We provide a variety of experimental protocols for deep-sequencing of RNA or DNA samples, depending on the requirements of your experiments. In many cases, multiple samples can be successfully analyzed in each lane of the sequencing run. The multiplicity for a given lane is limited by the read depth required for your experiment.

The following tables provide a guide to typical multiplicity and sequencing requirements for various kinds of experiments, the sample requirements of the Core, and estimated costs. For more detailed information, please call or email to set up a meeting with Core staff.

Please note that prices are subject to change without prior notice.

Service	Sample Type	Minimum Amount	Minimum CONCN (ng/µL)	Quality	Additional Requirement
RNA-seq
Total RNA Seq	Total RNA	1.5 µg	100	RIN>8.0	DNase treatment
mRNA Seq	Total RNA	2 µg	200	RIN>8.0	No DNase treatment required
miRNA Seq	Total RNA	2 µg	200	RIN>8.0	No DNase treatment required

^{*Note: Both RRBS and WGBS libraries are prepared by the DNA Methylation Analysis Core and sequenced by the Science Park NGS Core.}

Service Type	Sequencing	Multiplicity (samples/lane)	Expected # Reads	Cost/lane**
RNA-seq
Differential Expression (TruSeq Stranded Total RNA)	76 nt, paired end	8	>20M	$3,372
Differential Expression (TruSeq Stranded mRNA)	76 nt, paired end	8	>20M	$2,684
Novel Transcript (TruSeq Stranded Total RNA)	76 nt, paired end	4	>40M	$2,516
miRNA*	36nt, single read	12	>8M	$2,836
DNA-seq
Human Exome	76 nt, paired end	4	>40M	$2,820
Mouse Exome	76 nt, paired end	4	>40M	$3,120
ChIP-seq	36 nt, single read	6	>18M	Inquire
Reduced Representation Bisulfite Sequencing (RRBS)	36 nt, paired end	4	>24M (20X coverage)	$1,810
Whole Genome Bisulfite Sequencing (WGBS)	76 nt, paired end or 100 nt, paired end***	1	Inquire	Inquire

^{*Note:  miRNA samples can be typically multiplexed up to 48 samples per lane.
**Note: Cost is calculated based on using HiSeq 3000.  This estimate will be different if NextSeq 500 is used instead.  The costs are the sum of sample preparation and sequencing costs. Once you decide on the type of sequencing (read length, single or paired end) and on the multiplicity (number of samples per lane), the cost can be calculated from the parameters in the tables below. 
***Note: Depending on the size range of a prepared WGBS library.}

Sample Preparation	NGS User Group Member Price	MD Anderson Faculty non-NGS User Group Member Price	UT System / External In-Network Price	*External non-NGS User Goup Member Price	Quantity
RNA-seq (TruSeq Stranded Total RNA**)	$254.19	$391.30	$391.30	$572.30	per sample
mRNA (TruSeq Stranded mRNA)	$170.19	$307.30	$307.30	$488.30	per sample
Ultra Low Input RNA cDNA Synthesis (Clontech SMART-Seq v4)	$162	$202	$202	$256	per sample
Library Prep for Ultra Low Input RNA (Illumina NexteraXT) (not including cDNA synthesis)	$55	$100	$100	$160	per sample
TruSeq RNA Access Library Prep (for human RNA isolated from FFPE tissues)	$275	$444	$444		per sample
microRNA-seq (Illumina kit)	$176.34	$286.03	$286.03	$430.83	per sample
microRNA-seq (NEB kit)	$122.80				per sample
ChIP-seq (KAPA Hyper kit)	$124.13	$238.67	$336.30	$538.08	per sample
ChIP-seq (KAPA kit)	$ 94.11	$203.78	$203.78	$348.58	per sample
ChIP-seq (Bioo kit)	$126.96	$236.65	$236.65	$381.45	per sample
Exome-seq	$175.09	$312.19	$312.19	$493.19	per sample (not including capture)
Mouse exome capture	$875.79	$985.46	$985.46	$1,130.26	per sample (1-4 samples/capture)
Human exome capture	$566.19	$675.86	$675.86	$820.66	per sample (1-4 samples/capture)
Reduced Representation Bisulfite Seq (RRBS)	$245				per sample
Whole Genome Bisulfite Sequencing (WGBS)	$255				per library

^{*Note:  These prices are not including any overhead costs that may be collected by our Institution.
**Note: Please contact Core staff for consultation on kit selection.}

Service	NGS User Group Member Price (per lane)	MD Anderson Faculty non-NGS User Group Member Price (per lane)	UT System / External In-Network  (per lane)	*External non-NGS User Group Member Price (per lane)
HiSeq 3000
50 bp, single read	$966.41	$1,100.71	$1,360.92	$2,177.47
75 bp, paired end	$1,746.41	$1,880.71	$2,140.92	$3,425.47
100 bp, paired end	$2,089.61	$2,223.91	$2,484.12	$3,974.59
150 bp, paired end	$2,431.25	$2,565.55	$2,825.76	$4,521.22
NextSeq 500
High Output:
75 bp, single read	$1,632.95	$1,853.96	$2,023.82	$3,238.11
75 bp, paired end	$3,085.83	$3,306.84	$3,476.70	$5,562.72
150 bp, paired end	$4,904.79	$5,125.80	$5,295.66	$8,473.06
Mid Output:
75 bp, paired end	$1,232.55	$1,453.56	$1,623.42	$2,597.47
150 bp, paired end	$1,941.83	$2,162.84	$2,332.70	$3,732.32
MiSeq
50 bp, single read (v2 chemistry)	$948.99	$1,132.53	$1,132.53	$1,358.78
150 bp, paired end (v2 chemistry)	$1,202.19	$1,481.73	$1,481.73	$1,707.98
300 bp, single read (v2 chemistry)	$1,202.19	$1,481.73	$1,481.73	$1,707.98
300 bp, paired end (v3 chemistry)	$1,782.99	$2,177.73	$2,177.73	$2,403.98

^{*Note: These prices are not including any overhead costs that may be collected by our Institution.}