High-depth spatial transcriptome analysis by photo-isolation chemistry(Dataset ID: STDS0000069)

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PMID: 34285220
Summary
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Dataset information
Summary:
We established a transcriptome profiling method coupled with photo-isolation chemistry (PIC) that allows the determination of expression profiles specifically from photo-irradiated regions of interest.
Overall design:
We performed PIC to isolate expression profiles from small domain of the E14.5 mouse neural tube. We performed PIC to isolate expression profiles from small domain of HeLa cells or NIH3T3 cells. We performed PIC to isolate expression profiles from each of the major hippocmpal [CA1, CA2 and dentate gyrus (DG) ] in 8 weeks male mice.
Technology:
PIC-seq
Platform:
Illumina HiSeq 1500
Species:
Homo sapiens(hg38)
Mus musculus(mm10)
Tissues:
Cell line
Organ parts:
HeLa cells,NIH3T3 cells,Neural tube
Development stage:
E14.5
Sex:
Male
Submission date: 2020-01-10Update date: 2021-07-28
DOI: To be continue
Contributors
Mizuki Honda,Shinya Oki,Ryuichi Kimura,Akihito Harada,Kazumitsu Maehara,Kaori Tanaka,Chikara Meno,Ya
Contact: oki.shinya.3w@kyoto-u.ac.jp
Accessions
GEO Series Accessions: GSE143413
How to cite
  • Cite database of STOmicsDB:
    [1] Xu, Zhicheng et al. "STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization." Nucleic acids research vol. 52,D1 (2024): D1053-D1061. doi: 10.1093/nar/gkad933'
  • Cite visualization dataset:
    [2] Mizuki Honda,Shinya Oki,Ryuichi Kimura,Akihito Harada,Kazumitsu Maehara,Kaori Tanaka,Chikara Meno,Ya. High-depth spatial transcriptome analysis by photo-isolation chemistry[DS/OL]. STOmicsDB, 2020[2020-01-10]. https://db.cngb.org/stomics/datasets/STDS0000069/. doi: xxxxxx
    #Format: {contributors}. {title}[DS/OL]. STOmicsDB, {the year of submission data}[{submission data}]. {dataset link}. doi: {doi ID}
  • Cite original data article:
    Citation: Honda, Mizuki et al. “High-depth spatial transcriptome analysis by photo-isolation chemistry.” Nature communications vol. 12,1 4416. 20 Jul. 2021, doi:10.1038/s41467-021-24691-8