Sample Submission Guidelines

Requirements

The quality and quantity of the DNA/RNA sample are critical to the success of these procedures. Any contamination in the starting material will be directly reflected in the output library.

Ideally, the DNA/RNA sample should be checked to ensure the material is derived from the target organism and contains no other contaminating DNA. At a minimum, the DNA sample should meet the following criteria:

• DNA should not be degraded, and should contain no particulate matter
• OD260/280 ratio should be approximately 1.8
• Concentration should be 5 ng/ul or above, in TE or water (0.5 ng/ul for cloned or PCR-generated targets)
• Because DNA quantitation using OD260 is variable and dependent upon DNA purity, the input DNA concentration should be verified by fluorometry (PicoGreen/Ribogreen-based assay; Invitrogen Qubit) or densitometry (e.g., after gel electrophoresis on a 1 - 2% agarose gel using a DNA Mass Ladder).

Samples can be in water or TE. Samples can be shipped in a 1.5mL labeled tube, microtiter plate, or boxed. Samples and containers must be clearly labeled. If submitting unboxed 1.5mL tubes sample tubes can be sealed with parafilm, placed in a 50mL screw-top falcon tube packed with KimWipe, and shipped frozen on dry ice. Please include plenty of dry ice with your samples. Please include concentration, 260/280 readings, and a gel image for each submitted sample.

Pricing

Illumina GAII (Solexa)
* 1 Solexa cycle = 1bp
* Solexa lane run for 36-cycles typically generates 200-1000Mbp (5-25 million reads per lane)
* 7 lanes available for user samples per run; 1 lane used as control (all 7 lanes do not have to be from same user)
* Illumina currently offers 12 different library barcode indexes allowing 12 libraries to be run simultaneously in a single lane.
* Read length currently supported on Solexa: 18-100bp

36-cycle Solexa run without library preparation = $1,000.35 per lane
46-cycle Solexa run without library preparation = $1,172.34 per lane
56-cycle Solexa run without library preparation = $1,256.14 per lane
76-cycle Solexa run without library preparation = $1,511.93 per lane
100-cycles Solexa run without library preparation = $2,023.50 per lane
Standard Solexa DNAseq, RNAseq, or Paired-end library preparation = $425.40 per library
Standard Solexa ChIP-seq library preparation = $362.04 per library
2x36-cycle Solexa Paired-end run without library preparation = $1,881.24 per lane
2x54-cycle Solexa Paired-end run without library preparation = $2,392.81 per lane
2x76-cycle Solexa Paired-end run without library preparation = $2,610.05 per lane
2x100-cycle Solexa Paired-end run without library preparation = $3,338.86 per lane

Roche GS-FLX (454)
* Instrument can be run using either LR70 or XLR70 (Titanium) kits
* Only the shotgun DNAseq kit is currently available for XLR70 chemistry (Amplicon and Paired-end kits available late 2009)
* 454 Plate can be configured with 2, 4, 8, or 16-regions gaskets; 2-region gasket gives maximum Mbp output
* 12 Library Multiplex Identifier (MID) barcodes are available to allow for up to 12 libraries to be run per region.
* LR70 2-region output = ~400,000 reads with ~250bp mean fragment length (Total output = ~100Mbp)
* XLR70 2-region output = ~1,000,000 reads with ~400bp mean fragment length (Total output = ~400Mbp)
LR70 Standard 454 shotgun DNAseq library preparation = $539.74 per library
LR70 454 Sequencing Run = $13,390.35
XLR70 (Titanium) standard 454 shotgun DNAseq or cDNA library preparation = $496.77
XLR70 (Titanium) 454 Sequencing Run = $13,073.29

Microarray
Current slide processing full costs below:
- 1 array/slide hyb only (Tecan):  $154.91
- 4 array/slide hyb only (Tecan):  $154.91
- 1 array/slide hyb only (Manual):  $116.57
- 4 array/slide hyb only (Manual):  $116.57
- GE dual-color labeling:  $385.23
- GE single-color labeling:  $212.80
- ChIP-chip dual-color labeling: $255.41

Shipping Address

ATTN: IGSB HGAC Lab
Argonne National Laboratory
9700 South Cass Avenue
Building 202 Room A346
Argonne, IL 60439-4803
Phone: (630) 252-3993