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Services and Pricing
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- Experimental design assistance
- Type of arrays
- Array Pricing and Extent of Services
- Illumina 1G Pricing and Extent of Services
- LCM Pricing and Extent of Services
- Data Analysis
- Data Dissemination Via Online Repositories
- Education
- Manuscript Assistance and Consultation
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- Investigators can gather information regarding available platforms before submitting samples to the Consortium. Additionally, the four Centers will be available to review experimental design at any time prior to the submission of a project.
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- Affymetrix: human, rat, mouse, and more species (see list below)
- cDNA: songbird arrays - 18k arrays; brain full - length cDNAs from RIKEN
- oligo: Currently all Operon oligo sets are available.
- Agilent oligo: Human, mouse, rat, and more - see full list below.
- Illumina
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We offer four options for Expression Profiling Array
experiments:
- Start to Finish Profiling of total RNA;
- Partial Services from Hybridization through
Analysis;
- Custom Array creation and Data Analysis;
- DNA Array SNP Analysis
In additon,the Consortium has made it easier to access the data
produced via it's online repository, educational efforts and manuscript
consulting.
| Option
1: Start to Finish Profiling of total RNA* |
- The investigator may send total RNA to the designated
microarray center or travel to a center to learn techniques
for RNA isolation from tissue or Laser Capture Microdissection (LCM) samples.
- QC check for RNA quality
- Labeling of RNA
- Hybridization with arrays
- Scanning
- Data analysis
*NOTE: For
optimal experimental results, it is strongly recommended that
extramural investigator isolate the RNA, and that the total RNA,
rather than tissue, be sent to the NIH Neuroscience Microarray Consortium
center. See protocol for RNA isolation below. However, investigators
may also travel to a mircroarray center to isolate RNA with a
consortium scientist. RNA isolation at the centers will be performed only by special arrangement and the cost will be determined on a project
by project basis. |
| Affymetrix Gene 1.0 ST Arrays |
Cost Per Array |
Labeling per Array RNA ≥2µg |
QC per 12 Samples |
| Human |
$250.00 |
$80.00 |
$25.00 |
| Rat |
$250.00 |
$80.00 |
$25.00 |
| Mouse |
$250.00 |
$80.00 |
$25.00 |
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| * If you have less than 2ug of total RNA,
please contact Dr. Shrikant Mane (Shrikant.Mane@yale.edu)
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| Affymetrix Arrays |
Cost per Array |
Labeling per Array RNA ≥5µg |
Labeling per Array RNA ≤5µg |
QC per 12 samples |
Human Genome U133 Plus 2.0
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$400.00 |
$150.00 |
$300.00 |
$25.00 |
| Human U133 A or B |
$350.00 |
$150.00 |
$300.00 |
$25.00 |
| Human U133A 2.0 |
$250.00 |
$150.00 |
$300.00 |
$25.00 |
| Mouse Genome 430 2.0 |
$400.00 |
$150.00 |
$300.00 |
$25.00 |
| Mouse Genome 430A 2.0 |
$250.00 |
$150.00 |
$300.00 |
$25.00 |
| Mouse 430 A or B |
$350.00 |
$150.00 |
$300.00 |
$25.00 |
| Rat Genome 230 2.0 |
$375.00 |
$150.00 |
$300.00 |
$25.00 |
| Rat 230 A or B |
$325.00 |
$150.00 |
$300.00 |
$25.00 |
| Rat Neurobiology |
$250.00 |
$150.00 |
$300.00 |
$25.00 |
| Bovine Genome |
$250.00 |
$150.00 |
$300.00 |
$25.00 |
| C. Elegans Genome |
$275.00 |
$150.00 |
$300.00 |
$25.00 |
| Canine Genome 2.0 |
$375.00 |
$150.00 |
$300.00 |
$25.00 |
| Chicken Genome |
$375.00 |
$150.00 |
$300.00 |
