#  Experimental Design 

 



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The recommendations below are a good starting point for standard experiments, though individual experimental goals may require modifications. Please [request a consultation](/request-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](/instruments).



 

 RNA Sequencing DNA Sequencing 

## RNA Sequencing

 

 

##  RNA Sequencing 

Sort      **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

 

 

##  DNA Sequencing 

Sort    **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