Key Applications and Methods
Exome sequencing analyzes the protein-coding region of the genome, as a cost-effective alternative to whole-genome sequencing. With both rapid Run and High Output modes, HiSeq 2500 System is a flexible system that can sequence 5–75 exomes* per run.
*Assumes 100x coverage with 80% on target using 2 x 75 bp reads.
See how researchers are using exome sequencing on the HiSeq Series.
Prep
2.5 days/6 hours hands-on time
TruSeq DNA Exome
A cost-effective library preparation and exome enrichment solution with industry-leading accuracy.
Sequence
5 days/30 minutes hands-on
HiSeq SBS Kit V4
Ready-to-load reagents for sequencing by synthesis on enabled HiSeq sequencing systems.
HiSeq PE Cluster Kit v4 cBot
Reagents for paired-end cluster generation on the cBot cluster amplification system.
Analyze
2–3 hours
Enrichment BaseSpace App
Rapid alignment and variant detection for small, structural, and copy number variant calling, variant annotation, and enrichment metrics calculation.
Browse Sample Datasets in BaseSpace Sequence Hub
Analyze both coding RNA and multiple forms of noncoding RNA with total RNA sequencing (RNA-Seq) for a comprehensive view of the transcriptome. With 4 billion reads per dual flow cell HiSeq run using the HiSeq v4 chemistry, the HiSeq 2500 System can sequence up to 80 transcriptomes* per run.
*Assumes 50 million reads per sample.
See how researchers are using total RNA-Seq on the HiSeq Series.
Prep
10.5 hours/4.5 hours hands-on
TruSeq Stranded Total RNA Library Prep Kit
A clear, comprehensive view of the transcriptome with a streamlined, cost-efficient, and scalable solution for total RNA analysis.
Sequence
5 days/30 minutes hands-on
HiSeq SBS Kit V4
Ready-to-load reagents for sequencing by synthesis on enabled HiSeq sequencing systems.
HiSeq PE Cluster Kit v4 cBot
Reagents for paired-end cluster generation on the cBot cluster amplification system.
Analyze
~13 hours
RNA-Seq Alignment BaseSpace App
Performs read mapping, FPKM estimation of reference genes and transcripts, novel transcripts assembly, variant calling, and optional fusion calling.
Cufflinks Assembly & DE BaseSpace App
Quickly assess novel transcript isoforms and gene expression levels from RNA-Seq Alignment results.
Browse Sample Datasets in BaseSpace Sequence Hub
The HiSeq 2500 System has been obsolesced. We intend to continue to provide full support of the instrument and supply the reagents through February 28th, 2023. We also offer several instruments that support the same applications as the HiSeq 2500 System; we recommend using the Sequencing Platform Comparison Tool to find the best instrument for your needs.
More Applications and Methods
Gene Expression Profiling
mRNA sequencing (mRNA-Seq) detects known and novel transcripts and measures transcript abundance for accurate, comprehensive expression profiling.
Large Whole-Genome Sequencing
Sequencing large complex genomes (human, plant, or animal) provides a base-by-base view of genomic alterations to inform studies of disease or population genomics.
Researcher Interview
DNA-Protein Interaction Analysis
Combining chromatin immunoprecipitation (ChIP) assays with sequencing, ChIP-Seq is a powerful method for genome-wide surveys of gene regulation.
Methylation Sequencing
Perform epigenetic studies with high coverage density and flexibility enabled by sequencing-based DNA methylation analysis.
Researcher Interview
Coding Transcriptome Analysis
Detect both known and novel features of the RNA exome using sequence-specific capture of RNA coding regions.
De Novo Sequencing
With a unique mix of high output, long reads, and paired-end sequencing, HiSeq is a powerful tool for de novo sequencing of species without a reference genome.
Researcher Interview
Metagenomics
Perform metagenomic analyses by sequencing entire microbial communities to discover important taxonomic and functional information.
Researcher Interview
Genotyping by Sequencing
Genotyping by sequencing provides a low-cost genetic screening method to discover novel plant and animal SNPs and perform genotyping studies.
Researcher Interview
Small Whole-Genome Sequencing
Small genome sequencing provides comprehensive analysis of microbial or viral genomes for public health, epidemiology, and disease studies.
miRNA and Small RNA Analysis
Isolate and sequence small RNA species, such as microRNA, to study the role of noncoding RNA in gene silencing and posttranscriptional regulation.
Targeted Gene Panels
Targeted gene sequencing panels contain defined probe sets focused on specific genes of interest. Both predesigned and custom panels are available.
16S rRNA Sequencing
A culture-free method to identify and compare bacteria from complex microbiomes or environments that are difficult to study.
Translation Analysis
Ribosome profiling enables systematic monitoring of cellular translation processes and prediction of protein abundance.
Targeted RNA Expression Analysis
Targeted RNA sequencing (RNA-Seq) focuses on specific transcripts of interest, used to analyze gene expression and identify fusion genes.
Amplicon Sequencing
Ultra-deep sequencing of PCR amplicons enables cost-effective analysis of up to hundreds of target genomic regions in one assay.
Cytogenomics
Next-generation sequencing offers base-by-base, genome-wide detection of chromosomal variation to complement array-based cytogenomic analysis.
Population Studies
Population genomics programs integrate large-scale genomic and clinical data into a learning health system, driving health care innovation.
Researcher Interview
Sample Quality Control
Assess the quality of a sequencing library before committing it to a full-scale run, or perform quality control applications for bioproduction studies.
Methods Guide
Access the information you need—from BeadChips to library preparation for genome, transcriptome, or epigenome studies to sequencer selection, analysis, and support—all in one place. Select the best tools for your lab with our comprehensive guide designed specifically for research applications.
Access Guide