$25.00 |
| E. Coli Genome 2.0 |
$175.00 |
$150.00 |
$300.00 |
$25.00 |
| Rhesus Macaque Genome |
$400.00 |
$150.00 |
$300.00 |
$25.00 |
| Xenopus Genome |
$275.00 |
$150.00 |
$300.00 |
$25.00 |
| Yeast Genome 2.0 |
$175.00 |
$150.00 |
$300.00 |
$25.00 |
| Zebrafish Genome |
$275.00 |
$150.00 |
$300.00 |
$25.00 |
| Affymetrix Exon Arrays |
Cost |
Labeling per RNA ≥5µg |
Labeling per RNA ≤5µg |
QC per 12 samples |
| Human |
$400.00 |
$200.00 |
-- |
$25.00 |
| Mouse |
$400.00 |
$200.00 |
-- |
$25.00 |
| Rat |
$400.00 |
$200.00 |
-- |
$25.00 |
| Illumina Arrays |
Cost per Array |
Labeling per Array RNA ≥5µg |
Labeling per Array RNA ≤5µg |
QC per 12 samples |
Sentrix Human Ref-8v2
(8 samples/chip) |
$800.00 |
$400.00 |
$400.00 |
$25.00 |
Sentrix Human Ref-6v1
(6 samples/chip) |
$960.00 |
$300.00 |
$300.00 |
$25.00 |
Sentrix Mouse Ref-8v2
(8 samples/chip) |
$800.00 |
$400.00 |
$400.00 |
$25.00 |
Sentrix Mouse Ref-6v1
(6 samples/chip) |
$960.00 |
$300.00 |
$300.00 |
$25.00 |
Rat Genome
(12 samples/chip) |
$1200.00 |
$600.00 |
$600.00 |
$25.00 |
| Note that each Illumina array holds 6-12 samples thus the investigator must use the entire chip. |
| cDNA Arrays |
Cost per Array |
Labeling per Array RNA ≥5µg |
Labeling per Array RNA ≤5µg |
QC per 12 samples |
| Songbird (zebra finch) 18k |
$75.00 |
$87.50 |
$102.50 |
$25.00 |
| Neuro-specific growth factor signaling(3K) |
$50.00 |
$87.50 |
$102.50 |
$25.00 |
| Operon Oligo Arrays |
Cost per Array |
Labeling per Array RNA ≥5µg |
Labeling per Array RNA ≤5µg |
QC per 12 samples |
| Human |
$75.00 |
$87.50 |
$102.50 |
$25.00 |
| Mouse |
$75.00 |
$87.50 |
$102.50 |
$25.00 |
| Rat |
$75.00 |
$87.50 |
$102.50 |
$25.00 |
| Yeast |
$75.00 |
$87.50 |
$102.50 |
$25.00 |
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*Consortium is offering Ambion's new FirstChoice Human Brain reference RNA as the reference RNA for human arrays as brain genes are better represented in this reference source as opposed to Stratagenes Universal Human reference RNA.
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| Agilent Arrays |
Cost per Array |
10ug total RNA or 200ng mRNA |
~50-500 ng total RNA |
QC per 12 samples |
| Human 40K |
$450.00 |
$120.00 |
$245.00 |
$25.00 |
| Human |
$350.00 |
$120.00 |
$245.00 |
$25.00 |
| Mouse Development |
$315.00 |
$120.00 |
$245.00 |
$25.00 |
| Mouse Toxicology |
$315.00 |
$120.00 |
$245.00 |
$25.00 |
| Rat |
$315.00 |
$120.00 |
$245.00 |
$25.00 |
| Yeast |
$206.25 |
$120.00 |
$245.00 |
$25.00 |
| Magnaporthe |
$315.00 |
$120.00 |
$245.00 |
$25.00 |
| Human Whole Genome |
$400.00 |
$120.00 |
$245.00 |
$25.00 |
| Rat Whole Genome |
$400.00 |
$120.00 |
$245.00 |
$25.00 |
| Mouse Whole Genome |
$400.00 |
$120.00 |
$245.00 |
$25.00 |
| miRNA Arrays |
Cost per Array |
Labeling per Array for 10-20ug of total RNA enriched for small RNAs * |
Labeling per Array for 10-20ug of total RNA unenriched ** |
QC per 12 samples |
Ambion + Invitrogen (miRNA-AL)
Human, Rat, and Mouse |
$57.75 |
$146.00 |
$177.10 |
$25.00 |
Ambion + Invitrogen (miRNA3)
Human, Rat, and Mouse |
$57.00 |
$146.00 |
$177.10 |
$25.00 |
Exiquon (miRNA-EX)
Human, Rat, and Mouse |
$65.45 |
$146.00 |
$177.10 |
$25.00 |
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*Investigator must enrich 10-20 ug of total RNA using the Ambion mirVana RNA isolation kit. Consortium will then label all of their sample ($146.00 for processing).
**Investigators must submit 10-20 ug of total RNA (isolated via Ambion mirVana miRNA isolation kit or via Trizol, should NOT use Qiagen kits or any filter based isolation, will loose miRNA) for fractionation (isolates ~40nt fragments ). Consortium will label all miRNA isolated ($177.10 processing).
