HiSeq2000 - Next Level Hacking

We got a HiSeq 2000, Next Level Sequencing Machine from the Genomics Facility of Department of Biosystems Science and Engineering in Basel. Contact through Biozentrum, University of Basel. We got it for free with the only disclaimer: "The biohackers should understand that they are responsible to organize and pay for the transport as well as that there is no warranty or support that can be given neither by us nor the DBSSE."

This type of machine seems to be quite difficult to get up and running and also reagents, flowcell-kits and software licences can be expensive. Since more of these machines seem to show up in second hand (there are new machine generations by Illumina) it would be worth trying to find a way to make them work. Sequencing for all.

Specifications:
https://www.illumina.com/documents/products/datasheets/datasheet_hiseq2000.pdf
The HiSeq2000 (200Gb) was introduces in the year 2010. Followed by HiSeq2500 (500Gb) in 2012. And HiSeq X Ten (1000Gb) in 2014. In 2017 the NovaSeq series of machines was launched.
The machine is a quite early on, from March 2011, Serial Number is 700792, so the machine can not be updated to software and chemistry v4.

I made a first inspection on the machine. It seems very well made (2011). I still think it would be cool to make it run as is. It's basically a big microfluidic system. So if we get the pumps and the cameras to work we can hack it into anything we want 🙂. Even if it's not for sequencing - it's basically a holder for flow-cells with a fluorescence camera attached to it. And 32 channels with pumps and selector valves that attach to the flow cells. Plus a fridge and a computer. And peltier for heating and cooling (pcr). Now trying to get the control software. I also think the system is "relatively" open... the software can be downloaded and kind of installs, there is no ID checking on the supplies or anything. Looks very hackable. Also all the cases can be opened easily. Let's do a weekend hack-session on it.

I think it's great opportunity to learn about next level sequencing and about how theses machines work.

Fluidic System:

Some pictures from the inside of the machine:

Chemistry

Some images describing the Illumina Next-Generation Sequencing Chemistry:

Illumina uses a process called "Sequencing-by-synthesis"
The HiSeq (and MiSeq) use 4-colour SBS

The full DNA to Data solution:

Links and Information:

Illumina Next Level Sequencing:
https://www.youtube.com/watch?v=womKfikWlxM&feature=youtu.be
Expert Videos:
https://www.youtube.com/playlist?list=PLKRu7cmBQlai-GUWeAN-eHD5xRcCXDW-D
HiSeq2000 support page:
https://support.illumina.com/sequencing/sequencing_instruments/hiseq_2000.html

Discussion:

The goal is to make it work!
Let's discuss on the forum.. http://forum.hackteria.org/t/hiseq2000-next-level-hacking/325/1

- Where to get/buy the reagents and flow cells
- Hackquarium Lausanne got a similar machine and dissasembled it. We can get pointers from Gustavo on how to take it all apart!
- Muffatto there's a fluorescence microscope inside (afaik), the issue is to reduce it in size and still have it working
- Muffatto: erik from biocurious reverse engineered the chemistry of the system for BGI

Technical Descriptions / Findings:

The fluorescent readout system with lasers and CCD cameras:

The HiSeq uses an epifluorescence microscope design shown in the diagram. Light of the excitation wavelength is focused on the specimen through the objective lens and the fluorescence emitted by the specimen is focused back the detector by the same objective.

Here you can see the two camera units with even the letters A G T C written on it.

The laser calibration sheets that came with the machine: