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Genomic and RNA Profiling Core Facility

Houston, Texas

BCM faculty, staff and trainees are the heart of the organization.
Genomic and RNA Profiling Core
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DNA Sequencing Services

Illumina TruSeq DNA sequencing

Characterization of unknown or novel genomes is best achieved using a de novo sequencing approach. For small genomes, such as bacteria, archaea and viruses, Illumina’s Nextera XT sample prep kit is an ideal choice. This kit is also recommended to prepare PCR amplicons for sequencing on the HiSeq platforms. This method uses an enzymatic reaction to add Illumina-specific adapters to 1 ng of input DNA. Characterization of more complex genomes can be done by using Illumina’s TruSeq DNA Sample Prep kit using 1 µg of high-quality genomic DNA. Additionally, this kit can be used to construct high-quality sequencing libraries from 1 µg of cDNA generated from total RNA.

Illumina TruSeq and Nextera Input Amounts
Prep Type Total Input Minimum Concentration
TruSeq DNA Library Prep 1 μg (gDNA or cDNA) 20 ng/μl
Nextera Library Prep 1 ng (amplicons) 0.2 ng/μl

How does the Nextera XT assay work?

Agilent SureSelect Target Enrichment for DNA Sequencing

Utilizing Agilent Technologies SureSelect Target Enrichment kits partnered with Illumina’s next-generation sequencing technology, researchers can discover mutations associated with cancer and other diseases. Agilent’s in-solution hybridization capture technology enriches specific genomic regions of interest prior to sequencing. Researchers have a choice in kit formats. The SureSelect Human All Exon v5+UTRs covers 75 Mb of the human genome with 6 Gb of sequencing data. Alternatively, researchers can also customize which genomic regions to enrich using Agilent’s free web portal SureDesign or their design service. These kits require 3 µg of high quality DNA as measured by Picogreen to begin. The SureSelect All Exon target enrichment kits are also available for the mouse genome and other model organisms by request.

Agilent SureSelect Target Enrichment Input Amounts
Total gDNA Input Minimum Concentration
200 ng - 4 μg
8 ng/μl - 160 ng/μl

Agilent HaloPlex DNA Sequencing

Agilent’s HaloPlex technology is a hybrid approach between target enrichment and amplicon-based sequencing and is ideal for clinical research. It combines the speed of PCR with the sensitivity of hybridization providing a robust solution for targeting smaller capture regions. Researchers customize probe designs using Agilent’s SureDesign service. This protocol reduces sample preparation time by utilizing single-tube target amplification and eliminating library preparation, thereby greatly reducing sequencing cost. Currently available for human samples only, this protocol is ideal when genomic DNA is limited and there is not enough to proceed with Agilent SureSelect Target Enrichment. Only 4 Gb of sequencing per sample is required to achieve 80% coverage at 20X using only 225 ng of input DNA per sample. This provides the investigator with high specificity, uniformity and variant detection.

Agilent HaloPlex Input Amounts
Total gDNA Input Minimum Concentration
225 ng 5 ng/μl

Agilent SureSelect Methyl-Seq for DNA Sequencing

Analyzing under and over-methylated cytosine sites in the human genome can be accomplished using Agilent’s SureSelectXT Human Methyl-Seq kit. This kit combines Agilent’s leading target enrichment platform, SureSelect, with bisulfite sequencing, the gold standard for DNA methylation research. This tool enables researchers to focus on regions where methylation is known to impact gene regulation (CpG islands, CpG island shores, undermethylated regions promoters, and differentially methylated regions (DMRs)), analyzing over 3.7 million individual CpG dinucleotide sequences for their methylation state.

Agilent SureSelect Methyl-Seq Target Enrichment Input Amounts
Total gDNA Input Minimum Concentration
3 μg 60 ng/μl

DNA Sequencing for Bisulfite Treated Samples

Bisulfite sequencing provides the researcher with a powerful tool to study DNA methylation. Introducing changes in the DNA based on the methylation of the individual cytosine residues allows for unbiased genome-wide analysis of DNA methylation. Various analyses can then be performed on the altered DNA sequence. Whole genome bisulfite sequencing (WGBS) is a tool for examining the methylation status across the entire genome of a subject. Reduced representation bisulfite sequencing (RRBS) enriches those areas of the genome that are GC-rich which reduced the amount of sequencing needed yet captures the majority of promoters and other genomic regions of interest.

Illumina Bisulfite Treated DNA Seq Sample Amounts
Prep Type Total gDNA Input Minimum Concentration
RRBS Library Prep 2-5 μg 24-50 ng/μl
WGBS Library Prep 5 μg 100 ng/μl

Illumina WGBS & RRBS Library Prep Workflows for DNA Seq

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