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A. The Photo-oxidative damage mouse model

We used a mouse model developed by the Clear Vision Lab in 2016 [1], the model recapitulates critical pathologies seen in human AMD including photoreceptor cell death, inflammatory responses, choriocapillaris atrophy, and upregulation of oxidative stress. C57BLL/6J mice were treated with high intensity white LED light for 1, 3, and 5 days to demonstrate the different levels of photo-oxidative damage (PD), respectively. Dim-reared (DR) mice were kept under normal dim illumination and are considered as the negative control.

B. Cryosection and C. Staining and Imaging

Using the model in A, we obtained eight Visium spatial transcriptome profiles of parasagittal cross sections of the whole mouse eye.

D. Identifying 15 clusters in the whole eye

The sequenced gene and spot count matrices for eight samples were pre-processed and grouped into 15 clusters using the stLearn [2] Method.

E. 3-level analysis based on retina (Please go to 1. Retina Levels)

Based on the annotation above, we focus on the retinal region. We aim to investigate the retina reaction to PD. The mice retinas were explored from the following three levels:

1) Layer Level, which contains L1: Ganglion Cell Layer, L2: Inner Plexiform Layer, L3: Photoreceptor Layer, L4: RPE and Choroid Layer.

2) Location Level: which split the retina into superior and inferior side based on the location of optic nerve

3) Retina Schematic: which split the retina into 6 regions based on the distance from optic nerve to lesion site (Please refer to our paper: URL)

1. Retina Levels

The mice retinas could be explored from the following three levels:

1) Layer Level, which split the retina into L1: Ganglion Cell Layer, L2: Inner Plexiform Layer, L3: Photoreceptor Layer, L4: RPE and Choroid Layer.

2) Location Level: which split the retina into superior and inferior side based on the location of optic nerve

3) Retina Schematic: which split the retina into 6 regions based on the distance from the optic nerve to lesion site (Please refer to our paper: URL)