Integrative Genomics Core (Baylor) Menu of Services

	Platform/ Technology	Number of targets	Coverage	Limit of detction	Minimum total RNA sample requirements	Cost per sample
Targeted Gene Expression Analysis
	NanoString	~500	Study specific	0.5fM	200ng	Click here
Whole Genome Expression Analysis
Whole blood	iScan	~49,000	>25,000 annotated genes	5 fluor/µm2 (Cy3 or Cy5)	500ng	$160
Cell lysates		~49,000	>25,000 annotated genes	5 fluor/µm2 (Cy3 or Cy5)	500ng	$140
Small cell numbers		~49,000	>25,000 annotated genes	5 fluor/µm2 (Cy3 or Cy5)	50ng	$310
Whole Transcriptome Analysis
RNASeq	SOLiD v4	~50 million	All annotated and novel, coding and non-coding genes		5µg	$2,068

About the Technologies

Microarray

The high-value content on the Illumina Expression BeadChips provides genome-wide transcriptional coverage of well-characterized genes, gene candidates, and splice variants, with a significant portion targeting well-established sequences.

BIIR primarily employs the HumanHT-12 Expression BeadChip which targets more than 25,000 annotated genes with more than 48,000 probes derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq (Build 36.2, Rel 22) and the UniGene (Build 199) databases.

More information regarding the Illumina Expression BeadChip technology as well as other gene expression products currently used at BIIR can be found at: http://www.illumina.com/applications.ilmn#whole_genome_gene_expression

NanoString

The NanoString™ nCounter Analysis System® utilizes a novel digital technology that is based on direct multiplexed measurement of gene expression and offers high levels of precision and sensitivity.  This technology uses molecular "barcodes" and single molecule imaging to detect and count hundreds of unique transcripts in a single reaction. Each color-coded barcode is attached to a single target-specific probe corresponding to a gene of interest. Mixed together with spiked-in controls, they form a multiplexed CodeSet uniquely specific for your study of interest. The CodeSet consists of the probe pairs that will hybridize with your genes of interest.

This analysis system enables highly sensitive detection and quantification of gene expression from a wide variety of sample types including direct measurement from purified total RNA, cell and tissue lysates, RNA extracted from FFPE samples and blood without globin mitigation.

Assay Highlights:

• Multiplexed gene expression profiling of up to 550 genes in a single reaction
• Fully customizable
• High sensitivity, small starting sample requirement
• Wide dynamic range
• Compatible with multiple sample types

More information regarding the NanoString technology can be found at: http://www.nanostring.com/technology/

Next Generation High Throughput Sequencing (Development Phase)

The SOLiD™ 4 System is a revolutionary genetic analysis platform that enables massively parallel sequencing of clonally amplified DNA fragments linked to beads. The SOLiD™ sequencing methodology is based on sequential ligation with dye-labeled oligonucleotides. The SOLiD™ technology provides unmatched accuracy, ultra high throughput capability and application flexibility to empower translational research. 

SOLiD Chemistry: http://www3.appliedbiosystems.com/AB_Home/applicationstechnologies/SOLiDSystemSequencing/OverviewofSOLiDSequencingChemistry/index.htm

The SOLiD Whole Transcriptome Analysis Highlights

The sequencing-based SOLiD™ Total RNA-Seq kit enables you to detect all known and novel RNAs present in biological samples, with no bias toward known RNA molecules as with probe-based technologies.  The kit provides you with new views of a cell’s transcriptome, including:

• Expression of all coding and non-coding RNAs
• Identification of alternative splicing events
• Expressed SNPs (single nucleotide polymorphisms) or mutations
• Translocations and fusion transcripts
• Identify allele specific expression patterns

The SOLiD™ Total RNA-Seq kit and the ultra-high throughput SOLiD™ 4 System

• Conserve strandedness of cDNA, allowing you to discern between overlapping RNAs transcribed from the sense or antisense strand.
• Generate up to greater than 700 million sequence reads per run for RNA expression analysis.
• Facilitate detection of fusion transcripts and alternate splicing with paired-end sequencing
• Enable you to sequence up to 16 RNA libraries simultaneously (sample multiplexing), reducing the cost of analysis per sample.

SOLiD SAGE System Highlights

The SOLiD™ Serial Analysis of Gene Expression (SAGE™) System provides a highly sensitive, hypothesis-neutral method for quantifying gene expression levels on a genome-wide scale. This method, which determines mRNA expression levels by sequencing unique sequence tags isolated from the 3’ ends of mRNAs, has significant advantages over microarray technologies:

• Detects known and novel mRNAs.
• Is highly reproducible, with a dynamic range that is orders of magnitude greater than microarrays.
• Detects expression of transcripts from < 1 copy per cell to over 100,000 copies per cell, corresponding to a dynamic range of > 10⁵.

The sequencing-based SOLiD™ SAGE™ kit and analysis software provides an optimized and streamlined protocol enabling high-throughput analysis and quantification of genome-wide expression levels of both traditional poly(A) and non-poly(A) transcripts.  A limited number of steps developed for SAGE™ are used to generate a library of 27-bp “3’ tags” for all the transcripts in a cell, followed by SOLiD™ sequencing.  

Small RNA Analysis Highlights

The SOLiD™ Small RNA Solution is a robust method for hypothesis-neutral, whole genome analysis of expression patterns that enables you to discover novel RNA without the probe bias of microarrays. Using the SOLiD™ Total RNA-Seq Kit, you can convert total RNA into a library suitable for emulsion PCR in a single day. This simplified protocol reduces experimental variability and improves the detection of biologically relevant changes.

The SOLiD™ Total RNA-Seq kit is a single kit for the construction of libraries for either small RNA or whole transcriptome analysis. The expression profiles from these libraries are highly concordant with those from previous kits (SOLiD™ RNA Expression and SOLiD™ Whole Transcriptome Analysis kits).

More information regarding the SOLiD 4 Sequencing Technology can be found at: http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_061241.pdf