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| Option
2: Partial Services from Hybridization through Analysis* |
| Hybridizations, scanning,
and data analysis will be performed on labeled probes provided by
the investigators |
| Affymentrix |
Cost per chip |
Human Genome U133 Plus 2.0
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$400.00 |
| Human U133 A or B |
$300.00 |
| Human U133A 2.0 |
$300.00 |
| Mouse Genome 430 2.0 |
$400.00 |
| Mouse Genome 430A 2.0 |
$250.00 |
| Mouse 430 A & B |
$350.00 |
| Rat Genome 230 2.0 |
$375.00 |
| Rat 230 A & B |
$375.00 |
| Rat Neurobiology |
$250.00 |
| Bovine Genome |
$250.00 |
| C. Elegans Genome |
$275.00 |
| Canine Genome 2.0 |
$375.00 |
| Chicken Genome |
$375.00 |
| E. Coli Genome 2.0 |
$175.00 |
| Rhesus Macaque Genome |
$400.00 |
| Xenopus Genome |
$275.00 |
| Yeast Genome 2.0 |
$175.00 |
| Zebrafish Genome |
$275.00 |
| cDNA |
Cost per chip |
| Songbird (zebra finch) 18K |
$75.00 |
| Neuro-specific growth factor signaling (3K) |
$50.00 |
| Operon Oligo |
Cost per chip |
| Human |
$75.00 |
| Mouse |
$75.00 |
| Rat |
$75.00 |
| Yeast |
$75.00 |
| Agilent |
Cost per chip |
| Human 40K |
$450.00 |
| Human A or B |
$350.00 |
| Mouse Development |
$315.00 |
| Mouse Toxicology |
$315.00 |
| Rat |
$315.00 |
| Yeast |
$192.50 |
| Magnaporthe |
$315.00 |
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| Option 3 (only offered for cDNA and
oligo arrays) |
| Custom arrays and data
analysis are provided. All other services are performed by the
investigator. |
| cDNA |
Cost per Array |
| Songbird (zebra finch) 18K |
$75.00 |
| Neuro-specific growth factor signaling (3K) |
$50.00 |
| Operon Oligo |
Cost per Array |
| Human |
$75.00 |
| Mouse |
$75.00 |
| Rat |
$75.00 |
| Yeast |
$75.00 |
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| Option 4:
DNA Genotyping Arrays |
| Affymetrix Arrays |
Cost |
| Human Mapping 10K Array Xba 142 2.0 |
$185 per chip and sample reagents. |
| Human Mapping 100k system (consists of two 50k arrays) |
| Human mapping 50k Array Xba 240 |
$320 per chip and sample reagents. |
| Human mapping 50k Array Hind 240 |
$320 per chip and sample reagents. |
| Human Mapping 500k system (consists of two 250k arrays) |
| Human mapping 250k Sty Array |
$210 per chip and sample reagents. |
| Human mapping 250k Nsp Array |
$210 per chip and sample reagents. |
| Genome-Wide Human SNP 5.0 Array |
$350 per chip and sample reagents. |
| Genome-Wide Human SNP 6.0 Array |
$300 per chip and sample reagents. |
| Illumina Arrays * |
Cost ** |
| HumanCNV370-Duo Array |
$260 per chip and sample reagents. |
| Human Hap240S Array |
$260 per chip and sample reagents. |
| Human Exon510S-Duo Array |
$310 per chip and sample reagents. |
| Human Hap550-Duo Array |
$310 per chip and sample reagents. |
| Human Hap650Y Array |
$400 per chip and sample reagents. |
| Human 1M Array |
$600 per chip and sample reagents. |
** For projects with greater than 2000 samples, please contact Shrikant Mane at Yale University.
* Shipping fees are not included in the price of the Illumina arrays
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Genomic DNA should be sent to the Microarray Consortium. Also, Data Analysis is not currently offered for this option.
Notes on DNA preparation:
- Quantity: 50 uL of genomic DNA at concentration 50ng/uL. DNA
should be diluted in reduced EDTA TE buffer (0.1 mM EDTA, 10mM Tris
HCl, pH8.0).
- High quality genomic DNA will run as a major band at 10-20 kb
on a 1% gel.
- Quality: DNA must be double stranded and free of PCR inhibitors
and salts. DNA may not be pre-amplified or pre-digested. Please
download the following proposal form: Genotyping Proposal Form
Proposals can be emailed to Elizabeth Salomon.
- Please prepare samples in 96-well format.
Note: Data generated from the Human
Mapping arrays will be made publicly available 6-months after the last hybridization is complete. The NIH Neuroscience Microarray Consortium will warehouse the
data so that it can be referenced in publications.
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| User provides libraries to be sequenced on Illumina 1G |
The NIH Neuroscience Microarray Consortium is now offering massively parallel sequencing on the Illumina 1G sequencer. This technology provides the ability to generate 2-5 million 35 nucleotide reads per channel of the machine. Users should note that a specific number of reads is not guaranteed and highly depends on library generation. Not all reads will map to the portion of the genome attempting to be sequenced. The ability to perform paired end sequencing is also planned likely available in February 2008), which will permit the generation of 150 million bases of raw sequence per flow cell channel. Assays developed on this platform also permit:
- Deep counting based assessment of gene expression
- De novo sequencing
- Resequencing of genic intervals to detect rare variants
- Other genomic assays: Methylation analysis, Chromatin IP analysis, alternative splicing analysis, copy number, etc.
