Dr. Zhao Lai $600,000 NIH Shared Instrument grant
In March 2016, Dr. Zhao Lai was awarded $600,000 NIH Shared Instrument grant (S10 grant 1S10OD021805-01) to purchase Illumina HiSeq 3000 to upgrade the sequencing platform in GSF. Illumina HiSeq 3000/4000(3000 carries one flow cell vs HiSeq 4000 with two flow cell stations) is the latest and most efficient sequencing platform in Illumina NGS market. It provides greater efficiency in terms of high-throughput, faster turn-around-time and cheaper cost. We are very grateful to NIH funding support to continue the GSF’s NGS journey to the new exciting direction.
The enhanced sequencing performance of HiSeq 3000 is enabled by two new technologies: patterned flow cell and kinetic exclusion amplification. These two new technologies were only available on the X Ten sequencers for a single application, the re-sequencing of human genomic samples. In contrast to the random clustering employed previously (HiSeq 2500 and earlier models), the clusters in HiSeq 3000 are now generated in ordered nano-wells to allow for higher cluster densities and unambiguous cluster identification. Unlike Illumina X Ten line dedicated to human genome re-sequencing only, HiSeq 3000/4000 series are capable of processing samples derived from all organisms, making them very flexible and cost-effective sequencing platforms. The decreased cost and the increased capability will significantly benefit every user’s sequencing need and bring the type of genomic analyses once possible only in large-scale sequencing centers to research laboratories both large and small, and make scientific and translational genome sequencing applications closer to reality.
The table below compares with HiSeq 3000 (current) and HiSeq 2000 (previous)
For 50bp single reads sequencing
(most RNA-seq and ChIP-seq)
Instrument |
Run time1 |
# of reads/lane(millions) |
Read Length(base-pair) |
>Q30 |
Note |
| HiSeq 3000
(current) |
12 hour | 300-400 | 50 | 90-95% | New Chemistry |
| HiSeq 2000
(previous) |
3 days | 150-190 | 50 | 90-95% | V3 Chemistry3 |
For 100bp paired end sequencing
(most exome-seq and RNA-seq for splicing variants)
Instrument |
Run time1 |
# of reads/lane(millions) |
Read Length(base-pair) |
>Q30 |
Note |
| HiSeq 3000
(current) |
<2 days | 600-800 | 100 | 90%-95% | New Chemistry |
| HiSeq 2000
(previous) |
11 days | 300-380 | 100 | 85%-90% | V3 Chemistry3 |
The GSF has purchased HiSeq 3000 in May and installation and training have been completed in June 2016. If you are considering next generation sequencing for your research, please contact Dr. Zhao Lai for consultation on experimental design, pricing and scheduling.
Since 2004, UT Health San Antonio, Greehey Children’s Cancer Research Institute’s (Greehey CCRI) mission has been to advance scientific knowledge relevant to childhood cancer, contribute to understanding its causes, and accelerate the translation of knowledge into novel therapies. Greehey CCRI strives to have a national and global impact on childhood cancer by discovering, developing, and disseminating new scientific knowledge. Our mission consists of three key areas — research, clinical, and education.
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