Cho CS, Xi J, Si Y, Park SR, Hsu JE, Kim M, Jun G, Kang HM, Lee JH. Microscopic examination of spatial transcriptome using Seq-Scope. Cell. 2021 Jun 24;184(13):3559-3572.e22. doi: 10.1016/j.cell.2021.05.010. Epub 2021 Jun 10. PubMed PMID: 34115981; PubMed Central PMCID: PMC8238917. 

Do TH, Ma F, Andrade PR, Teles R, de Andrade Silva BJ, Hu C, Espinoza A, Hsu JE, Cho CS, Kim M, Xi J, Xing X, Plazyo O, Tsoi LC, Cheng C, Kim J, Bryson BD, O'Neill AM, Colonna M, Gudjonsson JE, Klechevsky E, Lee JH, Gallo RL, Bloom BR, Pellegrini M, Modlin RL. TREM2 macrophages induced by human lipids drive inflammation in acne lesions. Sci Immunol. 2022 Jul 22;7(73):eabo2787. doi: 10.1126/sciimmunol.abo2787. Epub 2022 Jul 22. PubMed PMID: 35867799; PubMed Central PMCID: PMC9400695

Xi J, Lee JH, Kang HM, Jun G. STtools: a comprehensive software pipeline for ultra-high-resolution spatial transcriptomics data. Bioinformatics Adv. 2022 Sep 1; 2(1):vbac061. doi: 10.1093/bioadv/vbac061.  PMCID: PMC9590442

Ma F, Plazyo O, Billi AC, Tsoi LC, Xing X, Wasikowski R, Gharaee-Kermani M, Hile G, Jiang Y, Harms PW, Xing E, Kirma J, Xi J, Hsu JE, Sarkar MK, Chung Y, Di Domizio J, Gilliet M, Ward NL, Maverakis E, Klechevsky E, Voorhees JJ, Elder JT, Lee JH, Kahlenberg JM, Pellegrini M, Modlin RL, Gudjonsson JE. Single cell and spatial sequencing define processes by which keratinocytes and fibroblasts amplify inflammatory responses in psoriasis. Nat Commun. 2023 Jun 12;14(1):3455. doi: 10.1038/s41467-023-39020-4. PubMed PMID: 37308489; PubMed Central PMCID: PMC10261041.

NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health. Nat Aging. 2022 Dec;2(12):1090-1100. doi: 10.1038/s43587-022-00326-5. Epub 2022 Dec 20. PubMed PMID: 36936385; PubMed Central PMCID: PMC10019484.

Kang HM, Lee JH. Spatial Single-Cell Technologies for Exploring Gastrointestinal Tissue Transcriptome. Compr Physiol. 2023 Jun 26;13(3):4709-4718. doi: 10.1002/cphy.c210053. PubMed PMID: 37358516; PubMed Central PMCID: PMC10386894.

Gurkar AU, Gerencser AA, Mora AL, Nelson AC, Zhang AR, Lagnado AB, Enninful A, Benz C, Furman D, Beaulieu D, Jurk D, Thompson EL, Wu F, Rodriguez F, Barthel G, Chen H, Phatnani H, Heckenbach I, Chuang JH, Horrell J, Petrescu J, Alder JK, Lee JH, Niedernhofer LJ, Kumar M, Königshoff M, Bueno M, Sokka M, Scheibye-Knudsen M, Neretti N, Eickelberg O, Adams PD, Hu Q, Zhu Q, Porritt RA, Dong R, Peters S, Victorelli S, Pengo T, Khaliullin T, Suryadevara V, Fu X, Bar-Joseph Z, Ji Z, Passos JF. Spatial mapping of cellular senescence: emerging challenges and opportunities. Nat Aging. 2023 Jul;3(7):776-790. doi: 10.1038/s43587-023-00446-6. Epub 2023 Jul 3. Review. PubMed PMID: 37400722.

Kim Y, Cheng W, Cho CS, Hwang Y, Si Y, Park A, Schrank M, Hsu JE, Anacleto A, Xi J, Kim M, Pedersen E, Koues OI, Wilson T, Lee C, Jun G, Kang HM, Lee JH. Seq-Scope: repurposing Illumina sequencing flow cells for high-resolution spatial transcriptomics. Nat Protoc. 2024 Oct 31;. doi: 10.1038/s41596-024-01065-0. PubMed PMID: 39482362

Si Y, Lee C, Hwang Y, Yun JH, Cheng W, Cho CS, Quiros M, Nusrat A, Zhang W, Jun G, Zöllner S, Lee JH, Kang HM. FICTURE: scalable segmentation-free analysis of submicron-resolution spatial transcriptomics. Nat Methods. 2024 Oct;21(10):1843-1854. doi: 10.1038/s41592-024-02415-2. Epub 2024 Sep 12. PubMed PMID: 39266749; PubMed Central PMCID: PMC11466694. 

Software Package for Processing Seq-Scope using NovaSeq6000 Flow Cell (https://seqscope.github.io/NovaScope/)

Step-by-step Experimental Protocols using NovaSeq6000 Flow Cell (https://rdcu.be/dYJhg)

[Deprecated] Software Package for Processing Seq-Scope and Other Spatial Transcriptome Data (https://github.com/jyxi7676/STtools)

[Deprecated] Step-by-step Experimental Protocols (Version M1.0.0)

[Deprecated] Video Demonstration of Key Procedures (https://www.youtube.com/playlist?list=PLRwwF9JZ_f5P7wXjgt90o52Jz9JyMYWf4)

[Deprecated] Custom Codes Initially used for Seq-Scope Analysis (https://github.com/leeju-umich/Cho_Xi_Seqscope)

Seq-Scope liver and colon raw sequencing data and digital gene expression (DGE) matrix
(https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169706)

Seq-Scope liver and colon processed datasets (annotated RDS) and H&E images
(https://doi.org/10.7302/cjfe-wa35)

Seq-Scope acne skin raw sequencing data and digital gene expression (DGE) matrix
(https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE186601)

Seq-Scope acne skin processed datasets (annotated RDS) and H&E images
(https://doi.org/10.7302/eb9w-ch66)