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  • Seq-Scope Protocol: Repurposing Illumina Sequencing Flow Cells for High-Resolution Spatial Transcriptomics”

    work
    Creator:
    Kim, Yongsung, Cheng, Weiqiu, Cho, Chun-Seok, Kang, Hyun Min, and Lee, Jun Hee
    Description:
    This dataset contains a typical example of Seq-Scope dataset that investigators would generate after examining the initial sequence data. If the quality of the initial Seq-Scope dataset looks great, one may decide to sequence the library much more deeply to maximize the information content. (see NovaScope tutorial at  https://seqscope.github.io/NovaScope/ for more details). The spatial barcode sequences and the initial version of the sequenced cDNA library are deposited separate repository, which is described in the NovaScope documentation ( https://seqscope.github.io/NovaScope/). This data repository contains a deeper sequencing of the same library. A shallower version of sequencing, which does not have overlapping data with the current repository can be found at  https://doi.org/10.5281/zenodo.10840695
    Keyword:
    Seq-Scope, Spatial Transcriptomics
    Citation to related publication:
    Yongsung Kim, Weiqiu Cheng, Chun-Seok Cho, Yongha Hwang, Yichen Si, Anna Park, Mitchell Schrank, Jer-En Hsu, Jingyue Xi, Myungjin Kim, Ellen Pedersen, Olivia I. Koues, Thomas Wilson, Goo Jun, Hyun Min Kang2, Jun Hee Lee, “Seq-Scope Protocol: Repurposing Illumina Sequencing Flow Cells for High-Resolution Spatial Transcriptomics” (submitted)
    Discipline:
    Science

  • Seq-Scope processed datasets for skin results (RDS) and H&E images

    work
    Creator:
    Hsu, Jer-En, Cho, Chun-Seok, Kim, Myungjin, Xi, Jingyue, and Lee, Jun Hee
    Description:
    There are three experimental outputs from Seq-Scope. (1) High definition map coordinate identifier (HDMI) sequence, tile and spatial coordinate information from 1st-Seq, (2) HDMI sequence, coupled with cDNA sequence from 2nd-Seq, and (3) Histological image obtained from Hematoxylin and Eosin (H&E) staining of the tissue slice. (1) and (2) were uploaded to GEO ( https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE186601). (3) is deposited here. In addition, this deposit includes the processed RDS (single R object) data files.
    Citation to related publication:
    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. PMID: 35867799; PMCID: PMC9400695.
    Discipline:
    Health Sciences