PAN_NGS

PAN: Protein and Nucleic Acid Facility

» Next Gen Sequencing

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Genomic Services

• Next Gen Sequencing

• DNA Sequencing
& Fragment Analysis

• Single Cell Genomics

Protein Services

Located in rooms
B065 and B017

• SAMPLE SUBMISSION REQUIREMENTS

Before submitting your order online, please follow our minimum requirements for the samples being submitted for each service below:

Full Service
MiSeq Run

Full Service: (back to top)

• Sample QC --

You need to check the quality of your samples before submitting them to us. QC can be done on Agilent Bioanalyzer, and the data can be submitted through our online order form.

• Required Amount of Starting Material --

The amount required will be dependent of the library preparation kit chosen. PAN is currently supporting sample prep kits from Illumina.If you are unsure of which kit to use, we will work with you to determine the kit best suited for your project.

The following table can be used as a guide to choose an appropriate kit for your project.
(Click on the name of each kit for more detailed information)

Starting Material	Application	Project Type	Sample Prep Kit Option(s)	Sample Type	Input Quantity
• DNA	• DNA Sequencing	Whole Genome	*TruSeq DNA (LT or HT)	gDNA	1ug
			*TruSeq DNA PCR-Free (LT or HT)	gDNA	1-2ug
			Nextera DNA	gDNA	50ng
			Nextera Mater Pair	gDNA	1-4ug
		** Targeted Resequencing (Enrichment) -Hybrid capture -Metagenomics (16S rRNA) -Clone checking	Nextera Rapid Capture Exome	gDNA	50ng
			Nextera Rapid Capture Expanded Exome	gDNA	50ng
			TruSeq Custom Enrichment	gDNA	1ug
			Nextera Custom Enrichment	gDNA	50ng
			Nextera Rapid Capture Custom Enrichment	gDNA	50ng
		Small Genome	Nextera XT	gDNA	1ng
		Amplicon	Nextera XT	PCR amplicons (at least 300bp)	1ng
			TSCA	gDNA	250ng
			TSACP	gDNA, FFPE DNA	150-250ng
	• Gene Regulation Analysis	ChIP-SEQ	TruSeq ChIP -Seq	ChIP DNA	5-10ng
• RNA	• Transcriptome Analysis	mRNA-SEQ	TruSeq RNA v2	Total RNA	1-4ug
			TruSeq RNA v2	mRNA	entire fraction of mRNA
			*TruSeq Stranded mRNA (LT or HT)	Total RNA	0.1-10ug
			*TruSeq Stranded mRNA (LT or HT)	mRNA	10-400ng
		Total RNA-SEQ ( mRNA + non-coding RNA)	*TruSeq Stranded Total RNA (LT or HT)	Total RNA (human, mouse or rat or other eukaryote)	0.1-1ug
		Total RNA-SEQ ( mRNA + non-coding RNA)	*TruSeq Stranded Total RNA (LT or HT)	Low quality or FFPE RNA	0.1-1ug
		Small RNA	TruSeq Small RNA (48rxns)	small RNA	entire fraction of small RNA purified from 1-10ug of total RNA.

*TruSeq LT: 24-plex; TruSeq HT: 96-plex
** For exome capture, you need to specify the total number of samples for pre-enrichment pooling.

• Library QC on MiSeq --

We offer further QC of the prepared library(ies) on our MiSeq machine. For more information, you can refer to the information in the MiSeq Run section below.

MiSeq Run : (back to top)

• Sample QC --

It is important that you check the quality and quantity of your samples before submitting them to us. For best results and accurate readings, use Bioanalyzer and Qubit to determine the library's size and concentration, respectively. We will ask for the results if they are availble.

We will also run your sample on our Agilent Bioanalyzer as part of our initial QC step for MiSeq Run. If the sample failed QC and/or the results are not the same as those provided by you, we may ask for sample resubmission or a written confirmation (email will suffice) stating that it is okay for us to proceed with MiSeq run as is.

• Desired Run Cycle and Expected Read Length --

Depending on the application and the read length needed, you need to choose the right run cycle for your sample.

The table below will give you guidance to choose the right run cycle based on the application needed.

Application/Project Type

Recommended Read Length

Targeted Resequencing

Amplicon (tens of targets)

Amplicon (hundreds of targets)

Hybrid Capture (thousands of targets)

16S Metagenomics

Clone Checking

1 x 250

2 x 250

2 x 75

2 x 150

1 x 36

Small Genome

De novo

Resequencing

Plasmids

2 x 250

RNA Sequencing

Small RNA

RNA-Seq (microbial)

2 x 25

2 x 50-250

ChIP Seq

2 x 25

Library QC

2 x 25

** For more information on other applications and recommended sample prep kits, please refer to this brochure and Illumina website.

• Order Submission --

For the library being submitted, please place an order online, then email us detailed information including library's size, library's concentration, index barcodes and sequences (if any). You can download this template and then email it to Elizabeth Zuo .