# Chemistry and Imaging on iSeq 100

The iSeq 100 System combines complementary metal-oxide semiconductor (CMOS) technology with innovative one-channel sequencing by synthesis (SBS) chemistry to deliver high-accuracy data in a compact system.

The system uses a patterned flow cell with nanowells fabricated over a CMOS chip (Figure 1).

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-c7415b756cc8103744f993aa3cf1e85cd7952ae8%2Fimage1.png?alt=media\&token=95db2df3-bd99-4850-99f0-7c0fb16f8c21)

Figure 1: Illumina CMOS Flow Cell.

Clustering and sequencing occur in the nanowells with direct alignment of single clusters over each photodiode (pixel). Using a CMOS sensor embedded in the consumable is a simple and fast detection method.

Unlike four-channel SBS chemistry, where sequencers use a different dye for each nucleotide, the iSeq 100 System uses one dye, two chemistry steps, and two imaging steps per sequencing cycle (Figure 2). In one-channel chemistry, adenine has a removable label and is labeled in the first image only. Cytosine has a linker group that can bind a label and is labeled in the second image only. Thymine has a permanent fluorescent label and is therefore labeled in both images, and guanine is permanently dark.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-98374c2c2361670e6d05d13e0ac3196b4cde8497%2Fimage2.png?alt=media\&token=ab32a4e1-b535-442e-937a-a86c4c74f4af)

Figure 2: One-Channel Chemistry by schematic representation.

Nucleotides are identified by analysis of the different emission patterns for each base across the combination of Image 1 and Image 2 that are processed by image analysis software to identify which bases are incorporated at each cluster position.

![](https://761066130-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGM9W2DuBTgEXv1ClCm8H%2Fuploads%2Fgit-blob-0d006f3203e3ede2ad6d90c6ede872af976a6d88%2Fimage3.png?alt=media\&token=d7b3c0de-7330-45a2-80de-7e01699e5c61)

Figure 3: Image analysis during SBS Chemistry with One-Channel Detection.

The iSeq 100 System uses during cluster generation, a proprietary ExAmp chemistry to ensure that each well in the flow cell generates a single, clonal cluster. During each imaging step, light emissions are detected by the CMOS photodiodes.

For more information, see the Sequencing by Synthesis page [here](https://www.illumina.com/science/technology/next-generation-sequencing/sequencing-technology/2-channel-sbs.html).

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