Experimental Design

The recommendations below are a good starting point for standard experiments, though individual experimental goals may require modifications. Please request a consultation to tailor the design to your particular experimental aims. Output per lane/flow cell varies by instrument and run mode. These details are outlined in our list of Instruments.

RNA Sequencing

Experiment type	Application	Organism	Output	Read Type
RNAseq (polyA)	Gene bundance	mammalian	15M reads	2 x 38+
RNAseq (polyA)	Transcript abundance,variant detection	mammalian	25M reads	2 x 75
RNAseq (polyA)	Transcriptome assembly		50M reads	2 x125+
RNAseq (ribo-depletion)	Transcript abundance,variant detection, lnc RNA	mammalian	50M reads	2 x 75
RNAseq (ribo- depletion)	Gene abundance	bacterial	10M reads	2 x 38+
small RNA	Expression profiling		1-2M reads	1 x 50
RIPseq	RNA-Protein Complex binding sites	mammalian	20M reads	1 x 50
RIPseq	RNA-Protein Complex binding sites	drosophila	10M reads	1 x 50
Ribosomal Profiling		mammalian	40M reads	1 x 50
16S Amplicon	Genus-level identification; Note: low diversity	mixed bacterial	15K-100K+ reads/sample	2 x150+

DNA Sequencing

Experiment type	Application	Organism	Output	Read Type
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
CUT&RUN	chromatin/histone profiling		5M reads	2 x 25
ATACseq	differences in open chromatin		50M reads	2 x 50
ATACseq	TF footprinting		200M reads	2 x 50
WGS	SNV detection		30X Coverage	2 x 100
WGBS	Note: low diversity	mammalian	120GB	2 x 75
RRBS	Note: low diversity	mammalian	3-5GB	2 x 75
Shallow Shotgun	species-level identification	mixed bacterial	500K reads/sample	2 x 150

Bauer Core Facility

FAS Division of Science

Experimental Design

RNA Sequencing

DNA Sequencing