Services
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.
Sample Requirements
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 |
Service | Sample Type | Minimum Amount | Minimum CONCN (ng/µL) |
Quality/Additional Requirement |
---|---|---|---|---|
DNA-seq | ||||
Human Exome | Genomic DNA | 2 µg | 15 | OD 260/280 1.8-2.0 |
Mouse Exome | Genomic DNA | 2 µg | 15 | OD 260/280 1.8-2.0 |
ChIP-seq (Bioo kit) | ChIP DNA | 10 ng | 0.25 | Fragmented to 100-300 bp |
ChIP-seq (KAPA kit) | ChIP DNA | 20 ng | 0.25 | Fragmented to 100-300 bp |
Service | Sample Type | Minimum Amount |
Minimum CONCN (ng/µL) |
Quality | Additional Requirement |
---|---|---|---|---|---|
DNA Methylation |
|||||
Reduced Representation Bisulfit Sequencing (RRBS)* | Genomic DNA | 2 µg | 25 | OD260/280 1.8-2.0; OD260/230 >2.0 | High MW DNA on a gel image |
Whole Genome Bisulfite Sequencing (WGBS)* | Genomic DNA | 2 µg | 25 | OD260/280 1.8-2.0; OD260/230 >2.0 | High MW DNA on a gel image |
*Note: Both RRBS and WGBS libraries are prepared by the DNA Methylation Analysis Core and sequenced by the Science Park NGS Core.
Typical Protocols and Costs
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 Costs
Sample Preparation | NGS User Group Member Price |
MDACC Faculty, UT System, BCM w/ MOU Price |
*External Out-of-Network Price | Quantity |
---|---|---|---|---|
RNA-seq (TruSeq Stranded Total RNA**) |
$266.05 | $321.47 | $514.35 | per sample |
mRNA (TruSeq Stranded mRNA) | $182.05 | $237.47 | $379.95 | per sample |
QuantSeq 3' mRNA-Seq Library Prep (Lexogen) | $58.83 | $77.98 | $124.77 | per sample |
Ultra Low Input RNA cDNA Synthesis (Clontech SMART-Seq v4) | $162 | $202 | $256 | per sample |
Library Prep for Ultra Low Input RNA (Illumina NexteraXT) (not including cDNA synthesis) | $55 | $100 | $160 | per sample |
TruSeq RNA Access Library Prep (for human RNA isolated from FFPE tissues) | $275 | $444 | $710.40 | per sample |
microRNA-seq (Illumina kit) | $176.34 | $286.03 | $430.83 | per sample |
microRNA-seq (NEB kit) | $122.80 | per sample | ||
ChIP-seq (NEB Ultra kit) (Pricing with beads clean-up) | $118.96 | $163.30 | $261.28 | per sample |
ChIP-seq (KAPA Hyper kit) (Pricing with beads clean-up) | $117.82 | $162.15 | $259.45 | per sample |
Exome-seq | $175.09 | $312.19 | $493.19 | per sample (not including capture) |
Mouse exome capture | $875.79 | $985.46 | $1,130.26 | per sample (1-4 samples/capture) |
Human exome capture | $566.19 | $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.
Sequencing Costs
Service | NGS User Group Member Price (per lane) |
MDACC Faculty, UT System, BCM w/ MOU Price (per lane) |
*External Out-of-Network Price (per lane) |
---|---|---|---|
HiSeq 3000 | |||
50 bp, single read | $966.41 | $1,100.71 | $2,177.47 |
75 bp, paired end | $1,746.41 | $1,880.71 | $3,425.47 |
100 bp, paired end | $2,089.61 | $2,223.91 | $3,974.59 |
150 bp, paired end | $2,431.25 | $2,565.55 | $4,521.22 |
NextSeq 500 |
|||
High Output: | |||
75 bp, single read | $1,632.95 | $1,853.96 | $3,238.11 |
75 bp, paired end | $3,085.83 | $3,306.84 | $5,562.72 |
150 bp, paired end | $4,904.79 | $5,125.80 | $8,473.06 |
Mid Output: | |||
75 bp, paired end | $1,232.55 | $1,453.56 | $2,597.47 |
150 bp, paired end | $1,941.83 | $2,162.84 | $3,732.32 |
MiSeq | |||
50 bp, single read (v2 chemistry) | $948.99 | $1,132.53 | $1,358.78 |
150 bp, paired end (v2 chemistry) | $1,202.19 | $1,481.73 | $1,707.98 |
300 bp, single read (v2 chemistry) | $1,202.19 | $1,481.73 |
$1,707.98 |
300 bp, paired end (v3 chemistry) | $1,782.99 | $2,177.73 | $2,403.98 |
*Note: These prices are not including any overhead costs that may be collected by our Institution.
NGS Core Service Requests
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Contact Us
The Virginia Harris Cockrell Cancer Research Center at the University of Texas MD Anderson Cancer Center, Science Park
Department of Epigenetics and Molecular Carcinogenesis
Mailing Address: P.O. Box 389, Smithville, Texas 78957
Physical Address: 1808 Park Road 1C, Smithville, Texas 78957
Jianjun (J-J) Shen, Ph.D.
Director, Science Park NGS Facility
Professor, Epigenetics and Molecular Carcinogenesis
512-237-9558
jianshen@mdanderson.org