Consortium will provide informatics support to call sequences and has established BLAT tools for mapping to genomic sequences that are known. Counting based gene expression data will be performed as counts for each gene. De novo assemblies will not be performed at this time, but sequence can be returned to the investigator.
Note: Investigator must pay for processing samples even if the run does not prove useful to the project and if the run was unsuccessful due to poor sample quality. If a technical or machine problem results in failure at the Consortium center, then the samples are rerun free of additional charge. There is limited capacity, and thus, samples are run on a first come first served basis.
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| Cost |
| $1000/ sample |
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Recommended Protocols for Isolating Samples:
Please download the following proposal form: Illumina 1G Proposal Form. Email back to Elizabeth Salomon.
For further questions, please contact Dr. Stan Nelson.
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NIH Neuroscience funded investigators have access to the following Laser Capture Microdissection services through the NIH Neuroscience Microarray Consortium.
| Option 1: Standard LCM in preparation for
microarray analysis through the Consortium |
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Appropriate for the isolation of cells or tissue regions that can be identified using standard histology, or are labeled by expression of a fluorescent reporter protein (e.g., GFP) or axonal tracers. Whole tissue should be frozen in OCT according to protocols provided, and shipped to the Duke center for processing. Tissues will be sectioned and stained, and 100-200 cells captured by LCM. Ideally the investigator will provide an example of the target cells unambiguously labeled using GFP or other staining protocols. Investigators will receive an image of the region from which the cells were captured as confirmation that the cells of interest were identified correctly. Service includes RNA extraction and amplification in preparation for microarray analysis through the Consortium. |
| Cost |
| $150/ sample |
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| Option 2: Investigator-supervised LCM in preparation for microarray analysis through the Consortium |
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An option for situations in which identification of the cells of interest requires specialized expertise. The investigator would need to arrange a time to travel to the Duke facility with tissue samples for LCM analysis in order to identify the target region. Investigators can also use option 2 if he or she would like training on LCM services. Subsequent RNA extraction and amplification will be performed as in the standard service (Option 1). This option may be combined with LCM training. |
| Cost |
| $150/ sample + $50/hour |
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| Option 3: LCM services without use of microarray services through Consortium |
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Investigators can also use the LCM services through the Consortium without subsequent microarray analysis. LCM will be carried out as described in Option 1, but amplified RNA will be returned to the investigator rather than submitted for microarray analysis through the Consortium. |
| Cost |
| $150/ sample + $100/hour |
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| Option 4: LCM training without use of microarray services through Consortium |
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Training in the use of LCM for isolating samples from standard sections or neuronal cultures, plus RNA extraction and amplification. Individual training available @ $50 per hour (time varies with procedures included). Training in standard procedures from tissue processing through RNA extraction requires approximately 2 days ($800) and $200 in reagent costs. Availability limited. |
| Cost |
| $50/ hour + reagent costs |
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- Statistical software packages are available for requisite
analyses
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All data that has gone through the process and publicly available can be searched via the Navigate Repository link to the left. Quick searches based on pre-defined, populated criteria (Project State, Platform, Species and those tied to Manuscripts)
or user-driven criteria against available species, organ, organ region, cell type, investigator last name and project key words that fall anywhere in the "abstract" of the
public project. The abstract pertains to the data filled in for the Study Relevance, Hypothesis, Specific Aim, or Experimental Design. Investigators should also review the data and analysis policies of the consortium. |
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- Protocols
- Protocol for total RNA isolation from mammalian cells and tissue:
- Trizol
RNA extraction protocol available from Invitrogen
- Followed by RNA purification with the RNeasy
cleanup kit from Qiagen
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Absolutely
RNA® RT-PCR Miniprep Kit from Stratagene for RNA isolation
from small tissue samples
Note: All RNA sent to the NIH Neuroscience
Microarray Consortium will be run on the Agilent Bioanalyzer to
assess quality of extracted RNA. Distinct ribosomal RNA bands should
be present. Non-distinct ribosomal RNA bands indicate RNA
degradation. The quantity ratio of the 28s band to the 18s band
should be around 2:1. RNA must pass these QC standards before it will
be labeled.
- Protocol for LCM and subsequent RNA isolation
- On-site Wet-lab Training: Investigators are invited to observe
the wet-lab work behind their experiments and to receive "hands-on"
experience working with the various platforms
- Data Analysis Training
- On-site interactive training: Investigators receive one-on-one
advice on the statistical analysis of their experiments
- Web-based: Investigators can
view
online lectures
on several statistical software packages
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- Submitting investigators can seek consultation on papers in preparation for a
fee of $100 per half-hour of phone time.
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