+ reads/sample

2 x 150 +

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