GeneSifter® Analysis Edition:
Digital gene Expression using Next Generation Sequencing
Digital gene expression (DGE) is a novel approach to genome-wide expression profiling using next generation sequencing rather than hybridization methodologies. This approach allows researchers to identify, quantify, and annotate the expression of any transcript from any organism.
Since DGE is not dependent upon hybridization, it has virtually no background signals impeding its detection capabilities making it extremely useful for identifying low abundance and novel transcripts often missed or ignored in microarray analysis. The ability to survey gene expression in an unbiased approach is very useful for a broad range of applications from studying new organisms with no previous genome wide expression analysis to exploring human diseases such as cancer, which have inherently unstable genomes.
From Data to Information
Geospiza’s DGE analysis kits streamlines this overwhelming process by taking millions of raw next generation sequencing reads and transforming them in to meaningful and easy to visualize data. Geospiza’s DGE analysis kits can analyze reads produced from whole mRNA or discrete segments of mRNA produced in tag-profiling (NlaIII or DpnI preps). The output will include a gene list representing all identified transcripts along with expression values and links to public data sources such as Entrez Gene.
Moreover, GeneSifter will take you to the next level of analysis with your DGE data allowing you to identify biologically significant data over multiple DGE experiments. GeneSifter utilizes consensus “best” standard gene expression analysis algorithms to provide statistical comparisons for two or more samples. All of this is done through a web-based platform allowing you to perform your analysis anywhere, anytime, and with any computer system using a standard web browser.
Altogether, Geospiza’s DGE analysis kit will empower you to easily and efficiently go from sample(s) to meaningful results using data from a single experiment or many experiments.
Input Requirements:
GeneSifter Analysis Edition utilizes standard file formats for the following systems:
ABI - SOLiD
csfasta color space files, 10-50 million reads
Illumina - Genome Analyzer
FASTA, FASTQ or ELAND files, 10-50 million reads
Intuitive Reports
GeneSifter DGE pipelines return an informative gene list summary and several quality control reports to researchers. Reports include:
Gene List Summary Report: This dashboard view of the analysis allows researchers to quickly account for and survey all the reads in a sample with information for each transcript identified.
Number of hits per transcript, per kilobase million, and per million
Live-link to Entrez Gene
Thumbnail summary read map linked to detailed pileup, base by base mapping of reads across mRNA transcript
RefSeq ID, Gene Title, and Gene ID
Chromosomal location and RNA type
Quality Control Reports: These reports allow researchers to visualize QC metrics and determine whether technical problems could confound results.
Mapping summaries - mapped, unmapped, and uniquely mapped reads, as well as read distribution of reads by chromosome.
Transcript coverage plot - distribution of reads per transcript.
Color composition analysis – nucleotide usage per cycle during sequencing run.
Integrated Statistical Analysis
For even more powerful analysis of your data, results generated by the DGE pipeline are immediately available for statistical analysis in GeneSifter®, allowing researchers to gain biologically relevant results from multiple experiments in a single step.
Contact us for more information or to find out how Geospiza can help with your analysis or lab automation. 877.Web.Gene or info@geospiza.com or Request More Info |
